bluuebunny/crossref_metadata_2025_split huggingface dataset:
SIRPα+dendritic cells regulate homeostasis of fibroblastic reticular cells via TNF receptor ligands in the adult spleen
Authors: Saito Yasuyuki , Respatika Datu , Komori Satomi , Washio Ken , Nishimura Taichi , Kotani Takenori , Murata Yoji , Okazawa Hideki , Ohnishi Hiroshi , Kaneko Yoriaki , Yui Katsuyuki , Yasutomo Koji , Nishigori Chikako , Nojima Yoshihisa , Matozaki Takashi 
Published: November 2017

SignificanceHomeostasis of Pdpn+fibroblastic reticular cells (FRCs) is thought to be regulated by hematopoietic cells. However, the cellular and molecular mechanisms of such homeostasis have been poorly understood, especially under the steady-state condition in adults. We show that dendritic cells, particularly CD4+conventional dendritic cells (cDCs), are crucial for the homeostasis of FRCs in the adult spleen under the steady-state condition. The production of TNF receptor ligands by CD4+cDCs regulates such homeostasis of FRCs, with SIRPα and CD47 likely being indispensable for the production of TNFR ligands by CD4+cDCs. The CD47–SIRPα interaction on CD4+cDCs may thus control the homeostasis of FRCs, which in turn maintain homeostasis of T cells in the white pulp of the spleen.
Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily
Authors: Crow Allister , Greene Nicholas P. , Kaplan Elise , Koronakis Vassilis 
Published: November 2017

Significance
Bacterial ABC transporters typically mediate transport of substrates across the cytoplasmic membrane, using either alternating access or toppling-based mechanisms. The noncanonical ABC transporter MacB does not behave in this manner, but instead couples cytoplasmic ATP hydrolysis with periplasmic conformational changes that drive substrates from the periplasm to the extracellular space via the TolC exit duct. Here we describe the mechanotransmission mechanism of MacB in molecular detail by comparing ATP-bound and nucleotide-free structures. We further show that MacB shares its structural architecture with an entire superfamily of ABC transporters responsible for fundamental bacterial processes, including cell division and outer membrane biogenesis, suggesting a common mode of operation, and raise the possibility of targeting such proteins for the development of new antibiotics.
Coordinated regulation of heterochromatin inheritance by Dpb3–Dpb4 complex
Authors: He Haijin , Li Yang , Dong Qianhua , Chang An-Yun , Gao Feng , Chi Zhongxuan , Su Min , Zhang Faben , Ban Hyoju , Martienssen Rob , Chen Yu-hang , Li Fei 
Published: November 2017

Significance
Epigenetic modifications, such as histone methylation, are crucial for gene expression, chromatin organization, and cellular identity. These modifications can be faithfully transmitted to daughter cells during the cell cycle. How epigenetic marks are inherited through DNA replication remains poorly understood. Histone hypoacetylation and histone H3 lysine 9 (H3K9) methylation are two conserved epigenetic marks of heterochromatin, a transcriptionally repressive form of chromatin. Here we demonstrate that the two conserved small histone-fold subunits of the DNA polymerase epsilon complex, Dpb3 and Dpb4, form a heterodimer and play an important role in coordinating the inheritance of histone hypoacetylation and H3K9 methylation during replication. This study provides mechanistic insights into how epigenetic marks in heterochromatin are transmitted through the cell cycle.
Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired
Authors: Wanrooij Paulina H. , Engqvist Martin K. M. , Forslund Josefin M. E. , Navarrete Clara , Nilsson Anna Karin , Sedman Juhan , Wanrooij Sjoerd , Clausen Anders R. , Chabes Andrei 
Published: November 2017

