bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ornithine decarboxylase regulates M1 macrophage activation and mucosal inflammation via histone modifications
Authors: Hardbower Dana M. , Asim Mohammad , Luis Paula B. , Singh Kshipra , Barry Daniel P. , Yang Chunying , Steeves Meredith A. , Cleveland John L. , Schneider Claus , Piazuelo M. Blanca , Gobert Alain P. , Wilson Keith T. 
Published: January 2017

SignificanceThe pathogenesis of many bacteria is enhanced by the ability to establish persistent infection. Macrophages, particularly classically activated M1 macrophages, provide essential functions in the initiation of antibacterial immune responses. The regulation of macrophage activation is still poorly understood. Here, we demonstrate that ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine synthesis, regulates M1 activation duringHelicobacter pyloriandCitrobacter rodentiuminfection. Deletion ofOdcin macrophages resulted in increased inflammation and decreased bacterial persistence in mouse models. The enhanced M1 response was due to alterations in histone modifications, resulting in changes in chromatin structure and up-regulated transcription. These findings represent a novel mechanism by which ODC directly regulates macrophage activation and provides new insights into understanding bacterial persistence.
Recognition of protein-linked glycans as a determinant of peptidase activity
Authors: Noach Ilit , Ficko-Blean Elizabeth , Pluvinage Benjamin , Stuart Christopher , Jenkins Meredith L. , Brochu Denis , Buenbrazo Nakita , Wakarchuk Warren , Burke John E. , Gilbert Michel , Boraston Alisdair B. 
Published: January 2017

Significance
Protein glycosylation is one of the most abundant and important posttranslational modifications where the protein-linked glycans can impart specific physiochemical properties to the glycoprotein and/or the glycans themselves can mediate particular biological functions. The degradation of glycosylated proteins in normal or pathogenic processes, therefore, is an important biological process. This study reveals the molecular basis of how peptidases can use the O-glycans present on glycoproteins as a critical determinant of peptidase activity and, in doing so, provides unique insight into how peptidases may directly use posttranslational modifications present on their substrates to influence recognition and peptide bond cleavage.
Rhythm judgments reveal a frequency asymmetry in the perception and neural coding of sound synchrony
Authors: Wojtczak Magdalena , Mehta Anahita H. , Oxenham Andrew J. 
Published: January 2017

Significance
Why music developed in the way it did is of fundamental interest across the sciences, arts, and humanities. A recent study reported that rhythm perception was enhanced for low-pitch sounds, and suggested that this enhancement may provide a biological explanation for why low-pitch instruments generally provide the beat in music. Our results refute this hypothesis, but reveal a robust asymmetry in the perception and cortical coding of synchrony between low and high tones. Synchrony is an important and ubiquitous property of sounds emanating from the same source. Our findings suggest a way in which the veridical perception of simultaneous events is maintained in the face of delays produced both by cochlear processing and by the inherent properties of acoustic sources.
Eight-coordinate fluoride in a silicate double-four-ring
Authors: Goesten Maarten G. , Hoffmann Roald , Bickelhaupt F. Matthias , Hensen Emiel J. M. 
Published: January 2017

Significance
Although strain and bonding are often antagonists in chemistry, they may also work together. When fluoride enters a silicate double-four-ring (D4R), their conjoined effect leads to fluoride binding to 8 silicon atoms. The strain comes from D4R, a molecular unit that acts (and looks) like a box. And, as we can expect from that geometrical constraint, it experiences strain when being deformed. Avoiding such deformation, the box pushes fluoride toward its center. Yet even there, fluoride engages in orbital overlap (hypervalent bonding) with the highly delocalized antibonding orbitals of D4R, and significant charge transfer occurs. The unusual number of bonds, around the smallest existing anion, leaves us pondering the limits of hypervalence.
Trogocytosis of peptide–MHC class II complexes from dendritic cells confers antigen-presenting ability on basophils
Authors: Miyake Kensuke , Shiozawa Nozomu , Nagao Toshihisa , Yoshikawa Soichiro , Yamanishi Yoshinori , Karasuyama Hajime 
Published: January 2017

