bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species
Authors: Adams Matthew P. , Collier Catherine J. , Uthicke Sven , Ow Yan X. , Langlois Lucas , O’Brien Katherine R. 
Published: January 2017

AbstractWhen several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (Topt) for maximum photosynthetic rate (Pmax). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.
Self-steering partially coherent beams
Authors: Chen Yahong , Ponomarenko Sergey A. , Cai Yangjian 
Published: January 2017

AbstractWe introduce a class of shape-invariant partially coherent beams with a moving guiding center which we term self-steering partially coherent beams. The guiding center of each such beam evolves along a straight line trajectory which can be engineered to make any angle with the x-axis. We show that the straight line trajectory of the guiding center is the only option in free space due to the linear momentum conservation. We experimentally generate a particular subclass of new beams, self-steering Gaussian Schell beams and argue that they can find applications for mobile target tracing and trapped micro- and/or nanoparticle transport.
Mechanisms of Yersinia YopO kinase substrate specificity
Authors: Lee Wei Lin , Singaravelu Pavithra , Wee Sheena , Xue Bo , Ang Khay Chun , Gunaratne Jayantha , Grimes Jonathan M. , Swaminathan Kunchithapadam , Robinson Robert C. 
Published: January 2017

AbstractYersiniabacteria cause a range of human diseases, including yersiniosis, Far East scarlet-like fever and the plague.Yersiniaemodulate and evade host immune defences through injection ofYersiniaouter proteins (Yops) into phagocytic cells. One of the Yops, YopO (also known as YpkA) obstructs phagocytosis through disrupting actin filament regulation processes - inhibiting polymerization-promoting signaling through sequestration of Rac/Rho family GTPases and by using monomeric actin as bait to recruit and phosphorylate host actin-regulating proteins. Here we set out to identify mechanisms of specificity in protein phosphorylation by YopO that would clarify its effects on cytoskeleton disruption. We report the MgADP structure ofYersinia enterocoliticaYopO in complex with actin, which reveals its active site architecture. Using a proteome-wide kinase-interacting substrate screening (KISS) method, we identified that YopO phosphorylates a wide range of actin-modulating proteins and located their phosphorylation sites by mass spectrometry. Using artificial substrates we clarified YopO’s substrate length requirements and its phosphorylation consensus sequence. These findings provide fresh insight into the mechanism of the YopO kinase and demonstrate that YopO executes a specific strategy targeting actin-modulating proteins, across multiple functionalities, to compete for control of their native phospho-signaling, thus hampering the cytoskeletal processes required for macrophage phagocytosis.
The larvicide pyriproxyfen blamed during the Zika virus outbreak does not cause microcephaly in zebrafish embryos
Authors: Dzieciolowska Stefania , Larroque Anne-Laure , Kranjec Elizabeth-Ann , Drapeau Pierre , Samarut Eric 
Published: January 2017

AbstractAlthough the zika virus (ZIKV) has now been strongly correlated with emerging cases of microcephaly in the Americas, suspicions have been raised regarding the use of pyriproxyfen, a larvicide that prevents mosquito development, in drinking water. The effects of this compound on neurodevelopment have not yet been addressed specifically in vertebrates. As a result, we aimed at addressing the effects, if any, of pyriproxyfen on neurodevelopment in the zebrafish embryo as a vertebrate model. Using zebrafish transgenic lines expressing GFP in different cell populations (elavl3 in newborn neurons, gfap and nestin in neural stem cells), we focused on the analysis of whole embryonic brain volume after confocal 3D-reconstruction and the quantification of purified neural stem cells during early neurodevelopment by FACS-cell sorting from whole in vivo embryos. Interestingly, though lethal at very high doses, pyriproxyfen did not cause brain malformation nor any significant changes in the number of observed stem cells in the developing central nervous system. Our data indicate that pyriproxyfen does not affect central nervous system development in zebrafish, suggesting that this larvicide on its own, may not be correlated with the increase in microcephaly cases reported recently.
AuPt Alloy Nanostructures with Tunable Composition and Enzyme-like Activities for Colorimetric Detection of Bisulfide
Authors: He Weiwei , Han Xiangna , Jia Huimin , Cai Junhui , Zhou Yunlong , Zheng Zhi 
Published: January 2017

