bluuebunny/crossref_metadata_2025_split huggingface dataset:
LA INVESTIGACIÓN Y LA CONSERVACIÓN DEL PATRIMONIO ARQUEOLÓGICO EN TEOTIHUACAN: PROBLEMAS, PERSPECTIVAS Y PROPUESTAS
Authors: Chávez Sergio Gómez 
Published: December 2015

AbstractTeotihuacan es reconocido mundialmente como uno de los sitios arqueológicos más importantes para la investigación de las sociedades complejas, sin embargo, y a pesar de estar incluido desde 1987 en la lista de Patrimonio Cultural de la Humanidad por la UNESCO, en la actualidad enfrenta severos problemas que inciden directa y desfavorablemente en la conservación de los vestigios arqueológicos. Diversas situaciones de carácter administrativo también afectan los acervos que se resguardan de manera muy precaria en las instalaciones, bodegas y los dos museos ubicados dentro de la zona de monumentos.En los últimos años la exigencia de las cada vez más pobladas comunidades aledañas a la zona arqueológica por tener y mejorar los servicios públicos tanto como el crecimiento de la mancha urbana, ha provocado graves afectaciones al patrimonio arqueológico. Aunado a los problemas económicos del país, la ausencia de una política institucional, la falta de planes de trabajo a mediano y largo plazo encaminados a la preservación de los bienes arqueológicos del sitio, así como de programas dirigidos a las comunidades para concientizarlas e involucrarlas directamente en la conservación, han generado una actitud hostil y de desprecio de los pobladores para con los restos arqueológicos. Sin una estrategia institucional y alternativas viables para los habitantes de las comunidades, la mayor destrucción es ocasionada por los propios pobladores del valle o peor aún, por las instancias de gobierno estatal y municipal encargadas de dotar de los servicios a las comunidades.En este artículo se analizan algunos de problemas que afectan el patrimonio arqueológico de Teotihuacan. Se hace hincapié en la carencia de planes y programas de trabajo con objetivos a largo y mediano plazo, que ayuden a la preservación de los bienes arqueológicos, así como de la información que constituye los distintos acervos.
Climate challenges, vulnerabilities, and food security
Authors: Nelson Margaret C. , Ingram Scott E. , Dugmore Andrew J. , Streeter Richard , Peeples Matthew A. , McGovern Thomas H. , Hegmon Michelle , Arneborg Jette , Kintigh Keith W. , Brewington Seth , Spielmann Katherine A. , Simpson Ian A. , Strawhacker Colleen , Comeau Laura E. L. , Torvinen Andrea , Madsen Christian K. , Hambrecht George , Smiarowski Konrad 
Published: December 2015

Significance
Climate-induced disasters are impacting human well-being in ever-increasing ways. Disaster research and management recognize and emphasize the need to reduce vulnerabilities, although extant policy is not in line with this realization. This paper assesses the extent to which vulnerability to food shortage, as a result of social, demographic, and resource conditions at times of climatic challenge, correlates with subsequent declines in social and food security. Extreme climate challenges are identified in the prehispanic US Southwest and historic Norse occupations of the North Atlantic Islands. Cases with such different environmental, climatic, demographic, and cultural and social traditions allow us to demonstrate a consistent relationship between vulnerability and consequent social and food security conditions, applicable in multiple contexts.
Genetic contributions to circadian activity rhythm and sleep pattern phenotypes in pedigrees segregating for severe bipolar disorder
Authors: Pagani Lucia , St. Clair Patricia A. , Teshiba Terri M. , Service Susan K. , Fears Scott C. , Araya Carmen , Araya Xinia , Bejarano Julio , Ramirez Margarita , Castrillón Gabriel , Gomez-Makhinson Juliana , Lopez Maria C. , Montoya Gabriel , Montoya Claudia P. , Aldana Ileana , Navarro Linda , Freimer Daniel G. , Safaie Brian , Keung Lap-Woon , Greenspan Kiefer , Chou Katty , Escobar Javier I. , Ospina-Duque Jorge , Kremeyer Barbara , Ruiz-Linares Andres , Cantor Rita M. , Lopez-Jaramillo Carlos , Macaya Gabriel , Molina Julio , Reus Victor I. , Sabatti Chiara , Bearden Carrie E. , Takahashi Joseph S. , Freimer Nelson B. 
Published: December 2015