Significance
Recent studies have revealed that basophils, the rarest granulocytes, have crucial roles in various immune responses. Among their properties, the MHC class II (MHC-II) expression and their function as antigen-presenting cells are matters of considerable controversy. Here we show that basophils indeed express MHC-II on the cell surface, but with little transcription of corresponding genes. This could be achieved by the acquisition of peptide–MHC-II complexes from dendritic cells via cell contact-dependent trogocytosis in vitro and in vivo. The acquired complexes enabled basophils to stimulate and differentiate T cells toward Th2 cells. Thus, the present study clarified the mechanism by which basophils display MHC-II on the cell surface and appears to reconcile some discrepancies observed in previous studies.
Measurement of cortical elasticity in
Drosophila melanogaster
embryos using ferrofluids
Authors: Doubrovinski Konstantin , Swan Michael , Polyakov Oleg , Wieschaus Eric F. 
Published: January 2017

Significance
A physically realistic understanding of any morphogenetic process requires the knowledge of material properties of the tissue, almost all of which we currently lack. This paper introduces a technique that allows measuring physical properties of the interior constituents of a fruit fly embryo. To interpret our measurements, we developed a computational framework that allowed us to deduce underlying material properties of embryonic tissues from the measured data. Using our protocol we have determined a number of key physical properties of embryonic tissue (e.g., cytoplasmic viscosity and the timescale of elastic stress relaxation). Finally, we used pharmacological perturbations to examine which cellular structures are responsible for the observed elastic response.
RFamide-related peptide-3 (RFRP-3) suppresses sexual maturation in a eusocial mammal
Authors: Peragine Diana E. , Pokarowski Martha , Mendoza-Viveros Lucia , Swift-Gallant Ashlyn , Cheng Hai-Ying M. , Bentley George E. , Holmes Melissa M. 
Published: January 2017

SignificanceNaked mole rats exhibit the most profound case of socially induced infertility among mammals. They live in sizable colonies where breeding is monopolized by two to four dominant animals; all other colony members retain prepubertal gonadal quiescence until death or removal from the colony. Proximate mechanisms underlying this phenomenon are unknown but presumably involve integration of environmental cues by the brain into neuroendocrine signals that impact the gonadotropin-releasing hormone (GnRH) system. The role of RFamide-related peptide-3 (RFRP-3) in modulating the reproductive axis in vertebrates has been well documented, making it a prime candidate as a gatekeeper for puberty onset. Here, we present evidence for RFRP-3–mediated social delay of puberty and define a previously unidentified neuroendocrine component of social control of sexual maturation.
Helical structure, stability, and dynamics in human apolipoprotein E3 and E4 by hydrogen exchange and mass spectrometry
Authors: Chetty Palaniappan S. , Mayne Leland , Lund-Katz Sissel , Englander S. Walter , Phillips Michael C. 
Published: January 2017

Significance
Apoliprotein E (apoE) serves as a cholesterol transport protein in both the peripheral circulation and the brain. In humans, the less common apoE4 isoform, which differs from the most abundant parent apoE3 by a single C112R substitution, is associated with increased incidence of cardiovascular disease and Alzheimer’s disease. To understand the structural basis for the altered functionality, we used hydrogen exchange mass spectrometry to compare the structure, stability, and molecular dynamics of these isoforms. The C112R substitution in apoE4 leads to unfolding of certain helical segments that reduces self-association and is expected to enhance the binding of apoE4 to triglyceride-rich lipoprotein particles in plasma and to amyloid-β deposits in the brain.
Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage
Authors: Lehtinen Sonja , Blanquart François , Croucher Nicholas J. , Turner Paul , Lipsitch Marc , Fraser Christophe 
Published: January 2017

Significance
The relationship between a population’s antibiotic consumption and the frequency of antibiotic resistance among bacteria colonizing that population is not fully understood. Antibiotic resistant and sensitive strains compete for available hosts—we would therefore expect the fitter strain to dominate. Instead, we observe stable coexistence of both strains. In this work, we propose an explanation for this coexistence by showing the fitness advantage of resistance depends on a bacterial strain’s duration of carriage. This finding ties the evolution of resistance to any genetic mechanism affecting duration of carriage. These insights could allow more accurate prediction of future resistance levels and play a role in informing strategies to prevent the spread of resistance.
Transmembrane protein 108 is required for glutamatergic transmission in dentate gyrus
Authors: Jiao Hui-Feng , Sun Xiang-Dong , Bates Ryan , Xiong Lei , Zhang Lei , Liu Fang , Li Lei , Zhang Hong-Sheng , Wang Shun-Qi , Xiong Ming-Tao , Patel Mihir , Stranahan Alexis M. , Xiong Wen-Cheng , Li Bao-Ming , Mei Lin 
Published: January 2017

