bluuebunny/crossref_metadata_2025_split huggingface dataset:
TLR Costimulation Causes Oxidative Stress with Unbalance of Proinflammatory and Anti-Inflammatory Cytokine Production
Authors: Lavieri Rosa , Piccioli Patrizia , Carta Sonia , Delfino Laura , Castellani Patrizia , Rubartelli Anna 
Published: April 2014

Abstract
IL-1β acts in concert with anti-inflammatory cytokines, in particular, IL-1R antagonist (IL-1Ra), to ensure the correct development and outcome of the inflammation: imbalance in the IL-1β/IL-1Ra ratio is implicated in many human diseases and may lead to dramatic consequences. In this article, we show that single TLR engagement induces IL-1β and, with a little delay, IL-1Ra. Differently, costimulation of TLR2, TLR4, and TLR7/8 enhances IL-1β secretion but severely inhibits IL-1Ra production. The IL-1β/IL-1Ra unbalance after activation of multiple TLRs depends on the insurgence of oxidative stress, because of enhanced production of reactive oxygen species and failure of the antioxidant systems. Increased reactive oxygen species levels increase ATP externalization by monocytes, resulting in enhanced inflammasome activation and IL-1β secretion. Oxidative stress then induces cell responses to stress, including inhibition of protein synthesis, which, in turn, is responsible for the impaired production of IL-1Ra. IL-1Ra secretion is restored by exogenous antioxidants that oppose oxidative stress. Similar effects are evident also on other cytokines: TNF-α is induced, whereas IL-6 is inhibited by costimulation. Our findings provide a molecular basis to the imbalance between proinflammatory and regulatory cytokine circuits that occur in various pathologic conditions, and suggest new strategies for controlling inflammation.
Human Lymphoid Development in the Absence of Common γ-Chain Receptor Signaling
Authors: Kohn Lisa A. , Seet Christopher S. , Scholes Jessica , Codrea Felicia , Chan Rebecca , Zaidi-Merchant Sania , Zhu Yuhua , De Oliveira Satiro , Kapoor Neena , Shah Ami , Abdel-Azim Hisham , Kohn Donald B. , Crooks Gay M. 
Published: April 2014

Abstract
Despite the power of model systems to reveal basic immunologic mechanisms, critical differences exist between species that necessitate the direct study of human cells. Illustrating this point is the difference in phenotype between patients with SCID caused by mutations affecting the common γ-chain (γc) cytokine signaling pathway and mice with similar mutations. Although in both species, null mutations in either IL-2RG (which encodes γc), or its direct downstream signaling partner JAK3, result in T and NK cell deficiency, an associated B cell deficiency is seen in mice but not in humans with these genetic defects. In this study, we applied recent data that have revised our understanding of the earliest stages of lymphoid commitment in human bone marrow (BM) to determine the requirement for signaling through IL-2RG and JAK3 in normal development of human lymphoid progenitors. BM samples from SCID patients with IL-2RG (n = 3) or JAK3 deficiency (n = 2), which produce similar “T-NK-B+” clinical phenotypes, were compared with normal BM and umbilical cord blood as well as BM from children on enzyme treatment for adenosine deaminase–deficient SCID (n = 2). In both IL-2RG– and JAK3-SCID patients, the early stages of lymphoid commitment from hematopoietic stem cells were present with development of lymphoid-primed multipotent progenitors, common lymphoid progenitors and B cell progenitors, normal expression patterns of IL-7RA and TLSPR, and the DNA recombination genes DNTT and RAG1. Thus, in humans, signaling through the γc pathway is not required for prethymic lymphoid commitment or for DNA rearrangement.
Myeloid PTEN Deficiency Protects Livers from Ischemia Reperfusion Injury by Facilitating M2 Macrophage Differentiation
Authors: Yue Shi , Rao Jianhua , Zhu Jianjun , Busuttil Ronald W. , Kupiec-Weglinski Jerzy W. , Lu Ling , Wang Xuehao , Zhai Yuan 
Published: April 2014