Significance
Mitochondria are essential for energy production. However, a number of defects that affect the cellular levels of deoxyribonucleoside triphosphates (dNTPs), the building blocks of DNA, threaten the proper maintenance of mitochondrial DNA (mtDNA) and lead to human disease. We show that imbalances in the total cellular dNTP pool are transmitted into the mitochondria and that they alter the frequency of ribonucleotides, the building blocks of RNA, that are incorporated into mtDNA in yeast. We further show that yeast mitochondria lack repair pathways that remove embedded ribonucleotides. Because ribonucleotides are a known cause of genome instability, our findings may explain why altered cellular dNTP pools lead to defects in mtDNA but not in nuclear DNA in certain human diseases.
Peptidyl arginine deiminase immunization induces anticitrullinated protein antibodies in mice with particular MHC types
Authors: Arnoux Fanny , Mariot Charlotte , Peen Elisa , Lambert Nathalie C. , Balandraud Nathalie , Roudier Jean , Auger Isabelle 
Published: November 2017

SignificanceThe presence and development of autoantibodies to citrullinated proteins (ACPAs) are highly associated with rheumatoid arthritis (RA). The mechanisms leading to the production of ACPAs are unknown. Here, we propose a model to explain the emergence of anticitrullinated protein autoantibodies in RA. Indeed, we could trigger the development of anticitrullinated fibrinogen autoantibodies in normal mice by immunization with peptidyl arginine deiminase (PAD), most likely through a hapten/carrier mechanism in which the carrier is the PAD enzyme that performs citrullination and the hapten is any protein being citrullinated (hence bound) by PAD. Our results allow us to understand the birth of anticitrullin autoimmunity.
Near-infrared remotely triggered drug-release strategies for cancer treatment
Authors: Goodman Amanda M. , Neumann Oara , Nørregaard Kamilla , Henderson Luke , Choi Mi-Ran , Clare Susan E. , Halas Naomi J. 
Published: November 2017

Significance
Gold-based nanoparticles that absorb near-infrared light have shown the potential to selectively target and treat cancer through highly efficient light-to-heat conversion. This study shows that gold-based nanoparticles can be coated with drug-bearing host biomolecules for remotely triggerable release. Near-infrared light-triggered release of docetaxel from a nanoshell-based DNA host complex, and lapatinib from nanoshell-based DNA and human serum albumin host complexes, is demonstrated. There is a strong dependence upon the type of near-infrared illumination––continuous wave or pulsed––specific to the drug-laden host molecules. Localizing drug delivery both spatially and temporally by combining nanoshell-based complexes and pulsed-laser irradiation is a promising strategy for highly controlled drug delivery that can apply to a myriad of therapeutic applications.
Syntenin mediates SRC function in exosomal cell-to-cell communication
Authors: Imjeti Naga Sailaja , Menck Kerstin , Egea-Jimenez Antonio Luis , Lecointre Celine , Lembo Frederique , Bouguenina Habib , Badache Ali , Ghossoub Rania , David Guido , Roche Serge , Zimmermann Pascale 
Published: November 2017

Significance
Viral-like nanovesicles of endosomal origin, or “exosomes,” are newly recognized vehicles of signals that cells use to communicate, in various systemic diseases, including cancer. Yet the molecular mechanisms that regulate the biogenesis and activity of exosomes remain obscure. Here, we establish that the oncogenic protein SRC stimulates the secretion of exosomes loaded with syntenin and syndecans, known co-receptors for a plethora of signaling and adhesion molecules. SRC phosphorylates conserved tyrosine residues in the syndecans and syntenin and stimulates their endosomal budding. Moreover, SRC-dependent exosomes have a promigratory activity that strictly depends on syntenin expression. This work sheds light on a function of SRC in cell-to-cell communication and mechanisms of exosome biogenesis and activity, with potential broad impact for physiopathology.
Poaceae-specificMS1encodes a phospholipid-binding protein for male fertility in bread wheat
Authors: Wang Zheng , Li Jian , Chen Shaoxia , Heng Yanfang , Chen Zhuo , Yang Jing , Zhou Kuanji , Pei Jiawei , He Hang , Deng Xing Wang , Ma Ligeng 
Published: November 2017