AbstractTuning the enzyme-like activity and studying the interaction between biologically relevant species and nano-enzymes may facilitate the applications of nanostructures in mimicking natural enzymes. In this work, AuPt alloy nanoparticles (NPs) with varying compositions were prepared through a facile method by co-reduction of Au3+ and Pt2+ in aqueous solutions. The composition could be tuned easily by adjusting the molar ratios of added Pt2+ to Au3+. It was found that both peroxidase-like and oxidase-like activity of AuPt alloy NPs were highly dependent on the alloy compositions, which thus suggesting an effective way to tailor their catalytic properties. By investigating the inhibitory effects of HS− on the enzyme-like activity of AuPt alloy NPs and natural enzyme, we have developed a method for colorimetric detection of HS− and evaluation of the inhibiting effects of inhibitors on natural and artificial enzymes. In addition, the responsive ability of this method was influenced largely by the composition: AuPt alloy NPs show much lower limit of detection for HS− than Pt NPs while Pt NPs show wider linear range than AuPt alloy NPs. This study suggests the facile way not only for synthesis of alloy nanostructures, but also for tuning their catalytic activities and for use in bioanalysis.
Neurogenetics of developmental dyslexia: from genes to behavior through brain neuroimaging and cognitive and sensorial mechanisms
Authors: Mascheretti S , De Luca A , Trezzi V , Peruzzo D , Nordio A , Marino C , Arrigoni F 
Published: January 2017

AbstractDevelopmental dyslexia (DD) is a complex neurodevelopmental deficit characterized by impaired reading acquisition, in spite of adequate neurological and sensorial conditions, educational opportunities and normal intelligence. Despite the successful characterization of DD-susceptibility genes, we are far from understanding the molecular etiological pathways underlying the development of reading (dis)ability. By focusing mainly on clinical phenotypes, the molecular genetics approach has yielded mixed results. More optimally reduced measures of functioning, that is, intermediate phenotypes (IPs), represent a target for researching disease-associated genetic variants and for elucidating the underlying mechanisms. Imaging data provide a viable IP for complex neurobehavioral disorders and have been extensively used to investigate both morphological, structural and functional brain abnormalities in DD. Performing joint genetic and neuroimaging studies in humans is an emerging strategy to link DD-candidate genes to the brain structure and function. A limited number of studies has already pursued the imaging–genetics integration in DD. However, the results are still not sufficient to unravel the complexity of the reading circuit due to heterogeneous study design and data processing. Here, we propose an interdisciplinary, multilevel, imaging–genetic approach to disentangle the pathways from genes to behavior. As the presence of putative functional genetic variants has been provided and as genetic associations with specific cognitive/sensorial mechanisms have been reported, new hypothesis-driven imaging–genetic studies must gain momentum. This approach would lead to the optimization of diagnostic criteria and to the early identification of ‘biologically at-risk’ children, supporting the definition of adequate and well-timed prevention strategies and the implementation of novel, specific remediation approach.
Weight‐transducerless control strategy based on active disturbance rejection theory for gearless elevator drives
Authors: Wang Gaolin , Wang Bowen , Li Chen , Xu Dianguo 
Published: January 2017

Direct‐drive traction systems applying the permanent magnet synchronous motor have become the trend of modern gearless elevators. To estimate and reject the non‐linear and uncertain load disturbance effectively during the elevator startup, a novel active disturbance rejection control (ADRC) strategy adopting extended state observer (ESO) and non‐linear error feedback (NLEF) controller is proposed to attenuate the elevator car sliding without using weight‐transducer. By using the weight‐transducerless control strategy, the sliding distance and speed can be suppressed to the extent that it could ensure the riding comfort. The proposed ADRC scheme will also accelerate the dynamic response and enhance the system robustness. Both the parameter selection and the stability of ESO are analysed according to the application requirements, and the contrastive analysis of the functions selected in NLEF controller is performed via Lyapunov theory. The feasibility of the proposed strategy is verified by the experimental results on an 11.7 kW elevator traction machine.
Period spacings in red giants
Authors: Mosser B. , Pinçon C. , Belkacem K. , Takata M. , Vrard M. 
Published: January 2017