Abstract
Although the role of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) in regulating cell proliferation is well established, its function in immune responses remains to be fully appreciated. In the current study, we analyzed myeloid-specific PTEN function in regulating tissue inflammatory immune response in a murine liver partial warm ischemia model. Myeloid-specific PTEN knockout (KO) resulted in liver protection from ischemia reperfusion injury (IRI) by deviating the local innate immune response against ischemia reperfusion toward the regulatory type: expression of proinflammatory genes was selectively decreased and anti-inflammatory IL-10 was simultaneously increased in ischemia reperfusion livers of PTEN KO mice compared with those of wild-type (WT) mice. PI3K inhibitor and IL-10–neutralizing Abs, but not exogenous LPS, recreated liver IRI in these KO mice. At the cellular level, Kupffer cells and peritoneal macrophages isolated from KO mice expressed higher levels of M2 markers and produced lower TNF-α and higher IL-10 in response to TLR ligands than did their WT counterparts. They had enhanced Stat3- and Stat6-signaling pathway activation, but diminished Stat1-signaling pathway activation, in response to TLR4 stimulation. Inactivation of Kupffer cells by gadolinium chloride enhanced proinflammatory immune activation and increased IRI in livers of myeloid PTEN KO mice. Thus, myeloid PTEN deficiency protects livers from IRI by facilitating M2 macrophage differentiation.
Environmental controls of anammox and denitrification in southern New England estuarine and shelf sediments
Authors: Brin Lindsay D. , Giblin Anne E. , Rich Jeremy J. 
Published: April 2014

We measured denitrification and anammox potential rates in homogenized sediments over two annual cycles from two estuarine sites (Providence River estuary and Narragansett Bay) and two continental shelf sites (Block Island and Rhode Island sounds). Denitrification varied both spatially and seasonally, but anammox only varied spatially. Denitrification ranged from 2.5 to 112 nmol N h−1 mL−1 sediment, and anammox from 0 to 8.7 nmol N h−1 mL−1 sediment, with the contribution of anammox to N2 fluxes (ra) ranging from undetectable to 4% in estuarine sites and 8–42% on the shelf. Oxygen microprofiles were analyzed in intact cores and concentrations of nitrate, nitrite, and ammonium were measured in the sediment slice corresponding to the depth layer in which potential rates were measured. Denitrification rates correlated positively with diffusive O2 consumption and temperature and potential anammox rates correlated positively with pore‐water concentrations. Anammox was positively correlated with denitrification in shelf sediments where anammox was regularly detected, but not in estuarine sediments. ra was negatively correlated with diffusive O2 consumption and positively correlated with pore‐water nitrate. Both organic matter and nitrate were important factors regulating the contribution of anammox to N2 production. As a whole, our results demonstrate that incorporating processes that control these two factors into models of N cycling, rather than focusing on organic matter availability alone, may improve predictions of the relative importance of anammox to N2 production in marine sediments.
The in situ light microenvironment of corals
Authors: Wangpraseurt Daniel , Polerecky Lubos , Larkum Anthony W.D. , Ralph Peter J. , Nielsen Daniel A. , Pernice Mathieu , Kühl Michael 
Published: April 2014

We used a novel diver‐operated microsensor system to collect in situ spectrally resolved light fields on corals with a micrometer spatial resolution. The light microenvironment differed between polyp and coenosarc tissues with scalar irradiance (400–700 nm) over polyp tissue, attenuating between 5.1‐ and 7.8‐fold from top to base of small hemispherical coral colonies, whereas attenuation was at most 1.5‐fold for coenosarc tissue. Fluctuations in ambient solar irradiance induced changes in light and oxygen microenvironments, which were more pronounced and faster in coenosarc compared with polyp tissue. Backscattered light from the surrounding benthos contributed > 20% of total scalar irradiance at the coral tissue surface and enhanced symbiont photosynthesis and the local O2 concentration, indicating an important role of benthos optics for coral ecophysiology. Light fields on corals are species and tissue specific and exhibit pronounced variation on scales from micrometers to decimeters. Consequently, the distribution, genetic diversity, and physiology of coral symbionts must be coupled with the measurements of their actual light microenvironment to achieve a more comprehensive understanding of coral ecophysiology.
Famine and feast in a common freshwater calanoid: Effects of diet and temperature on fatty acid dynamics of Eudiaptomus gracilis
Authors: Koussoroplis Apostolos-Manuel , Nussbaumer Julia , Arts Michael T. , Guschina Irina A. , Kainz Martin J. 
Published: April 2014