SignificanceHeterosis provides an important strategy for increasing crop yield, and breeding and adoption of hybrid crops is a feasible way to increase crop yields. Male sterility is an essential trait in hybrid seed production for monoclinous crops, including wheat. Heterosis in wheat was observed approximately 100 y ago. However, very little commercial hybrid wheat is planted in the world because of the lack of a suitable male sterility trait. Therefore, understanding the molecular nature of male fertility in wheat is critical for hybrid wheat development. Here, we report the cloning and molecular, biochemical, and cell-biological characterizations ofMale Sterility 1(Ms1) in bread wheat, and provide a foundation for large-scale commercial hybrid wheat breeding and hybrid seed production.
PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences
Authors: Avvaru Akshay Kumar , Sowpati Divya Tej , Mishra Rakesh Kumar 
Published: November 2017

Abstract

Motivation
Microsatellites or Simple Sequence Repeats (SSRs) are short tandem repeats of DNA motifs present in all genomes. They have long been used for a variety of purposes in the areas of population genetics, genotyping, marker-assisted selection and forensics. Numerous studies have highlighted their functional roles in genome organization and gene regulation. Though several tools are currently available to identify SSRs from genomic sequences, they have significant limitations.

Results
We present a novel algorithm called PERF for extremely fast and comprehensive identification of microsatellites from DNA sequences of any size. PERF is several fold faster than existing algorithms and uses up to 5-fold lesser memory. It provides a clean and flexible command-line interface to change the default settings, and produces output in an easily-parseable tab-separated format. In addition, PERF generates an interactive and stand-alone HTML report with charts and tables for easy downstream analysis.

Availability and implementation
PERF is implemented in the Python programming language. It is freely available on PyPI under the package name perf_ssr, and can be installed directly using pip or easy_install. The documentation of PERF is available at https://github.com/rkmlab/perf. The source code of PERF is deposited in GitHub at https://github.com/rkmlab/perf under an MIT license.

Supplementary information
Supplementary data are available at Bioinformatics online.
How Am I Doing? Perceived Financial Well-Being, Its Potential Antecedents, and Its Relation to Overall Well-Being
Authors: Netemeyer Richard G , Warmath Dee , Fernandes Daniel , Lynch John G 
Published: November 2017

Abstract
Though perceived financial well-being is viewed as an important topic of consumer research, the literature contains no accepted definition of this construct. Further, there has been little systematic examination of how perceived financial well-being may affect overall well-being. Using consumer financial narratives, several large-scale surveys, and two experiments, we conceptualize perceived financial well-being as two related but separate constructs: 1) stress related to the management of money today (current money management stress), and 2) a sense of security in one’s financial future (expected future financial security). We develop and validate measures of these constructs (web appendix A) and then demonstrate their relationship to overall well-being, controlling for other life domains and objective measures of the financial domain. Our findings demonstrate that perceived financial well-being is a key predictor of overall well-being and comparable in magnitude to the combined effect of other life domains (job satisfaction, physical health assessment, and relationship support satisfaction). Further, the relative importance of current money management stress to overall well-being varies by income groups and due to the differing antecedents of current money management stress and expected future financial security. Implications for financial well-being and education efforts are offered.
The immediate environment of an astrophysical black hole
Authors: Contopoulos I 
Published: November 2017

Abstract
In view of the upcoming observations with the Event Horizon Telescope (EHT), we present our thoughts on the immediate environment of an astrophysical black hole. We are concerned that two approximations used in general relativistic magnetohydrodynamic numerical simulations, namely numerical density floors implemented near the base of the black hole jet, and a magnetic field that comes from large distances, may mislead our interpretation of the observations. We predict that three physical processes will manifest themselves in EHT observations, namely dynamic pair formation just above the horizon, electromagnetic energy dissipation along the boundary of the black hole jet, and a region of weak magnetic field separating the black hole jet from the disc wind.
Bipolar H ii regions produced by cloud–cloud collisions
Authors: Whitworth Anthony , Lomax Oliver , Balfour Scott , Mège Pierre , Zavagno Annie , Deharveng Lise 
Published: November 2017