Significance
Characterizing the abnormalities in sleep and activity that are associated with bipolar disorder (BP) and identifying their causation are key milestones in unraveling the biological underpinnings of this severe and highly prevalent disorder. We have conducted the first systematic evaluation of sleep and activity phenotypes in pedigrees that include multiple BP-affected members. By delineating specific sleep and activity measures that are significantly heritable in these families, and those whose variation correlated with the BP status of their members, and by determining the chromosomal position of loci contributing to many of these traits, we have taken the first step toward discovery of causative genetic variants. These variants, in turn, could provide clues to new approaches for both preventing and treating BP.
Biochemical evidence of a role for matrix trimerization in HIV-1 envelope glycoprotein incorporation
Authors: Tedbury Philip R. , Novikova Mariia , Ablan Sherimay D. , Freed Eric O. 
Published: December 2015

Significance
The HIV matrix domain of Gag is known to play a key role in the incorporation of the envelope glycoprotein into viral particles. Here we provide evidence that matrix is organized as a trimer in HIV-1 particles, and that the ability of matrix to form trimers is essential for the packaging of the envelope glycoprotein. The requirement for matrix trimerization depends on steric constraints between matrix and the cytoplasmic tail of envelope and matrix. This represents a novel model of envelope incorporation in this family of viruses, and suggests that the matrix trimer interface may represent a novel drug target to inhibit the production of infectious viral particles and combat the spread of AIDS.
Protein carbamylation is a hallmark of aging
Authors: Gorisse Laëtitia , Pietrement Christine , Vuiblet Vincent , Schmelzer Christian E. H. , Köhler Martin , Duca Laurent , Debelle Laurent , Fornès Paul , Jaisson Stéphane , Gillery Philippe 
Published: December 2015

Significance
Human longevity is increasing worldwide because of the advances in scientific knowledge and patient care, which leads to the frequent development of age-related pathologies. Aging remains an elusive process associated with genetic and environmental features, and better understanding would promote sustained wellbeing. We show here for the first time, to our knowledge, that carbamylation, a nonenzymatic posttranslational modification of proteins characterized by the spontaneous binding of isocyanic acid mainly derived from urea, is highly associated with aging and life expectancy in three mammalian species. Carbamylation promotes molecular aging through alteration of protein functions, especially long-lived extracellular matrix proteins. Tissue accumulation of carbamylated proteins may be considered a general hallmark of aging, enabling us to establish a link between cumulative metabolic alterations and age-related complications.
A second transmissible cancer in Tasmanian devils
Authors: Pye Ruth J. , Pemberton David , Tovar Cesar , Tubio Jose M. C. , Dun Karen A. , Fox Samantha , Darby Jocelyn , Hayes Dane , Knowles Graeme W. , Kreiss Alexandre , Siddle Hannah V. T. , Swift Kate , Lyons A. Bruce , Murchison Elizabeth P. , Woods Gregory M. 
Published: December 2015

SignificanceTransmissible cancers are somatic cell lineages that are spread between individuals via the transfer of living cancer cells. Only three transmissible cancers have been reported in nature, suggesting that such diseases emerge rarely. One of the known transmissible cancers affects Tasmanian devils, and is threatening this species with extinction. Here we report the discovery of a second transmissible cancer in Tasmanian devils. This cancer causes facial tumors that are grossly indistinguishable from those caused by the first-described transmissible cancer in this species; however, tumors derived from this second clone are genetically distinct. These findings indicate that Tasmanian devils have spawned at least two different transmissible cancers, and suggest that transmissible cancers may arise more frequently in nature than previously considered.
Prevalence, genetics, and transmissibility in ferrets of Eurasian avian-like H1N1 swine influenza viruses
Authors: Yang Huanliang , Chen Yan , Qiao Chuanling , He Xijun , Zhou Hong , Sun Yu , Yin Hang , Meng Shasha , Liu Liping , Zhang Qianyi , Kong Huihui , Gu Chunyang , Li Chengjun , Bu Zhigao , Kawaoka Yoshihiro , Chen Hualan 
Published: December 2015

Significance
Animal influenza viruses continue to challenge human public health; surveillance of these viruses and evaluation of their pandemic potential are important for future influenza pandemic preparedness. Pigs are intermediate hosts for novel influenza generation and transfer to humans. Two lineages of H1N1 swine influenza viruses (SIVs), classical H1N1 SIVs and Eurasian avian-like H1N1 (EAH1N1) SIVs, have been circulating in pigs since 1918 and 1979, respectively. The classical H1N1 SIVs emerged in humans as a reassortant and caused the 2009 H1N1 influenza pandemic. Here, we found that, after long-term evolution in pigs, the EAH1N1 SIVs have obtained the traits to cause a human influenza pandemic.
Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses
Authors: Yan Liying , Huang Lei , Xu Liya , Huang Jin , Ma Fei , Zhu Xiaohui , Tang Yaqiong , Liu Mingshan , Lian Ying , Liu Ping , Li Rong , Lu Sijia , Tang Fuchou , Qiao Jie , Xie X. Sunney 
Published: December 2015

