bluuebunny/crossref_metadata_2025_split huggingface dataset:
CONTEXTUAL AND COMPOSITIONAL COMPARISONS OF ABANDONMENT-RELATED, ON-FLOOR DEPOSITS AT CHAN CHICH, BELIZE
Authors: Houk Brett A. 
Published: May 2020

AbstractAt Chan Chich, Belize, archaeologists have encountered Terminal Classic artifact scatters and piled artifact deposits in elite residential compounds near the epicenter of the site. This article presents a detailed comparison of four artifact deposits’ contexts and compositions to highlight similarities and differences among them. Commonly classified as “problematic deposits” in the field, all four examples considered here formed directly on floors or steps. Although they exhibit compositional variability, all four deposits appear to be abandonment-related features, which unknown actors deliberately created, specifically targeting elite residential architecture rather than monumental public structures in the site core.
APPLYING REGIONAL, CONTEXTUAL, ETHNOHISTORIC, AND ETHNOGRAPHIC APPROACHES FOR UNDERSTANDING THE SIGNIFICANCE OF PERI-ABANDONMENT DEPOSITS IN WESTERN BELIZE
Authors: Awe Jaime J. , Helmke Christophe , Aimers James J. , Ebert Claire E. , Stemp W. James , Hoggarth Julie A. 
Published: May 2020

AbstractThe discovery of cultural remains on or above the floors of rooms and courtyards at several Maya sites has been interpreted by some archaeologists as problematic deposits, squatter's refuse, as evidence for feasting, termination rituals,de factorefuse, or rapid abandonment as a result of warfare. Investigations by the Belize Valley Archaeological Reconnaissance Project have recorded similar deposits at several surface and subterranean sites in Western Belize. Our regional, contextual, and methodological approaches for studying these deposits, coupled with ethnohistoric and ethnographic information, provide limited support for the interpretation of these remains asde factorefuse or due to rapid abandonment. Instead, we argue that these deposits are more likely the result of peri-abandonment activities such as propitiation rituals and/or pilgrimages during and after the gradual abandonment of sites in the Belize River Valley.
TO EAT, DISCARD, OR VENERATE: FAUNAL REMAINS AS PROXY FOR HUMAN BEHAVIORS IN LOWLAND MAYA PERI-ABANDONMENT DEPOSITS
Authors: Burke Chrissina C. , Tappan Katie K. , Wisner Gavin B. , Hoggarth Julie A. , Awe Jaime J. 
Published: May 2020

AbstractInterpreting middens, feasting events, ritual, or terminal deposits in the Maya world requires an evaluation of faunal remains. Maya archaeologists consistently evaluate other artifact classes, but often offer simply number of identified specimens values for skeletal elements recovered from these deposits. To further understand their archaeological significance, we analyzed faunal materials from deposits at the sites of Baking Pot and Xunantunich in the Upper Belize River Valley. We identified the species, bone elements, bone or shell artifacts, taphonomic signatures, and quantitative ratios recovered to test whether a deposit can be identified as a midden, part of a feasting ritual, terminal ritual, or other rituals significant to the Maya. Our analyses allow us to begin building a system for using faunal remains as a proxy for interpreting the significance of these deposits. In this paper, we present our results and hope to open the conversation for future evaluations of faunal remains in similar deposits.
RECONSTRUCTING THE FORMATION OF PERI-ABANDONMENT DEPOSITS AT BAKING POT, BELIZE
Authors: Hoggarth Julie A. , Davis J. Britt , Awe Jaime J. , Helmke Christophe 
Published: May 2020

AbstractArchaeological research in the Maya lowlands has identified special deposits that offer essential information about the abandonment of Classic Maya centers. We argue that some of the “problematical deposits” associated with terminal architecture may be more accurately described as peri-abandonment deposits since they temporally and behaviorally relate to the activities associated with the final use of ceremonial space. Here, we describe several peri-abandonment deposits that were identified in Group B at the site of Baking Pot, located in western Belize. Using detailed stratigraphic and contextual information, artifact assemblages, and calendar dates recorded on polychrome vessels recovered in the deposits, we describe the nature of activities associated with the formation of peri-abandonment deposits at Baking Pot in the eighth to ninth centuries. We find patterning in the spatial locations of deposits in the corners of plazas and courtyards at Baking Pot, with variability in artifact assemblages between specific deposits.
Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations
Authors: Ping Derek , Wang Tong , Fraebel David T , Maslov Sergei , Sneppen Kim , Kuehn Seppe 
Published: May 2020