We investigated the effects of temperature (4°C, 8°C, and 12°C) on structural and storage dynamics, as measured by changes in fatty acids (FA) associated with cell membrane phospholipids (PL) and triacylglycerols (TAG), respectively, as well as on body weight and survival of a freshwater calanoid copepod (Eudiaptomus gracilis) during fasting (10 d) and refeeding (10 d) with two algae of differing nutritional quality (Cryptomonas ozolinii and Scenedesmus obliquus). Fasting led to 50% loss in body weight, a near total depletion of TAG, and a drastic decrease of the polyunsaturated FA (PUFA) in TAG and PL, indicating their preferential utilization and alterations in membrane function, respectively. Higher temperatures accelerated the decrease of body weight and of PUFA in PL and TAG, and decreased survival. After 10 d of refeeding, copepods partially recovered their initial lipid stores and cell membrane composition. The effects of food quality were temperature dependent: Cryptomonas promoted better recovery (i.e., return to or close to the levels at the beginning of the experiment) of both body weight and TAG at only the two higher temperatures (8°C and 12°C), whereas no recovery was observed at 4°C. Higher temperatures and refeeding on Cryptomonas also had a positive, but minor, influence on the recovery of membrane FA composition. Survival differed among treatments but was lowest at the intermediate temperature (8°C) for both diets. We conclude that temperature changes on the order of 4–8°C significantly influence TAG and PL during fasting periods and interact with food quality to determine the extent of recovery in copepod lipids.
Influence of cyanobacteria blooms on sediment biogeochemistry and nutrient fluxes
Authors: Gao Yonghui , Cornwell Jeffrey C. , Stoecker, Diane K. , Owens Michael S. 
Published: April 2014

To explore the influence of cyanobacteria blooms on internal nutrient loading and sediment biogeochemistry, we conducted a 3 yr (2008–2010) field investigation in the upper Sassafras River, a shallow tidal freshwater tributary of Chesapeake Bay, Maryland. During 2010 a dense diazotrophic cyanobacteria bloom was accompanied by abnormally high pH (9.0–10.5) and supersaturated oxygen throughout the summer. With the persistence of high pH in the water column and organic matter inputs from sedimented phytoplankton detritus, flux rates of NH+4 and soluble reactive phosphate were significantly higher during the summer of the bloom year than the same period in nonbloom years. Although low summer N2‐N flux rates generally coincided with reduced water‐column NO−3 concentrations, the efficiency of nitrification was constrained by elevated pH that converted NH+4 to more toxic NH3. Denitrification was subsequently limited by nitrate supply, elevated pH, and the deepening of the oxic layer in the sediment. During blooms, we observed increases in bioavailable nutrient release from the sediment, coupled with decreases in inorganic N : P flux ratios and inhibition of N2 loss from the ecosystem. These changes in sediment nutrient recycling created positive feedbacks that may have fueled the prolonged blooms and selectively fostered growth of diazotrophic cyanobacteria.
Stratigraphic controls on fluid and solute fluxes across the sediment—water interface of an estuary
Authors: Sawyer Audrey H. , Lazareva Olesya , Kroeger Kevin D. , Crespo Kyle , Chan Clara S. , Stieglitz Thomas , Michael Holly A. 
Published: April 2014

Shallow stratigraphic features, such as infilled paleovalleys, modify fresh groundwater discharge to coastal waters and fluxes of saltwater and nutrients across the sediment—water interface. We quantify the spatial distribution of shallow surface water—groundwater exchange and nitrogen fluxes near a paleovalley in Indian River Bay, Delaware, using a hand resistivity probe, conventional seepage meters, and pore‐water samples. In the interfluve (region outside the paleovalley) most nitrate‐rich fresh groundwater discharges rapidly near the coast with little mixing of saline pore water, and nitrogen transport is largely conservative. In the peat‐filled paleovalley, fresh groundwater discharge is negligible, and saltwater exchange is deep (∼1 m). Long pore‐water residence times and abundant sulfate and organic matter promote sulfate reduction and ammonium production in shallow sediment. Reducing, iron‐rich fresh groundwater beneath paleovalley peat discharges diffusely around paleovalley margins offshore. In this zone of diffuse fresh groundwater discharge, saltwater exchange and dispersion are enhanced, ammonium is produced in shallow sediments, and fluxes of ammonium to surface water are large. By modifying patterns of groundwater discharge and the nature of saltwater exchange in shallow sediments, paleovalleys and other stratigraphic features influence the geochemistry of discharging groundwater. Redox reactions near the sediment—water interface affect rates and patterns of geochemical fluxes to coastal surface waters. For example, at this site, more than 99% of the groundwater‐borne nitrate flux to the Delaware Inland Bays occurs within the interfluve portion of the coastline, and more than 50% of the ammonium flux occurs at the paleovalley margin.
Increased Genomic Integrity of an Improved Protein-Based Mouse Induced Pluripotent Stem Cell Method Compared With Current Viral-Induced Strategies
Authors: Park Hansoo , Kim Dohoon , Kim Chun-Hyung , Mills Ryan E. , Chang Mi-Yoon , Iskow Rebecca Cheryl , Ko Sanghyeok , Moon Jung-Il , Choi Hyun Woo , Man Yoo Paulo Sng , Do Jeong Tae , Han Min-Joon , Lee Eun Gyo , Jung Joon Ki , Zhang Chengsheng , Lanza Robert , Kim Kwang-Soo 
Published: April 2014