Context. The power of asteroseismology relies on the capability of global oscillations to infer the stellar structure. For evolved stars, we benefit from unique information directly carried out by mixed modes that probe their radiative cores. This third article of the series devoted to mixed modes in red giants focuses on their coupling factors, which have remained largely unexploited up to now.
Aims. With the measurement of coupling factors, we intend to give physical constraints on the regions surrounding the radiative core and the hydrogen-burning shell of subgiants and red giants.
Methods. A new method for measuring the coupling factor of mixed modes was implemented, which was derived from the method recently implemented for measuring period spacings. This new method was automated so that it could be applied to a large sample of stars.
Results. Coupling factors of mixed modes were measured for thousands of red giants. They show specific variation with mass and evolutionary stage. Weak coupling is observed for the most evolved stars on the red giant branch only; large coupling factors are measured at the transition between subgiants and red giants as well as in the red clump.
Conclusions. The measurement of coupling factors in dipole mixed modes provides a new insight into the inner interior structure of evolved stars. While the large frequency separation and the asymptotic period spacings probe the envelope and core, respectively, the coupling factor is directly sensitive to the intermediate region in between and helps determine its extent. Observationally, the determination of the coupling factor is a prior to precise fits of the mixed-mode pattern and can now be used to address further properties of the mixed-mode pattern, such as the signature of buoyancy glitches and core rotation.
Bilateral Vertebral Artery Dissection after a Chiropractic Therapy Session
Authors: Romero Flavio , Vieira Rodolfo , Freitas Carlos 
Published: January 2017

AbstractVertebral artery dissection (VAD) is a rare and sometimes unrecognized cause of stroke in patients younger than 45 years. Herein, we describe a very rare case of bilateral vertebral artery dissection after a session of cervical therapy manipulation (chiropractic).
Late-term Effects of Surgery on Nasal Functions in Patients who Underwent Total Laryngectomy Surgery
Authors: Karaoglu Deniz , Kocyigit Murat , Ortekin Safiye , Adali Mustafa 
Published: January 2017

Introduction There is a common opinion that losing airway functions in total laryngectomy patients cause changes in nasal physiological rates. Studies conducted to review the subject present gaps, especially in terms of objective measurements.
Objective We evaluated late-term effects of surgery on nasal functions in patients who underwent total laryngectomy surgery more than two years ago.
Methods We included in the study 22 patients who had undergone total laryngectomy, as well as 24 healthy subjects with similar demographic characteristics as the control group. We performed acoustic rhinometry for intranasal volume and cross-sectional area measurements, saccharin test for measurement of nasal mucociliary clearance, and smell identification test for evaluation of olfactory function in the patient and control groups. We compared and statistically analyzed the data obtained from the groups.
Results In our study, although late-term (>2 years) measurements were not statistically significant, we detected more nasal passage patency in the patient group than in the control group. In smell identification test, lower scores were obtained in the patient group. The difference between measurements in both groups was statistically significant.
Conclusion We believe that since the upper respiratory tract is disabled due to tracheostomy in patients with total laryngectomy, atrophy occurs in the late term and, consequently, nasal mucociliary clearance is impaired. We also see diminished olfactory function in total laryngectomy patients.
Contribution of propriospinal neurons to recovery of hand dexterity after corticospinal tract lesions in monkeys
Authors: Tohyama Takamichi , Kinoshita Masaharu , Kobayashi Kenta , Isa Kaoru , Watanabe Dai , Kobayashi Kazuto , Liu Meigen , Isa Tadashi 
Published: January 2017