Abstract
Natural bacterial populations are subjected to constant predation pressure by bacteriophages. Bacteria use a variety of molecular mechanisms to defend themselves from phage predation. However, since phages are nonmotile, perhaps the simplest defense against phage is for bacteria to move faster than phages. In particular, chemotaxis, the active migration of bacteria up attractant gradients, may help the bacteria escape slowly diffusing phages. Here we study phage infection dynamics in migrating bacterial populations driven by chemotaxis through low viscosity agar plates. We find that expanding phage–bacteria populations supports two moving fronts, an outermost bacterial front driven by nutrient uptake and chemotaxis and an inner phage front at which the bacterial population collapses due to phage predation. We show that with increasing adsorption rate and initial phage population, the speed of the moving phage front increases, eventually overtaking the bacterial front and driving the system across a transition from a regime where bacterial front speed exceeds that of the phage front to one where bacteria must evolve phage resistance to survive. Our data support the claim that this process requires phage to hitchhike with moving bacteria. A deterministic model recapitulates the transition under the assumption that phage virulence declines with host growth rate which we confirm experimentally. Finally, near the transition between regimes we observe macroscopic fluctuations in bacterial densities at the phage front. Our work opens a new, spatio-temporal, line of investigation into the eco-evolutionary struggle between bacteria and phage.
Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression
Authors: Silva-Fisher Jessica M. , Dang Ha X. , White Nicole M. , Strand Matthew S. , Krasnick Bradley A. , Rozycki Emily B. , Jeffers Gejae G. L. , Grossman Julie G. , Highkin Maureen K. , Tang Cynthia , Cabanski Christopher R. , Eteleeb Abdallah , Mudd Jacqueline , Goedegebuure S. Peter , Luo Jingqin , Mardis Elaine R. , Wilson Richard K. , Ley Timothy J. , Lockhart Albert C. , Fields Ryan C. , Maher Christopher A. 
Published: May 2020

AbstractColorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of patients develop metastatic disease (mCRC). Despite our understanding of long non-coding RNAs (lncRNAs) in primary colon cancer, their role in mCRC and treatment resistance remains poorly characterized. Therefore, through transcriptome sequencing of normal, primary, and distant mCRC tissues we find 148 differentially expressed RNAs Associated with Metastasis (RAMS). We prioritizeRAMS11due to its association with poor disease-free survival and promotion of aggressive phenotypes in vitro and in vivo. A FDA-approved drug high-throughput viability assay shows that elevatedRAMS11expression increases resistance to topoisomerase inhibitors. Subsequent experiments demonstrateRAMS11-dependent recruitment of Chromobox protein 4 (CBX4) transcriptionally activates Topoisomerase II alpha (TOP2α). Overall, recent clinical trials using topoisomerase inhibitors coupled with our findings ofRAMS11-dependent regulation of TOP2α supports the potential use ofRAMS11as a biomarker and therapeutic target for mCRC.
Role of the nuclear membrane protein Emerin in front-rear polarity of the nucleus
Authors: Nastały Paulina , Purushothaman Divya , Marchesi Stefano , Poli Alessandro , Lendenmann Tobias , Kidiyoor Gururaj Rao , Beznoussenko Galina V. , Lavore Stefania , Romano Orso Maria , Poulikakos Dimos , Lagomarsino Marco Cosentino , Mironov Alexander A. , Ferrari Aldo , Maiuri Paolo 
Published: May 2020