Abstract
It has recently been shown that genomic integrity (with respect to copy number variants [CNVs]) is compromised in human induced pluripotent stem cells (iPSCs) generated by viral-based ectopic expression of specific transcription factors (e.g., Oct4, Sox2, Klf4, and c-Myc). However, it is unclear how different methods for iPSC generation compare with one another with respect to CNV formation. Because array-based methods remain the gold standard for detecting unbalanced structural variants (i.e., CNVs), we have used this approach to comprehensively identify CNVs in iPSC as a proxy for determining whether our modified protein-based method minimizes genomic instability compared with retro- and lentiviral methods. In this study, we established an improved method for protein reprogramming by using partially purified reprogramming proteins, resulting in more efficient generation of iPSCs from C57/BL6J mouse hepatocytes than using protein extracts. We also developed a robust and unbiased 1 M custom array CGH platform to identify novel CNVs and previously described hot spots for CNV formation, allowing us to detect CNVs down to the size of 1.9 kb. The genomic integrity of these protein-based mouse iPSCs (p-miPSCs) was compared with miPSCs developed from viral-based strategies (i.e., retroviral: retro-miPSCs or lentiviral: lenti-miPSCs). We identified an increased CNV content in lenti-miPSCs and retro-miPSCs (29∼53 CNVs) compared with p-miPSCs (9∼10 CNVs), indicating that our improved protein-based reprogramming method maintains genomic integrity better than current viral reprogramming methods. Thus, our study, for the first time to our knowledge, demonstrates that reprogramming methods significantly influence the genomic integrity of resulting iPSCs.
Concise Review: Unraveling Stem Cell Cocultures in Regenerative Medicine: Which Cell Interactions Steer Cartilage Regeneration and How?
Authors: de Windt Tommy S. , Hendriks Jeanine A.A. , Zhao Xing , Vonk Lucienne A. , Creemers Laura B. , Dhert Wouter J.A. , Randolph Mark A. , Saris Daniel B.F. 
Published: April 2014

Abstract

Cartilage damage and osteoarthritis (OA) impose an important burden on society, leaving both young, active patients and older patients disabled and affecting quality of life. In particular, cartilage injury not only imparts acute loss of function but also predisposes to OA. The increase in knowledge of the consequences of these diseases and the exponential growth in research of regenerative medicine have given rise to different treatment types. Of these, cell-based treatments are increasingly applied because they have the potential to regenerate cartilage, treat symptoms, and ultimately prevent or delay OA. Although these approaches give promising results, they require a costly in vitro cell culture procedure. The answer may lie in single-stage procedures that, by using cell combinations, render in vitro expansion redundant. In the last two decades, cocultures of cartilage cells and a variety of (mesenchymal) stem cells have shown promising results as different studies report cartilage regeneration in vitro and in vivo. However, there is considerable debate regarding the mechanisms and cellular interactions that lead to chondrogenesis in these models. This review, which included 52 papers, provides a systematic overview of the data presented in the literature and tries to elucidate the mechanisms that lead to chondrogenesis in stem cell cocultures with cartilage cells. It could serve as a basis for research groups and clinicians aiming at designing and implementing combined cellular technologies for single-stage cartilage repair and treatment or prevention of OA.
Botanical Evidence of Paleodietary and Environmental Change: Drought on the Channel Islands, California
Authors: Arnold Jeanne E. , Martin Lana S. 
Published: April 2014