Significance
One missing or wrong nucleotide out of six billion in a human genome can cause a genetic disease. Detecting such a point mutation in a single human germ cell has been a daunting challenge in in vitro fertilization, yet one cannot afford to make any mistakes in selecting a viable embryo for transfer. Mutated allele revealed by sequencing with aneuploidy and linkage analyses (MARSALA) combines next-generation sequencing and single-cell whole-genome amplification methodologies, allowing embryo diagnosis with a single-molecule precision, significantly reducing false-positive or false-negative errors. MARSALA can benefit couples who desire to avoid transmitting their genetic diseases to their offspring.
Genetically targeted single-channel optical recording reveals multiple Orai1 gating states and oscillations in calcium influx
Authors: Dynes Joseph L. , Amcheslavsky Anna , Cahalan Michael D. 
Published: December 2015

Significance
Calcium ions serve as intracellular signals controlling many aspects of cell behavior. Here, we create fusions of genetically encoded calcium indicators and cell surface Orai calcium channels that report calcium influx through the channel. These fluorescent fusion proteins will allow us to see in living cells Orai signals that underlie cell functions, especially those essential for mounting an adaptive immune response. Their output is bright enough to record the intermittent openings of a single Orai channel for the first time to our knowledge. Our recordings reveal several patterns of channel activity, including oscillations. These responses help us understand Orai channels as molecular machines, and our work enables Orai calcium signals to be identified, mapped, and related to the functional systems of the body.
Spatio-temporal genetic structure of the rodent Calomys venustus in linear, fragmented habitats
Authors: Chiappero Marina B. , Sommaro Lucía V. , Priotto José W. , Wiernes María Paula , Steinmann Andrea R. , Gardenal Cristina N. 
Published: December 2015

AbstractStudies about habitat fragmentation, in terms of how it affects gene flow and genetic variability, have traditionally been conducted on island-like systems in which the remaining habitats form patches embedded in a matrix. However, in agroecosystems, remaining habitats usually form linear strips along fence lines, roads, and water courses (“border” habitats). We used the rodent Calomys venustus , a species inhabiting borders in central Argentina agroecosystems, as a model to address how genetic variability is structured in linear habitats. A total of 359 rodents were captured seasonally from spring 2005 to winter 2006. Genetic variability at microsatellite loci was uniformly high, despite significant variation in population size during the sampling period. Genetic differentiation, spatial autocorrelation, and causal modeling analyses suggested that dispersion patterns in this species depend mainly on geographic distance, with unfavorable habitat like dirt roads and crop fields posing only weak (or no) resistance to dispersal. Small-scale spatial genetic structure was related to different space use patterns by females and males. Our results showed that, although greatly reduced in area, border habitats can support stable populations of species without loss of either variability or genetic connectivity.Los efectos de la fragmentación del hábitat sobre el flujo génico y la variabilidad genética, se han estudiado tradicionalmente en sistemas tipo islas, en los cuales los hábitats remanentes forman parches embebidos en una matriz. Sin embargo, en los agroecosistemas, éstos suelen tener forma lineal a lo largo de alambrados, caminos y corrientes de agua (hábitats de “borde”). En este trabajo, utilizamos al roedor Calomys venustus , especie típica de ambientes de borde en los agroecosistemas del centro de Argentina, como modelo para estudiar cómo la variabilidad genética se estructura en hábitats lineales. Un total de 359 roedores se capturaron estacionalmente desde la primavera de 2005 hasta el invierno de 2006. La variabilidad genética encontrada en loci de microsatélites fue siempre alta, a pesar de una variación significativa del tamaño poblacional a lo largo del período de estudio. Los análisis de diferenciación genética, autocorrelación genética espacial y modelado causal sugieren que los patrones de dispersión en esta especie dependen principalmente de la distancia geográfica, y que los hábitats desfavorables como caminos de tierra y campos de cultivo representan una barrera débil (o nula) para la dispersión. La estructura genética a escala pequeña estuvo relacionada al diferente uso del espacio por parte de machos y hembras. Nuestros resultados mostraron que a pesar de tener un área reducida, los hábitat de bordes pueden mantener poblaciones estables sin pérdida de variabilidad genética o reducción del flujo génico.
Estimating the age of Risso’s dolphins ( Grampus griseus ) based on skin appearance
Authors: Hartman Karin L. , Wittich Anja , Cai Juan Juan , van der Meulen Frank H. , Azevedo José M. N. 
Published: December 2015