Abstract
We suggest that bipolar H ii regions may be the aftermath of collisions between clouds. Such a collision will produce a shock-compressed layer, and a star cluster can then condense out of the dense gas near the center of the layer. If the clouds are sufficiently massive, the star cluster is likely to contain at least one massive star, which emits ionizing radiation, and excites an H ii region, which then expands, sweeping up the surrounding neutral gas. Once most of the matter in the clouds has accreted onto the layer, expansion of the H ii region meets little resistance in directions perpendicular to the midplane of the layer, and so it expands rapidly to produce two lobes of ionized gas, one on each side of the layer. Conversely, in directions parallel to the midplane of the layer, expansion of the H ii region stalls due to the ram pressure of the gas that continues to fall towards the star cluster from the outer parts of the layer; a ring of dense neutral gas builds up around the waist of the bipolar H ii region, and may spawn a second generation of star formation. We present a dimensionless model for the flow of ionized gas in a bipolar H ii region created according to the above scenario, and predict the characteristics of the resulting free–free continuum and recombination-line emission. This dimensionless model can be scaled to the physical parameters of any particular system. Our intention is that these predictions will be useful in testing the scenario outlined above, and thereby providing indirect support for the role of cloud–cloud collisions in triggering star formation.
Technological Distractions (Part 2): A Summary of Approaches to Manage Clinical Alarms With Intent to Reduce Alarm Fatigue
Authors: Winters Bradford D. , Cvach Maria M. , Bonafide Christopher P. , Hu Xiao , Konkani Avinash , O’Connor Michael F. , Rothschild Jeffrey M. , Selby Nicholas M. , Pelter Michele M. , McLean Barbara , Kane-Gill Sandra L. 
Published: November 2017

Objective:
Alarm fatigue is a widely recognized safety and quality problem where exposure to high rates of clinical alarms results in desensitization leading to dismissal of or slowed response to alarms. Nonactionable alarms are thought to be especially problematic. Despite these concerns, the number of clinical alarm signals has been increasing as an everincreasing number of medical technologies are added to the clinical care environment.

Data Sources:
PubMed, SCOPUS, Embase, and CINAHL.

Study Selection:
We performed a systematic review of the literature focused on clinical alarms. We asked a primary key question; “what interventions have been attempted and resulted in the success of reducing alarm fatigue?” and 3-secondary key questions; “what are the negative effects on patients/families; what are the balancing outcomes (unintended consequences of interventions); and what human factor approaches apply to making an effective alarm?”

Data Extraction:
Articles relevant to the Key Questions were selected through an iterative review process and relevant data was extracted using a standardized tool.

Data Synthesis:
We found 62 articles that had relevant and usable data for at least one key question. We found that no study used/developed a clear definition of “alarm fatigue.” For our primary key question 1, the relevant studies focused on three main areas: quality improvement/bundled activities; intervention comparisons; and analysis of algorithm-based false and total alarm suppression. All sought to reduce the number of total alarms and/or false alarms to improve the positive predictive value. Most studies were successful to varying degrees. None measured alarm fatigue directly.

Conclusions:
There is no agreed upon valid metric(s) for alarm fatigue, and the current methods are mostly indirect. Assuming that reducing the number of alarms and/or improving positive predictive value can reduce alarm fatigue, there are promising avenues to address patient safety and quality problem. Further investment is warranted not only in interventions that may reduce alarm fatigue but also in defining how to best measure it.
Acute Physiologic Stress and Subsequent Anxiety Among Family Members of ICU Patients
Authors: Beesley Sarah J. , Hopkins Ramona O. , Holt-Lunstad Julianne , Wilson Emily L. , Butler Jorie , Kuttler Kathryn G. , Orme James , Brown Samuel M. , Hirshberg Eliotte L. 
Published: November 2017

Objectives:
The ICU is a complex and stressful environment and is associated with significant psychologic morbidity for patients and their families. We sought to determine whether salivary cortisol, a physiologic measure of acute stress, was associated with subsequent psychologic distress among family members of ICU patients.

Design:
This is a prospective, observational study of family members of adult ICU patients.

Setting:
Adult medical and surgical ICU in a tertiary care center.

Subjects:
Family members of ICU patients.

Interventions:
Participants provided five salivary cortisol samples over 24 hours at the time of the patient ICU admission. The primary measure of cortisol was the area under the curve from ground; the secondary measure was the cortisol awakening response. Outcomes were obtained during a 3-month follow-up telephone call. The primary outcome was anxiety, measured by the Hospital Anxiety and Depression Scale-Anxiety. Secondary outcomes included depression and posttraumatic stress disorder.

