bluuebunny/crossref_metadata_2025_split huggingface dataset:
OR14I1 is a receptor for the human cytomegalovirus pentameric complex and defines viral epithelial cell tropism
Authors: E Xiaofei , Meraner Paul , Lu Ping , Perreira Jill M. , Aker Aaron M. , McDougall William M. , Zhuge Ronghua , Chan Gary C. , Gerstein Rachel M. , Caposio Patrizia , Yurochko Andrew D. , Brass Abraham L. , Kowalik Timothy F. 
Published: March 2019

Significance
Identifying cell-surface receptors required for viral infection is important for developing antiviral therapies and effective vaccines. Human cytomegalovirus (HCMV) infects epithelial cells during interhost transmission. The pentameric protein complex (PC) was identified as being required for infection of this clinically relevant cell type. The majority of neutralizing antibody responses are directed against the PC. Here we describe an HCMV receptor, OR14I1, which binds to the PC and defines epithelial tropism. Importantly, we identified a peptide representing the N terminus of OR14I1 that blocks HCMV infection of epithelial cells. Moreover, an adenylate cyclase signaling pathway functioning downstream of OR14I1 contributes to HCMV infection and endocytosis. These findings reveal information useful for the development of new anti-HCMV therapies and vaccines.
Growth factor stimulation promotes multivesicular endosome biogenesis by prolonging recruitment of the late-acting ESCRT machinery
Authors: Quinney Kyle B. , Frankel Elisa B. , Shankar Raakhee , Kasberg William , Luong Peter , Audhya Anjon 
Published: March 2019

Significance
The formation of multivesicular endosomes (MVEs) enables the sequestration of numerous membrane-associated cargo molecules, including signaling receptors, to downregulate signal transduction pathways initiated by various stimuli. In this work, we demonstrate that the machinery responsible for MVE biogenesis responds to growth factor stimulation by extending its duration of action at endosomes. Specifically, we show that endosomal sorting complex required for transport-I (ESCRT-I) and Vps4 accumulation at MVEs is dramatically prolonged following growth factor stimulation. Additionally, we demonstrate that native ESCRT complexes exhibit an oscillatory behavior on endosomes, which is dependent on the sequential recruitment of downstream components. Our studies strongly suggest that components of the ESCRT machinery act cyclically and in a coordinated manner to enable a rapid response to changing environmental cues.
Host−guest complexation-mediated codelivery of anticancer drug and photosensitizer for cancer photochemotherapy
Authors: Yu Guocan , Zhu Benyue , Shao Li , Zhou Jiong , Saha Manik Lal , Shi Bingbing , Zhang Zibin , Hong Tao , Li Shijun , Chen Xiaoyuan , Stang Peter J. 
Published: March 2019

Significance
The combination of chemotherapy and photodynamic therapy opens up a promising way of overcoming drug resistance, incorporating different mechanisms of actions to achieve synergistic efficacy. However, the antitumor outcome of photodynamic therapy is greatly limited due to the unsatisfactory singlet oxygen generation caused by severe aggregation of the photosensitizer. To this end, we utilize a discrete metallacage containing therapeutic organoplatinum(II) to encapsulate a photosensitizer by forming an inclusion host–guest complex, facilitating the codelivery of chemotherapeutic agent and photosensitizer through nanoformulation. Benefiting from the enhanced permeability and retention effect and active targeting, the nanomedicine exhibits satisfactory antitumor performance against drug-resistant tumor. This pioneering work provides a distinct supramolecular methodology to prepare theranostic systems for multimodality imaging and therapy.
Transition from weak to strong turbulence in magnetized plasmas
Authors: Bratanov Vasil , Mahajan Swadesh , Hatch David 
Published: March 2019

Abstract
The scaling of turbulent heat flux with respect to electrostatic potential is examined in the framework of a reduced (4D) kinetic system describing electrostatic turbulence in magnetized plasmas excited by the ion temperature gradient instability. Numerical simulations were instigated by, and tested the predictions of generic renormalized turbulence models like the 2D fluid model for electrostatic turbulence (Zhang and Mahajan 1993 Phys. Fluids B 5 2000). A fundamental, perhaps, universal result of this theory-simulation combination is the demonstration that there exist two distinct asymptotic states (that can be classified as weak turbulence (WT) and strong turbulence (ST) states) where the turbulent diffusivity Q scales quite differently with the strength of turbulence measured by the electrostatic energy

∥
ϕ

∥

2

. In the case of WT

Q
∝
∥
ϕ

∥

2

, while in ST Q has a weaker dependence on the electrostatic energy and scales as