SignificanceDentate gyrus (DG) dysfunction has been implicated in schizophrenia, a disabling psychiatric disorder. However, underlying pathophysiological mechanisms are not clear. We provide evidence that Tmem108, a novel schizophrenia-associated gene, is highly enriched in DG granule neurons. Tmem108 is required for spine development and glutamatergic transmission. Further investigations indicate a critical role of Tmem108 for AMPA receptor expression in postsynaptic compartments. Mutation ofTmem108leads to schizophrenia-related behavioral deficits. These results provide insight into a potential pathophysiological mechanism for DG dysfunction in schizophrenia.
Kinetic assay shows that increasing red cell volume could be a treatment for sickle cell disease
Authors: Li Quan , Henry Eric R. , Hofrichter James , Smith Jeffrey F. , Cellmer Troy , Dunkelberger Emily B. , Metaferia Belhu B. , Jones-Straehle Stacy , Boutom Sarah , Christoph Garrott W. , Wakefield Terri H. , Link Mary E. , Staton Dwayne , Vass Erica R. , Miller Jeffery L. , Hsieh Matthew M. , Tisdale John F. , Eaton William A. 
Published: January 2017

SignificanceSickle cell disease can be treated by preventing polymerization of the mutant hemoglobin to form fibers during the time that red cells are transiting the smallest vessels of the tissues. However, most drugs in clinical trials are aimed at reducing the sequelae of fiber formation, such as inflammation and adhesion to the vascular endothelium. Searching for drugs that increase the delay before polymerization, which allows more cells to escape the small vessels before fibers form, has been hampered by the lack of a quantitative and sensitive assay, which we describe in this work. With this assay, we show that increasing the delay time by increasing red cell volume to reduce the intracellular hemoglobin concentration is a viable approach to therapy.
Antiviral screening identifies adenosine analogs targeting the endogenous dsRNALeishmaniaRNA virus 1 (LRV1) pathogenicity factor
Authors: Kuhlmann F. Matthew , Robinson John I. , Bluemling Gregory R. , Ronet Catherine , Fasel Nicolas , Beverley Stephen M. 
Published: January 2017

SignificanceThe endogenous double-stranded RNA virusLeishmaniavirus(LRV1) has been implicated as a pathogenicity factor for leishmaniasis in rodent models and human disease, and associated with drug-treatment failures. As a first step toward the identification of therapeutic LRV1 inhibitors, we identified two adenosine analogs that selectively inhibited LRV1 replication. These analogs were used as tools to confirm that viral inheritance is by random segregation, as well as to generate LRV1-cured lines ofLeishmania guyanensis,which correspondingly lost the increased pathogenicity conferred by LRV1. These compounds hold promise as leads to ameliorate the severity of LRV1-bearingLeishmaniainfections, and raise the possibility of targeting other protozoal infections whose pathogenicity may be exacerbated by similar endogenous viruses.
Continual renewal and replication of persistentLeishmania majorparasites in concomitantly immune hosts
Authors: Mandell Michael A. , Beverley Stephen M. 
Published: January 2017

SignificancePersistent parasites contribute to the maintenance of protective immune responses through concomitant immunity, but our understanding of how they do so has been limited by the difficulties associated with their low numbers. Our studies indicate that forLeishmaniasubstantial parasite replication occurs in persistent infections, with most parasites found within activated antigen-presenting cells. Parasite replication serves to maintain the infection and likely also provides a constant source of parasite antigens for immune stimulation and the maintenance of protective immunity. Collectively, these studies suggest a framework to understand concomitant immunity that may be applicable to other persistent pathogens.
The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events
Authors: Urbach Jonathan M. , Ausubel Frederick M. 
Published: January 2017