AbstractCell polarity refers to the intrinsic asymmetry of cells, including the orientation of the cytoskeleton. It affects cell shape and structure as well as the distribution of proteins and organelles. In migratory cells, front-rear polarity is essential and dictates movement direction. While the link between the cytoskeleton and nucleus is well-studied, we aim to investigate if front-rear polarity can be transmitted to the nucleus. We show that the knock-down of emerin, an integral protein of the nuclear envelope, abolishes preferential localization of several nuclear proteins. We propose that the frontally biased localization of the endoplasmic reticulum, through which emerin reaches the nuclear envelope, is sufficient to generate its observed bias. In primary emerin-deficient myoblasts, its expression partially rescues the polarity of the nucleus. Our results demonstrate that front-rear cell polarity is transmitted to the nucleus and that emerin is an important determinant of nuclear polarity.
Global CO2 emissions from dry inland waters share common drivers across ecosystems
Authors: Keller P. S. , Catalán N. , von Schiller D. , Grossart H.-P. , Koschorreck M. , Obrador B. , Frassl M. A. , Karakaya N. , Barros N. , Howitt J. A. , Mendoza-Lera C. , Pastor A. , Flaim G. , Aben R. , Riis T. , Arce M. I. , Onandia G. , Paranaíba J. R. , Linkhorst A. , del Campo R. , Amado A. M. , Cauvy-Fraunié S. , Brothers S. , Condon J. , Mendonça R. F. , Reverey F. , Rõõm E.-I. , Datry T. , Roland F. , Laas A. , Obertegger U. , Park J.-H. , Wang H. , Kosten S. , Gómez R. , Feijoó C. , Elosegi A. , Sánchez-Montoya M. M. , Finlayson C. M. , Melita M. , Oliveira Junior E. S. , Muniz C. C. , Gómez-Gener L. , Leigh C. , Zhang Q. , Marcé R. 
Published: May 2020

AbstractMany inland waters exhibit complete or partial desiccation, or have vanished due to global change, exposing sediments to the atmosphere. Yet, data on carbon dioxide (CO2) emissions from these sediments are too scarce to upscale emissions for global estimates or to understand their fundamental drivers. Here, we present the results of a global survey covering 196 dry inland waters across diverse ecosystem types and climate zones. We show that their CO2 emissions share fundamental drivers and constitute a substantial fraction of the carbon cycled by inland waters. CO2 emissions were consistent across ecosystem types and climate zones, with local characteristics explaining much of the variability. Accounting for such emissions increases global estimates of carbon emissions from inland waters by 6% (~0.12 Pg C y−1). Our results indicate that emissions from dry inland waters represent a significant and likely increasing component of the inland waters carbon cycle.
Genome-wide association study of MRI markers of cerebral small vessel disease in 42,310 participants
Authors: Persyn Elodie , Hanscombe Ken B. , Howson Joanna M. M. , Lewis Cathryn M. , Traylor Matthew , Markus Hugh S. 
Published: May 2020

AbstractCerebral small vessel disease is a major cause of stroke and dementia, but its genetic basis is incompletely understood. We perform a genetic study of three MRI markers of the disease in UK Biobank imaging data and other sources: white matter hyperintensities (N = 42,310), fractional anisotropy (N = 17,663) and mean diffusivity (N = 17,467). Our aim is to better understand the disease pathophysiology. Across the three traits, we identify 31 loci, of which 21 were previously unreported. We perform a transcriptome-wide association study to identify associations with gene expression in relevant tissues, identifying 66 associated genes across the three traits. This genetic study provides insights into the understanding of the biological mechanisms underlying small vessel disease.
PBRM1 loss defines a nonimmunogenic tumor phenotype associated with checkpoint inhibitor resistance in renal carcinoma
Authors: Liu Xian-De , Kong Wen , Peterson Christine B. , McGrail Daniel J. , Hoang Anh , Zhang Xuesong , Lam Truong , Pilie Patrick G. , Zhu Haifeng , Beckermann Kathryn E. , Haake Scott M. , Isgandrova Sevinj , Martinez-Moczygemba Margarita , Sahni Nidhi , Tannir Nizar M. , Lin Shiaw-Yih , Rathmell W. Kimryn , Jonasch Eric 
Published: May 2020