∥
ϕ
∥

.
The ecology and significance of below-ground bud banks in plants
Authors: Ott Jacqueline P , Klimešová Jitka , Hartnett David C 
Published: March 2019

AbstractBackgroundBelow-ground bud banks have experienced much recent interest due to discoveries that they (1) account for the majority of seasonal population renewal in many communities, (2) are crucial to regeneration following disturbance, and (3) have important consequences for plant population dynamics and plant and ecosystem function across a number of habitats.ScopeThis review presents an overview of the role of bud banks in plant population renewal, examines bud bank life history, summarizes bud bank traits and their potential ecological implications, synthesizes the response of bud banks to disturbance, and highlights gaps to guide future research. The characteristics and life history of buds, including their natality, dormancy, protection and longevity, provide a useful framework for advancing our understanding of bud banks. The fate of buds depends on their age, size, type, location, and biotic and abiotic factors that collectively regulate bud bank dynamics. A bud bank can provide a demographic storage effect stabilizing population dynamics, and also confer resistance to disturbance and invasion. Regeneration capacity following disturbance is determined by interactions among the rates of bud natality, depletion and dormancy (meristem limitation), and the resources available to support the regeneration process. The resulting response of plants and their bud banks to disturbances such as fire, herbivory and anthropogenic sources determines the community’s regenerative capacity.ConclusionsVegetation responses to environmental change may be mediated through changes in bud bank dynamics and phenology. Environmental change that depletes the bud bank or prohibits its formation likely results in a loss of vegetation resilience and plant species diversity. Standardization of bud sampling, examination of bud banks in more ecosystems and their response to environmental variation and disturbance regimes, employment of stage-structured bud bank modelling and evaluation of the cost of bud bank construction and maintenance will benefit this expanding field of research.
Sharing the burden: on the division of parental care and vocalizations during incubation
Authors: Kavelaars Marwa M , Lens Luc , Müller Wendt 
Published: March 2019

AbstractIn species with biparental care, individuals only have to pay the costs for their own parental investment, whereas the contribution of their partner comes for free. Each parent hence benefits if its partner works harder, creating an evolutionary conflict of interest. How parents resolve this conflict and how they achieve the optimal division of parental tasks often remains elusive. In this study, we investigated whether lesser black-backed gulls (Larus fuscus) divide parental care during incubation equally and whether this correlates with the extent of vocalizations between pair-members during incubation. We then investigated whether pairs showing more evenly distributed incubation behavior had a higher reproductive success. To this end, we recorded incubation behavior and vocalizations for 24-h time periods. Subsequently, we experimentally increased or decreased brood sizes in order to manipulate parental effort, and followed offspring development from hatching till fledging. Although incubation bouts were, on average, slightly longer in females, patterns varied strongly between pairs, ranging from primarily female incubation over equal sex contributions to male-biased incubation. Pairs contributing more equally to incubation vocalized more during nest relief and had a higher reproductive output when brood sizes were experimentally increased. Thus, vocalizations and a more equal division of parental care during incubation may facilitate higher levels of care during the nestling period, as suggested by a greater reproductive success when facing high brood demand, or they indicate pair quality.
Invasive shrubs modify rodent activity timing, revealing a consistent behavioral rule governing diel activity
Authors: Guiden Peter W , Orrock John L 
Published: March 2019