AbstractFluctuations in climatic regimes and biodiversity through time are linked in complex ways to human behavior and socioeconomic processes. We use macrobotanical evidence from Chumash village sites on California’s Channel Islands to investigate the relationship between late Holocene climatic perturbations and one region of the larger Chumash world. Carbonized plant remains provide evidence of the shifting availability of native plants during the Transitional period (A.D. 1150–1300), when droughts impacted island floral diversity and the Chumash had to cope with changes in vegetation regimes that likely curtailed food availability. We find that drought-resistant plant resources appear in higher relative frequencies in proveniences dating to the Transitional era, and at least one food resource was first imported from the mainland around that time. These findings support the proposition that the Chumash intensified cross-channel trade in part to respond to dietary needs during episodic resource stress. This is also the time when several economic specializations blossomed, including intensive shell bead making. These specializations persisted for six centuries and were central to the development of institutionalized leadership and political complexity in the region ca. A.D. 1200. Various strategies to preserve stability in the plant diet were important elements in the broader reorganization of labor in coastal southern California.
History, Monumentality, and Interaction in the Appalachian Summit Middle Woodland
Authors: Wright Alice P. 
Published: April 2014

AbstractThe Middle Woodland period in eastern North America witnessed a florescence of monumental architecture and material exchange linked to widespread networks of ritual interaction. Although these networks encompassed large geographic areas and persisted for several centuries, extant archaeological models have tended to characterize Middle Woodland interaction as an historically unitary process. Using new data from the Garden Creek site in North Carolina, I argue that these frameworks obscure important historical shifts in Middle Woodland interaction. Recent collections-based research, geophysical survey, targeted excavation, and14C dating (including Bayesian modeling) of this site reveal two coeval diachronic changes: a shift from geometric earthwork construction to platform mound construction; and a shift from the production of special artifacts {mica, crystal quartz) to the consumption of exotic artifacts in association with platform mound ceremonialism. These data hint at important changes in interregional relationships between the Appalachian Summit, the Hopewellian Midwest, and the greater Southeast during the Middle Woodland period, and provide a springboard for considering how processes of culture contact contributed to precolumbian cultural change.
Kansas and the Postrevolt Puebloan Diaspora: Ceramic Evidence from the Scott County Pueblo
Authors: Beck Margaret E. , Trabert Sarah 
Published: April 2014

AbstractNative American communities underwent significant upheaval, ethnic blending, and restructuring in the Spanish colonial period. One archaeological example is the appearance of a seven-room stone and adobe structure in western Kansas, known as the Scott County Pueblo (14SC1). Previous researchers used Spanish documents to attribute the site to Puebloan refugees from Taos or Picuris in the mid- to late 1600s. Here we examine the Smithsonian and Kansas Historical Society ceramic collections for evidence of Puebloan women at the site. We find a high proportion of bowls at 14SC1, suggesting the maintenance of Puebloan food-preparation and-serving patterns, as well as some vessels apparently made by Puebloan potters in western Kansas. We cannot falsify our null hypothesis that the Scott County Pueblo included people from one or more northern Rio Grande pueblos during the mid-1600s, or A.D. 1696–1706, or both.
Fault coupling and potential for earthquakes on the creeping section of the central San Andreas Fault
Authors: Maurer Jeremy , Johnson Kaj 
Published: April 2014

AbstractThe 150 km long central section of the San Andreas Fault (CSAF) in central California creeps at the surface and has not produced a large earthquake historically. However, sections of the San Andreas Fault to the north and south are known to have ruptured repeatedly inM~7–8 earthquakes. It is currently unclear whether the creeping CSAF could rupture in large earthquakes, either individually or along with earthquakes on the locked sections to the north and south. We invert Global Positioning System and interferometric synthetic aperture radar data with elastic block models to estimate the degree of locking on the CSAF and place bounds on the moment accumulation rate on the fault. We find that the inferred moment accumulation rate is highly dependent on the long‐term fault slip rate, which is poorly constrained along the CSAF. The inferred moment accumulation rate, normalized by shear modulus, ranges from 3.28 × 104to 5.85 × 107 m3/yr, which is equivalent to aMw = 5.5–7.2 earthquake every 150 years for a long‐term slip rate of 26 mm/yr andMw = 7.3–7.65 for a long‐term slip rate of 34 mm/yr. The comparisons of slip distributions with microseismicity and repeating earthquakes indicate a possible locked patch between 10 and 20 km depth on the CSAF that could potentially rupture withMw = 6.5.