AbstractA non-immunogenic tumor microenvironment (TME) is a significant barrier to immune checkpoint blockade (ICB) response. The impact of Polybromo-1 (PBRM1) on TME and response to ICB in renal cell carcinoma (RCC) remains to be resolved. Here we show that PBRM1/Pbrm1 deficiency reduces the binding of brahma-related gene 1 (BRG1) to the IFNγ receptor 2 (Ifngr2) promoter, decreasing STAT1 phosphorylation and the subsequent expression of IFNγ target genes. An analysis of 3 independent patient cohorts and of murine pre-clinical models reveals that PBRM1 loss is associated with a less immunogenic TME and upregulated angiogenesis. Pbrm1 deficient Renca subcutaneous tumors in mice are more resistance to ICB, and a retrospective analysis of the IMmotion150 RCC study also suggests that PBRM1 mutation reduces benefit from ICB. Our study sheds light on the influence of PBRM1 mutations on IFNγ-STAT1 signaling and TME, and can inform additional preclinical and clinical studies in RCC.
The kallikrein–kinin pathway as a mechanism for auto-control of brown adipose tissue activity
Authors: Peyrou Marion , Cereijo Rubén , Quesada-López Tania , Campderrós Laura , Gavaldà-Navarro Aleix , Liñares-Pose Laura , Kaschina Elena , Unger Thomas , López Miguel , Giralt Marta , Villarroya Francesc 
Published: May 2020

AbstractBrown adipose tissue (BAT) is known to secrete regulatory factors in response to thermogenic stimuli. Components of the BAT secretome may exert local effects that contribute to BAT recruitment and activation. Here, we found that a thermogenic stimulus leads to enhanced secretion of kininogen (Kng) by BAT, owing to induction of kininogen 2 (Kng2) gene expression. Noradrenergic, cAMP-mediated signals induce KNG2 expression and release in brown adipocytes. Conversely, the expression of kinin receptors, that are activated by the Kng products bradykinin and [Des-Arg9]-bradykinin, are repressed by thermogenic activation of BAT in vivo and of brown adipocytes in vitro. Loss-of-function models for Kng (the circulating-Kng-deficient BN/Ka rat) and bradykinin (pharmacological inhibition of kinin receptors, kinin receptor-null mice) signaling were coincident in showing abnormal overactivation of BAT. Studies in vitro indicated that Kng and bradykinin exert repressive effects on brown adipocyte thermogenic activity by interfering the PKA/p38 MAPK pathway of control of Ucp1 gene transcription, whereas impaired kinin receptor expression enhances it. Our findings identify the kallikrein–kinin system as a relevant component of BAT thermogenic regulation that provides auto-regulatory inhibitory signaling to BAT.
Room-temperature chemical synthesis of C2
Authors: Miyamoto Kazunori , Narita Shodai , Masumoto Yui , Hashishin Takahiro , Osawa Taisei , Kimura Mutsumi , Ochiai Masahito , Uchiyama Masanobu 
Published: May 2020

AbstractDiatomic carbon (C2) is historically an elusive chemical species. It has long been believed that the generation of C2 requires extremely high physical energy, such as an electric carbon arc or multiple photon excitation, and so it has been the general consensus that the inherent nature of C2 in the ground state is experimentally inaccessible. Here, we present the chemical synthesis of C2 from a hypervalent alkynyl-λ3-iodane in a flask at room temperature or below, providing experimental evidence to support theoretical predictions that C2 has a singlet biradical character with a quadruple bond, thus settling a long-standing controversy between experimental and theoretical chemists, and that C2 serves as a molecular element in the bottom-up chemical synthesis of nanocarbons such as graphite, carbon nanotubes, and C60.
Photoactivatable Cre recombinase 3.0 for in vivo mouse applications
Authors: Morikawa Kumi , Furuhashi Kazuhiro , de Sena-Tomas Carmen , Garcia-Garcia Alvaro L. , Bekdash Ramsey , Klein Alison D. , Gallerani Nicholas , Yamamoto Hannah E. , Park Seon-Hye E. , Collins Grant S. , Kawano Fuun , Sato Moritoshi , Lin Chyuan-Sheng , Targoff Kimara L. , Au Edmund , Salling Michael C. , Yazawa Masayuki 
Published: May 2020