Measurements and Main Results:
Among 100 participants, 92 completed follow-up. Twenty-nine participants (32%) reported symptoms of anxiety at 3 months, 15 participants (16%) reported depression symptoms, and 14 participants (15%) reported posttraumatic stress symptoms. In our primary analysis, cortisol level as measured by area under the curve from ground was not significantly associated with anxiety (odds ratio, 0.94; p = 0.70). In our secondary analysis, however, cortisol awakening response was significantly associated with anxiety (odds ratio, 1.08; p = 0.02).

Conclusions:
Roughly one third of family members experience anxiety after an ICU admission for their loved one, and many family members also experience depression and posttraumatic stress. Cortisol awakening response is associated with anxiety in family members of ICU patients 3 months following the ICU admission. Physiologic measurements of stress among ICU family members may help identify individuals at particular risk of adverse psychologic outcomes.
Memantine, an NMDA Receptor Antagonist, Prevents Thyroxin-induced Hypertension, but Not Cardiac Remodeling
Authors: Repas Steven J. , Saad Nancy S. , Janssen Paul M. L. , Elnakish Mohammad T. 
Published: November 2017

Abstract:Stimulation of glutamatergic tone has been causally linked to myocardial pathogenesis and amplified systemic blood pressure (BP). Memantine, a noncompetitiveN-methyl-d-aspartate glutamatergic receptor (NMDA-R) antagonist, has been proposed to be an active cardioprotective drug. However, the efficacy of memantine and subsequently the possible involvement of the NMDA-R in the thyroxin (T4)-induced cardiovascular complications have never been investigated. We examined the effect of memantine (30 mg·kg−1·d−1) on the T4 (500 μg·kg−1·d−1)-provoked increase in mouse BP, cardiac hypertrophy indicated by enlarged overall myocardial mass, and reformed reactions of the contractile myocardium both in vivo and ex vivo after 2 weeks of treatment. Memantine alone did not result in any cardiovascular pathology in mice. Instead, memantine significantly prevented the T4-triggered systemic hypertension. But, it did not reverse cardiac hypertrophy, coupled in vivo left ventricular dysfunction (LV) or ex vivo right ventricular (RV) papillary muscle contractile alterations of the T4-treated mice. Our results openly direct the cardiovascular safety and tolerability of memantine therapy. Yet, extra research is necessary to endorse these prospective advantageous outcomes. Also, we believe that this is the first study to inspect the possible role of NMDA-R in the T4-stimulated cardiovascular disorders and concluded that NMDA-R could play a key role in the T4-induced hypertension.
Trajectories and predictors of the long-term course of low back pain: cohort study with 5-year follow-up
Authors: Chen Ying , Campbell Paul , Strauss Victoria Y. , Foster Nadine E. , Jordan Kelvin P. , Dunn Kate M. 
Published: November 2017

Abstract
Low back pain (LBP) is a major health challenge globally. Research has identified common trajectories of pain over time. We aimed to investigate whether trajectories described in 1 primary care cohort can be confirmed in another, and to determine the prognostic value of factors collected 5 years prior to the identification of the trajectory. The study was conducted on 281 patients who had consulted primary care for LBP, at that point completed a baseline questionnaire, and then returned a questionnaire at 5-year follow-up plus at least 3 (of 6) subsequent monthly questionnaires. Baseline factors were measured using validated tools. Pain intensity scores from the 5-year follow-up and monthly questionnaires were used to assign participants into 4 previously derived pain trajectories (no or occasional mild, persistent mild, fluctuating, and persistent severe), using latent class analysis. Posterior probabilities of belonging to each cluster were estimated for each participant. The posterior probabilities for the assigned clusters were very high (>0.90) for each cluster except for the smallest “fluctuating” cluster (0.74). Lower social class and higher pain intensity were significantly associated with a more severe trajectory 5 years later, as were patients' perceptions of the greater consequences and longer duration of pain, and greater passive behavioural coping. Low back pain trajectories identified previously appear generalizable. These allow better understanding of the long-term course of LBP, and effective management tailored to individual trajectories needs to be identified.