Significance
Instances of convergent evolution in innate immune systems can reveal fundamental principles of immunity. We use phylogenetic reconstruction and tests of alternative evolutionary hypotheses combined with ancestral state reconstruction and an analysis of the phylogenetic distribution of the nucleotide binding site–leucine rich repeat (NBS-LRR) architecture to demonstrate that most likely, two distinct and separate evolutionary events gave rise to the NBS-LRR architecture in plant resistance proteins (R-proteins) and metazoan NOD-like receptors (NLRs), and furthermore, the STAND NTPase of both protein families was likely inherited from ancestral proteins with an NBS–tetratricopeptide (TPR) architecture. The implication is that the NBS-LRR architecture has special functionality for innate immune receptors.
Myosin-driven transport network in plants
Authors: Kurth Elizabeth G. , Peremyslov Valera V. , Turner Hannah L. , Makarova Kira S. , Iranzo Jaime , Mekhedov Sergei L. , Koonin Eugene V. , Dolja Valerian V. 
Published: January 2017

Significance
A key feature of plant cells is rapid cytoplasmic streaming that is driven by myosin motors. However, specific mechanisms of myosin-dependent streaming are poorly understood. Here, we characterize a dense network of plant myosins and their receptors and adaptors that, jointly with myosins, appear to mediate cytoplasmic streaming through distinct endomembrane compartments. We additionally present data suggestive of a myosin-dependent nucleocytoplasmic trafficking pathway. The myosin network is an ancient functional module that was already present in the common ancestor of green algae and land plants but underwent a major expansion in the latter, probably contributing to land colonization by plants.
Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish
Authors: Rabinowitz Jeremy S. , Robitaille Aaron M. , Wang Yuliang , Ray Catherine A. , Thummel Ryan , Gu Haiwei , Djukovic Danijel , Raftery Daniel , Berndt Jason D. , Moon Randall T. 
Published: January 2017

Significance
In vertebrates, proper patterning during appendage regeneration is regulated by positional memory—a cellular property hypothesized to rely on gradients of molecules present in uninjured limbs. Only one gene, exclusive to salamanders, has been shown to regulate positional memory and be expressed in a gradient in the uninjured limb. To identify new candidate effectors of positional memory, we mapped the abundance of RNAs, proteins, and metabolites along the uninjured zebrafish tail fin. We identified hundreds of molecular gradients and generated a high-confidence list of 32 genes and 42 metabolites that are candidate effectors of positional memory in zebrafish. Furthermore, expression patterns discovered here may help to explain how size-homeostasis and patterning are maintained in a complex adult tissue.
A functional endonuclease Q exists in the bacterial domain: identification and characterization of endonuclease Q from Bacillus pumilus
Authors: Shiraishi Miyako , Ishino Sonoko , Cann Isaac , Ishino Yoshizumi 
Published: January 2017

Abstract
DNA base deamination occurs spontaneously under physiological conditions and is promoted by high temperature. Therefore, hyperthermophiles are expected to have efficient repair systems of the deaminated bases in their genomes. Endonuclease Q (EndoQ) was originally identified from the hyperthermophlic archaeon, Pyrococcus furiosus, as a hypoxanthine-specific endonuclease recently. Further biochemical analyses revealed that EndoQ also recognizes uracil, xanthine, and the AP site in DNA, and is probably involved in a specific repair process for damaged bases. Initial phylogenetic analysis showed that an EndoQ homolog is found only in the Thermococcales and some of the methanogens in Archaea, and is not present in most members of the domains Bacteria and Eukarya. A better understanding of the distribution of the EndoQ-mediated repair system is, therefore, of evolutionary interest. We showed here that an EndoQ-like polypeptide from Bacillus pumilus, belonging to the bacterial domain, is functional and has similar properties with the archaeal EndoQs.
Isolation and identification of a humanTRPV1 activating compound from soy sauce
Authors: Oshida Mayu , Matsuura Yasunori , Hotta Shinnosuke , Watanabe Jun , Mogi Yoshinobu , Watanabe Tatsuo 
Published: January 2017

Abstract
Transient receptor potential vanilloid 1 (TRPV1) was identified as a receptor of capsaicin, which is a pungent ingredient in hot red peppers. Due to its relevance for nociception, a physiological and pharmacological study of TRPV1 has also been developed. Therefore, it is important to enrich scientific knowledge regarding the TRPV1 activating or inhibiting compounds. In this study, we fractionated soy sauce based on the human TRPV1 (hTRPV1) activity using column chromatography and purified 5-(9H-pyrido[3,4-b]indol-1-yl)-2-furanmethanol (perlolyrine) as an hTRPV1-activating compound. Additionally, perlolyrine activates the human transient receptor potential ankyrin 1 (hTRPA1). The EC50 of hTRPV1 and hTRPA1 were 2.87 and 1.67 μmol L−1, respectively. HPLC quantification of soy sauces showed that they contain 2.22–12.13 μmol L−1 of perlolyrine. The sensory evaluation revealed that perlolyrine has taste modification effect. The results of this study, for the first time, suggest that perlolyrine induces the activation of hTRPV1 and hTRPA1.
Discrete wave equation upscaling
Authors: Fichtner Andreas , Hanasoge Shravan M. 
Published: January 2017