Abstract
Animals adjust the timing of their activity to maximize benefits, such as access to resources, and minimize costs, such as exposure to predators. Despite many examples of invasive plants changing animal behavior, the potential for invasive plants to alter the timing of animal activity remains unexplored. In eastern North America, invasive shrubs might have particularly strong effects on animal activity timing during spring and fall, when many invasive shrubs retain their leaves long after native species’ leaves senesce. We experimentally removed an invasive shrub (buckthorn, Rhamnus cathartica) and monitored the activity timing of a ubiquitous small-mammal species (white-footed mouse, Peromyscus leucopus) in spring, summer, and fall. We captured nearly 3 times as many P. leucopus in plots invaded by R. cathartica compared with plots with R. cathartica removed, and P. leucopus were captured 2 h earlier in invaded plots. Regardless of invasion treatment, P. leucopus appear to follow a common rule to set activity timing: P. leucopus were only active below a threshold of ground-level moonlight illuminance (0.038 lux). Diel and monthly lunar cycles play an important role in regulating small-mammal activity, but our data suggest that decreased light penetration dampens the influence of moonlight illuminance in habitats invaded by R. cathartica, allowing P. leucopus to remain active throughout the night. By changing the temporal niche of ubiquitous native animals, invasive shrubs may have unappreciated effects on many ecological interactions, including processes that alter community diversity and affect human health.
BrAPI—an application programming interface for plant breeding applications
Authors: Selby Peter , Abbeloos Rafael , Backlund Jan Erik , Basterrechea Salido Martin , Bauchet Guillaume , Benites-Alfaro Omar E , Birkett Clay , Calaminos Viana C , Carceller Pierre , Cornut Guillaume , Vasques Costa Bruno , Edwards Jeremy D , Finkers Richard , Yanxin Gao Star , Ghaffar Mehmood , Glaser Philip , Guignon Valentin , Hok Puthick , Kilian Andrzej , König Patrick , Lagare Jack Elendil B , Lange Matthias , Laporte Marie-Angélique , Larmande Pierre , LeBauer David S , Lyon David A , Marshall David S , Matthews Dave , Milne Iain , Mistry Naymesh , Morales Nicolas , Mueller Lukas A , Neveu Pascal , Papoutsoglou Evangelia , Pearce Brian , Perez-Masias Ivan , Pommier Cyril , Ramírez-González Ricardo H , Rathore Abhishek , Raquel Angel Manica , Raubach Sebastian , Rife Trevor , Robbins Kelly , Rouard Mathieu , Sarma Chaitanya , Scholz Uwe , Sempéré Guilhem , Shaw Paul D , Simon Reinhard , Soldevilla Nahuel , Stephen Gordon , Sun Qi , Tovar Clarysabel , Uszynski Grzegorz , Verouden Maikel ,   The BrAPI consortium
Published: March 2019

Abstract

Motivation
Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge.

Results
To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases.

Availability and implementation
More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
Enhanced Waddington landscape model with cell–cell communication can explain molecular mechanisms of self-organization
Authors: Fooladi Hosein , Moradi Parsa , Sharifi-Zarchi Ali , Hosein Khalaj Babak 
Published: March 2019

Abstract

Motivation
The molecular mechanisms of self-organization that orchestrate embryonic cells to create astonishing patterns have been among major questions of developmental biology. It is recently shown that embryonic stem cells (ESCs), when cultured in particular micropatterns, can self-organize and mimic the early steps of pre-implantation embryogenesis. A systems-biology model to address this observation from a dynamical systems perspective is essential and can enhance understanding of the phenomenon.

Results
Here, we propose a multicellular mathematical model for pattern formation during in vitro gastrulation of human ESCs. This model enhances the basic principles of Waddington epigenetic landscape with cell–cell communication, in order to enable pattern and tissue formation. We have shown the sufficiency of a simple mechanism by using a minimal number of parameters in the model, in order to address a variety of experimental observations such as the formation of three germ layers and trophectoderm, responses to altered culture conditions and micropattern diameters and unexpected spotted forms of the germ layers under certain conditions. Moreover, we have tested different boundary conditions as well as various shapes, observing that the pattern is initiated from the boundary and gradually spreads towards the center. This model provides a basis for in-silico modeling of self-organization.

Availability and implementation
https://github.com/HFooladi/Self_Organization.

Supplementary information
Supplementary data are available at Bioinformatics online.
IsoCor: isotope correction for high-resolution MS labeling experiments
Authors: Millard Pierre , Delépine Baudoin , Guionnet Matthieu , Heuillet Maud , Bellvert Floriant , Létisse Fabien 
Published: March 2019

Abstract

Summary
Mass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines.

Availability and implementation
IsoCor v2 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/IsoCor/ and https://isocor.readthedocs.io/.
TISIDB: an integrated repository portal for tumor–immune system interactions
Authors: Ru Beibei , Wong Ching Ngar , Tong Yin , Zhong Jia Yi , Zhong Sophia Shek Wa , Wu Wai Chung , Chu Ka Chi , Wong Choi Yiu , Lau Chit Ying , Chen Ian , Chan Nam Wai , Zhang Jiangwen 
Published: March 2019

Abstract

Summary
The interaction between tumor and immune system plays a crucial role in both cancer development and treatment response. To facilitate comprehensive investigation of tumor–immune interactions, we have designed a user-friendly web portal TISIDB, which integrated multiple types of data resources in oncoimmunology. First, we manually curated 4176 records from 2530 publications, which reported 988 genes related to anti-tumor immunity. Second, genes associated with the resistance or sensitivity of tumor cells to T cell-mediated killing and immunotherapy were identified by analyzing high-throughput screening and genomic profiling data. Third, associations between any gene and immune features, such as lymphocytes, immunomodulators and chemokines, were pre-calculated for 30 TCGA cancer types. In TISIDB, biologists can cross-check a gene of interest about its role in tumor–immune interactions through literature mining and high-throughput data analysis, and generate testable hypotheses and high quality figures for publication.