AbstractOptogenetic genome engineering tools enable spatiotemporal control of gene expression and provide new insight into biological function. Here, we report the new version of genetically encoded photoactivatable (PA) Cre recombinase, PA-Cre 3.0. To improve PA-Cre technology, we compare light-dimerization tools and optimize for mammalian expression using a CAG promoter, Magnets, and 2A self-cleaving peptide. To prevent background recombination caused by the high sequence similarity in the dimerization domains, we modify the codons for mouse gene targeting and viral production. Overall, these modifications significantly reduce dark leak activity and improve blue-light induction developing our new version, PA-Cre 3.0. As a resource, we have generated and validated AAV-PA-Cre 3.0 as well as two mouse lines that can conditionally express PA-Cre 3.0. Together these new tools will facilitate further biological and biomedical research.
Ubiquitinated-PCNA protects replication forks from DNA2-mediated degradation by regulating Okazaki fragment maturation and chromatin assembly
Authors: Thakar Tanay , Leung Wendy , Nicolae Claudia M. , Clements Kristen E. , Shen Binghui , Bielinsky Anja-Katrin , Moldovan George-Lucian 
Published: May 2020

AbstractUpon genotoxic stress, PCNA ubiquitination allows for replication of damaged DNA by recruiting lesion-bypass DNA polymerases. However, PCNA is also ubiquitinated during normal S-phase progression. By employing 293T and RPE1 cells deficient in PCNA ubiquitination, generated through CRISPR/Cas9 gene editing, here, we show that this modification promotes cellular proliferation and suppression of genomic instability under normal growth conditions. Loss of PCNA-ubiquitination results in DNA2-dependent but MRE11-independent nucleolytic degradation of nascent DNA at stalled replication forks. This degradation is linked to defective gap-filling in the wake of the replication fork and incomplete Okazaki fragment maturation, which interferes with efficient PCNA unloading by ATAD5 and subsequent nucleosome deposition by CAF-1. Moreover, concomitant loss of PCNA-ubiquitination and the BRCA pathway results in increased nascent DNA degradation and PARP inhibitor sensitivity. In conclusion, we show that by ensuring efficient Okazaki fragment maturation, PCNA-ubiquitination protects fork integrity and promotes the resistance of BRCA-deficient cells to PARP-inhibitors.
Design of a broadly reactive Lyme disease vaccine
Authors: Kamp Heather D. , Swanson Kurt A. , Wei Ronnie R. , Dhal Pradeep K. , Dharanipragada Ram , Kern Aurelie , Sharma Bijaya , Sima Radek , Hajdusek Ondrej , Hu Linden T. , Wei Chih-Jen , Nabel Gary J. 
Published: May 2020

AbstractA growing global health concern, Lyme disease has become the most common tick-borne disease in the United States and Europe. Caused by the bacterial spirocheteBorrelia burgdorferisensu lato (sl), this disease can be debilitating if not treated promptly. Because diagnosis is challenging, prevention remains a priority; however, a previously licensed vaccine is no longer available to the public. Here, we designed a six component vaccine that elicits antibody (Ab) responses against allBorreliastrains that commonly cause Lyme disease in humans. The outer surface protein A (OspA) ofBorreliawas fused to a bacterial ferritin to generate self-assembling nanoparticles. OspA-ferritin nanoparticles elicited durable high titer Ab responses to the seven major serotypes in mice and non-human primates at titers higher than a previously licensed vaccine. This response was durable in rhesus macaques for more than 6 months. Vaccination with adjuvanted OspA-ferritin nanoparticles stimulated protective immunity from bothB. burgdorferiandB. afzeliiinfection in a tick-fed murine challenge model. This multivalent Lyme vaccine offers the potential to limit the spread of Lyme disease.
Evaluation of lateral diffusion length in InAs/GaSb superlattice detectors grown by MOCVD
Authors: Teng Yan , Hao Xiujun , Zhao Yu , Wu Qihua , Li Xin , Liu Jiafeng , Zhu He , Chen Ying , Zhu Hong , Huang Yong 
Published: May 2020

The lateral diffusion length (Lh) of minority carriers in LWIR InAs/GaSb superlattice detectors grown by metalorganic chemical vapour deposition was evaluated. The deeply‐etched PNn device exhibits a diffusion‐limited behaviour at 80 K, with a dark current density as low as 9.1 × 10−6 A/cm2 at −0.1 V and a 50% cut‐off of 10.1 μm. In shallow‐etched pixels with a common absorber, both the photo‐current and the dark current show a size‐dependent behaviour. Lh deduced from the two methods are 211 and 251 μm, respectively, which are longer than those in superlattice materials grown by molecular beam epitaxy.