Significance
There are different views about the targets of regenerative therapies to induce functional recovery in patients with motor paralysis following brain and spinal cord injury: whether we should aim at repairing the injured corticospinal tract or at facilitating compensation by other descending motor pathways. To help answer this question, we used double viral vectors to reversibly and selectively block the propriospinal neurons (PNs), one of the major intercalated neurons mediating cortical commands to motoneurons, in monkeys with partial spinal cord injury. We demonstrated causal roles of the PN-mediated pathway in promoting recovery of hand dexterity after the lesion. Thus, targeting the PNs might lead to developing effective treatment to facilitate recovery after spinal cord injury.
On-demand high-capacity ride-sharing via dynamic trip-vehicle assignment
Authors: Alonso-Mora Javier , Samaranayake Samitha , Wallar Alex , Frazzoli Emilio , Rus Daniela 
Published: January 2017

Significance
Ride-sharing services can provide not only a very personalized mobility experience but also ensure efficiency and sustainability via large-scale ride pooling. Large-scale ride-sharing requires mathematical models and algorithms that can match large groups of riders to a fleet of shared vehicles in real time, a task not fully addressed by current solutions. We present a highly scalable anytime optimal algorithm and experimentally validate its performance using New York City taxi data and a shared vehicle fleet with passenger capacities of up to ten. Our results show that 2,000 vehicles (15% of the taxi fleet) of capacity 10 or 3,000 of capacity 4 can serve 98% of the demand within a mean waiting time of 2.8 min and mean trip delay of 3.5 min.
Imaging individual neurons in the retinal ganglion cell layer of the living eye
Authors: Rossi Ethan A. , Granger Charles E. , Sharma Robin , Yang Qiang , Saito Kenichi , Schwarz Christina , Walters Sarah , Nozato Koji , Zhang Jie , Kawakami Tomoaki , Fischer William , Latchney Lisa R. , Hunter Jennifer J. , Chung Mina M. , Williams David R. 
Published: January 2017

Significance
Retinal ganglion cells are the primary output neurons of the retina that process visual information and transmit it to the brain. We developed a method to reveal these cells in the living eye that does not require the fluorescent labels or high light levels that characterize more invasive methods. The death of these cells causes vision loss in glaucoma, the second leading cause of blindness worldwide. The ability to image these cells in the living eye could accelerate our understanding of their role in normal vision and provide a diagnostic tool for evaluating new therapies for retinal disease.
Statistical mechanical model of gas adsorption in porous crystals with dynamic moieties
Authors: Simon Cory M. , Braun Efrem , Carraro Carlo , Smit Berend 
Published: January 2017

Significance
Some nanoporous, crystalline materials possess dynamic/flexible constituents, for example, a ligand that can rotate. Much like the induced-fit model of enzyme–substrate binding in biology, these dynamic moieties often change conformation when gas molecules adsorb. Such flexible constituents may endow nanoporous materials with enhanced properties for gas storage and separations, chemical sensing, drug delivery, and catalysis. We developed and solved a statistical mechanical model of gas adsorption in a porous material with a rotating ligand that is shared between cages. Our model contributes a more intimate understanding of gas adsorption in nanoporous materials with moving parts and lends insights into how to harness these dynamic constituents for adsorption-based processes.
GAS6 is a key homeostatic immunological regulator of host–commensal interactions in the oral mucosa
Authors: Nassar Maria , Tabib Yaara , Capucha Tal , Mizraji Gabriel , Nir Tsipora , Pevsner-Fischer Meirav , Zilberman-Schapira Gili , Heyman Oded , Nussbaum Gabriel , Bercovier Herve , Wilensky Asaf , Elinav Eran , Burstyn-Cohen Tal , Hovav Avi-Hai 
Published: January 2017