Abstract
We present homogenization technique for the uniformly discretized wave equation, based on the derivation of an effective equation for the low-wavenumber component of the solution. The method produces a down-sampled, effective medium, thus making the solution of the effective equation less computationally expensive. Advantages of the method include its conceptual simplicity and ease of implementation, the applicability to any uniformly discretized wave equation in 1-D, 2-D or 3-D, and the absence of any constraints on the medium properties. We illustrate our method with a numerical example of wave propagation through a 1-D multiscale medium and demonstrate the accurate reproduction of the original wavefield for sufficiently low frequencies.
Survey Results from Canada and Some Latin America Countries: 2016 National Pressure Ulcer Advisory Panel Changes in Terminology and Definitions
Authors: Ayello Elizabeth A. , Lobo Guadalupe Maria , Sibbald R. Gary 
Published: January 2017

ABSTRACT

OBJECTIVE:
Since the National Pressure Ulcer Advisory Panel (NPUAP) held its consensus conference in April 2016, various wound care specialists and professional organizations have been disseminating their response to the revised pressure injury staging definitions. The purpose of this survey was to get an objective perspective of the new NPUAP terminology and staging definitions changes from wound care colleagues outside the United States.

PARTICIPANTS:
In an attempt to obtain the opinions of wound care specialists outside the United States, a convenience sample from some countries in Latin America was invited to complete a survey during the Mexican Association for Integral Care and Wound Healing conference. In addition, students enrolled in the International Interprofessional Wound Care Course conducted in Toronto, Ontario, Canada, were also invited to participate in a revised NPUAP staging definition survey.

RESULTS:
Survey responses reveal strong support for the changes with consensus agreement greater than 80% on all survey items.

CONCLUSIONS:
These survey results can contribute to a universal agreement on terminology and definitions for pressure-related wounds, which may ultimately improve patient care.
Long-term Follow-up of Sexual Function in Women Before and After Tension-Free Vaginal Tape Operation for Stress Urinary Incontinence
Authors: Lindquist Anna Sofie Inger , Glavind Karin 
Published: January 2017

(Abstracted from Int Urogynecol J 2016;27:1571–1576)
A number of studies have investigated the effect of incontinence surgery on sexual function in women. Results have been conflicting; some studies have reported improvement, some deterioration, and others no difference.
Evaluation of Gene Expression Patterns in Micrografts Demonstrate Induction of Catagen-Like Processes During Storage
Authors: Krugluger Walter , Stiefsohn Karl , Moser Karl , Moser Claudia , Laciak Katarina 
Published: January 2017

BACKGROUND
Alterations of gene expression patterns may contribute to the commonly observed transient reduction of hair shaft elongation in hair restoration surgery.

OBJECTIVE
To elucidate the molecular causes, we evaluated changes in gene expression patterns in hair follicle micrografts during storage.

MATERIALS AND METHODS
Micrografts with different amounts of adjacent connective tissue (regular, skinny, and chubby) were stored for different periods, and the expression of key genes was determined: dermal papilla (DP): FGF7, alkaline phosphatase (ALP), versican; outer root sheath: Krt15; inner root sheath: Krt 25; cuticula: Krt85; Henle layer: filaggrin; genes related to apoptosis and growth/differentiation: Caspase 3, Ovol1, and Foxo1.

RESULTS
A significant decrease in FGF7 (4 × 10−4 fold) was observed after 4 hours, with further decrease after 48 hours. A significant decrease of versican (0.35 fold) and ALP (0.004 fold) was observed after 24 hours of storage. No differences relating to adjacent connective tissue were observed. No changes of different keratins genes or genes related to growth/differentiation and apoptosis were observed.

CONCLUSION
These data clearly demonstrate a reduction in the specific function of cells in the DP, which seem to be the causative for the induction of hair follicle cycling during micrograft preparation and storage.