Availability and implementation
http://cis.hku.hk/TISIDB

Supplementary information
Supplementary data are available at Bioinformatics online.
CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles
Authors: Leite Pereira Adrien , Lambotte Olivier , Le Grand Roger , Cosma Antonio , Tchitchek Nicolas 
Published: March 2019

Abstract

Motivation
Flow and mass cytometry are experimental techniques used to measure the level of proteins expressed by cells at the single-cell resolution. Several algorithms were developed in flow cytometry to increase the number of simultaneously measurable markers. These approaches aim to combine phenotypic information of different cytometric profiles obtained from different cytometry panels.

Results
We present here a new algorithm, called CytoBackBone, which can merge phenotypic information from different cytometric profiles. This algorithm is based on nearest-neighbor imputation, but introduces the notion of acceptable and non-ambiguous nearest neighbors. We used mass cytometry data to illustrate the merging of cytometric profiles obtained by the CytoBackBone algorithm.

Availability and implementation
CytoBackBone is implemented in R and the source code is available at https://github.com/tchitchek-lab/CytoBackBone.

Supplementary information
Supplementary data are available at Bioinformatics online.
Oxytocin involves in chronic stress-evoked melanoma metastasis via β-arrestin 2-mediated ERK signaling pathway
Authors: Ji Haoyi , Liu Na , Li Jing , Chen Dawei , Luo Dan , Sun Qian , Yin Yingchun , Liu Yanli , Bu Bing , Chen Xiaoyang , Li Jingxin 
Published: March 2019

Abstract
Stress is associated with an increased risk of lung metastasis in melanoma. However, the underlying mechanism is elusive. Oxytocin (OXT), a neurohormone produced by the hypothalamus, plays a vital role in laboring induction and lactation. Emerging evidence suggests that OXT also regulates human emotions, social cognition, social behaviors and stress-related disorders. Here, we reported that a significant up-regulation of oxytocin receptors (OXTRs) was observed in malignant melanoma. The activation of OXTRs dramatically promoted migration, invasion and angiogenesis but not the proliferation of melanoma cells in vitro and in vivo via β-arrestin 2-dependent ERK-VEGF/MMP-2 pathway. Next, chronic restraint stress significantly elevated the plasma level of OXT. Notably, 21 days chronic restraint stress facilitated lung metastasis of melanoma and reduced overall survival in mice, which were largely abrogated by knocking down either OXTR or β-arrestin 2. These findings provide evidence that chronic stress hormone-OXT promotes lung metastasis of melanoma via a β-arrestin 2-dependent mechanism and suggest that OXT, a novel pro-metastasis factor, is a potential therapeutic target for melanoma.
Dopamine Receptor Expression Among Local and Visual Cortex-Projecting Frontal Eye Field Neurons
Authors: Mueller Adrienne , Krock Rebecca M , Shepard Steven , Moore Tirin 
Published: March 2019

Abstract
Dopaminergic modulation of prefrontal cortex plays an important role in numerous cognitive processes, including attention. The frontal eye field (FEF) is modulated by dopamine and has an established role in visual attention, yet the underlying circuitry upon which dopamine acts is not known. We compared the expression of D1 and D2 dopamine receptors (D1Rs and D2Rs) across different classes of FEF neurons, including those projecting to dorsal or ventral extrastriate cortex. First, we found that both D1Rs and D2Rs are more prevalent on pyramidal neurons than on several classes of interneurons and are particularly prevalent on putatively long-range projecting pyramidals. Second, higher proportions of pyramidal neurons express D1Rs than D2Rs. Third, overall a higher proportion of inhibitory neurons expresses D2Rs than D1Rs. Fourth, among inhibitory interneurons, a significantly higher proportion of parvalbumin+ neurons expresses D2Rs than D1Rs, and a significantly higher proportion of calbindin+ neurons expresses D1Rs than D2Rs. Finally, compared with D2Rs, virtually all of the neurons with identified projections to both dorsal and ventral extrastriate visual cortex expressed D1Rs. Our results demonstrate that dopamine tends to act directly on the output of the FEF and that dopaminergic modulation of top-down projections to visual cortex is achieved predominately via D1Rs.