Significance
Understanding the mechanisms by which the immune system and local microorganisms coexist in the oral cavity is important, as disruption of this delicate balance could cause oral and systemic diseases. We revealed that growth arrest specific 6 (GAS6), a ligand of the TYRO3–AXL–MERTK signaling system, plays a critical role in this process. Upon birth, microorganisms residing in the oral cavity induce expression of GAS6 in oral tissues; GAS6 in turn regulates antibacterial function in these tissues. We also found that GAS6 expressed by cells of the immune system further contributes to its regulatory role in oral tissues. Collectively, this work proposes that GAS6 restrains the immune response in the oral cavity to maintain coexistence with favorable microorganisms residing within the oral cavity.
Glucocorticoid receptor in T cells mediates protection from autoimmunity in pregnancy
Authors: Engler Jan Broder , Kursawe Nina , Solano María Emilia , Patas Kostas , Wehrmann Sabine , Heckmann Nina , Lühder Fred , Reichardt Holger M. , Arck Petra Clara , Gold Stefan M. , Friese Manuel A. 
Published: January 2017

Significance
Reproduction in placental mammals relies on potent control of the mother’s immune system to not attack the developing fetus. As a bystander effect, pregnancy also potently suppresses the activity of the autoimmune disease multiple sclerosis (MS). Here, we report that T cells are able to directly sense progesterone via their glucocorticoid receptor (GR), resulting in an enrichment of regulatory T cells (Tregs). By using an MS animal model, we found that the presence of the GR in T cells is essential to increase Tregs and confer the protective effect of pregnancy, but not for maintaining the pregnancy itself. Better understanding of this tolerogenic pathway might yield more specific therapeutic means to steer the immunological balance in transplantation, cancer, and autoimmunity.
Forkhead box a2 (FOXA2) is essential for uterine function and fertility
Authors: Kelleher Andrew M. , Peng Wang , Pru James K. , Pru Cindy A. , DeMayo Francesco J. , Spencer Thomas E. 
Published: January 2017

Significance
These studies define biological roles for Forkhead box a2 (FOXA2) and glands of the uterus in female reproduction and fertility. FOXA2 is a critical regulator of uterine gland development in the neonate as well as of differentiated gland function in the adult uterus. Our findings provide clear in vivo evidence that FOXA2 regulates uterine expression of Leukemia inhibitory factor (Lif) for blastocyst implantation and that uterine glands play active roles in stromal cell decidualization and placental development. These findings support the idea that pregnancy loss and complications in women may have their origin in uterine gland dysfunction.
Characterization of cytopathic factors through genome-wide analysis of the Zika viral proteins in fission yeast
Authors: Li Ge , Poulsen Melissa , Fenyvuesvolgyi Csaba , Yashiroda Yoko , Yoshida Minoru , Simard J. Marc , Gallo Robert C. , Zhao Richard Y. 
Published: January 2017

Significance
The Zika virus (ZIKV) causes various neurologic defects including microcephaly and the Guillain-Barré syndrome. However, little is known about how ZIKV causes those diseases or which viral protein(s) is responsible for the observed cytopathic effects involved in restricted neuronal cellular growth, dysregulation of the cell cycle, and induction of cell hypertrophy or cell death. A genome-wide analysis of ZIKV proteins and peptides was conducted using fission yeast as a surrogate host. Seven ZIKV proteins conferred various cytopathic effects in which NS4A-induced cellular hypertrophy and growth restriction were mediated through the target of rapamycin (TOR) cellular stress-response pathway. These findings provide a foundation for identifying viral pathogenicity factors associated with the ZIKV diseases.
Resolution of single and double Holliday junction recombination intermediates by GEN1
Authors: Shah Punatar Rajvee , Martin Maria Jose , Wyatt Haley D. M. , Chan Ying Wai , West Stephen C. 
Published: January 2017

Significance

Holliday junction resolvases are required for the resolution of recombination intermediates to ensure proper chromosome segregation at mitosis. In human cells, the GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the cleavage of Holliday junction recombination intermediates. Here, we show that GEN1 cuts DNA substrates containing single or double Holliday junctions to generate cross-over or noncross-over recombination products. In contrast to the bacterial Holliday junction resolvase, RuvC, which prefers to cut junctions at the sequence 5′-
A
/
T
TT
G
/
C
- 3′, GEN1 shows only weak sequence specificity.