AbstractOne of Risso’s dolphin’s distinctive characteristics is the tendency to “lighten” with age due to the accumulation of unpigmented scars. These accumulated scars may provide an indication of age. Photographic skin recaptures gathered from 61 free-ranging animals over a period of 15 years were analyzed to develop a skin classification model in 6 skin stages. Classification of photographic skin captures following this model was tested by 15 experts and 13 nonexpert rankers, with a general probability of agreement of 79%. The duration of each skin stage was estimated using a statistical model based on the recorded dates in which individual animals were known to have entered and/or exited a given stage. A Bayesian approach was used to combine available photographic skin recapture data using expert knowledge as prior to predict the duration for each skin stage and thus the mean age at each stage. Results suggest that animals may live more than 45 years, which is in agreement with published information based on dental layers. The proposed skin stages can be correlated with reproduction, with the transition to stage 3 linked to the onset of maturity. Adult females are less scarified than males and were not observed in the whiter skin classes. The proposed skin stage model is noninvasive and easy to apply and could be a valuable tool in further studies of population structure and dynamics of Risso’s dolphins.
Genomic DNA preparation enabling multiple replicate reads for accurate nanopore sequencing
Authors: Tsavachidou Dimitra 
Published: December 2015

AbstractSequencing at single-nucleotide resolution using nanopore devices is performed with reported error rates 10.5–20.7% (Ip et al., 2015). Since errors occur randomly during sequencing, repeating the sequencing procedure for the same DNA strands several times can generate sequencing results based on consensus derived from replicate readings, thus reducing overall error rates.The method presented in this manuscript constructs copies of a nucleic acid molecule that are consecutively connected to the nucleic acid molecule. Such copies are useful because they can be sequenced by a nanopore device, enabling replicate reads, thus improving overall sequencing accuracy.
MPRAnator: a web-based tool for the design of Massively Parallel Reporter Assay experiments
Authors: Georgakopoulos-Soares Ilias , Jain Naman , Gray Jesse , Hemberg Martin 
Published: December 2015

AbstractDNA regulatory elements contain short motifs where transcription factors (TFs) can bind to modulate gene expression. Although the broad principles of TF regulation are well understood, the rules that dictate how combinatorial TF binding translates into transcriptional activity remain largely unknown. With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as Massively Parallel Reporter Assays (MPRAs) and similar methods remains challenging. We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences therefore allowing the user to investigate the rules that govern TF occupancy. MPRA SNP design can be used to investigate the functional effects of single or combinations of SNPs at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs.
An approximation of the error back-propagation algorithm in a predictive coding network with local Hebbian synaptic plasticity
Authors: Whittington James C.R. , Bogacz Rafal 
Published: December 2015

AbstractTo efficiently learn from feedback, cortical networks need to update synaptic weights on multiple levels of cortical hierarchy. An effective and well-known algorithm for computing such changes in synaptic weights is the error back-propagation algorithm. However, in the back-propagation algorithm, the change in synaptic weights is a complex function of weights and activities of neurons not directly connected with the synapse being modified, whereas the changes in biological synapses are determined only by the activity of pre-synaptic and post-synaptic neurons. Several models have been proposed that approximate the back-propagation algorithm with local synaptic plasticity, but these models require complex external control over the network or relatively complex plasticity rules. Here we show that a network developed in the predictive coding framework can efficiently perform supervised learning fully autonomously, employing only simple local Hebbian plasticity. Furthermore, for certain parameters, the weight change in the predictive coding model converges to that of the back-propagation algorithm. This suggests that it is possible for cortical networks with simple Hebbian synaptic plasticity to implement efficient learning algorithms in which synapses in areas on multiple levels of hierarchy are modified to minimize the error on the output.
The impact of amplification on differential expression analyses by RNA-seq
Authors: Parekh Swati , Ziegenhain Christoph , Vieth Beate , Enard Wolfgang , Hellmann Ines 
Published: December 2015

ABSTRACTCurrently quantitative RNA-Seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this effects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined via their mapping position, which does not distinguish PCR- from natural duplicates and hence it is unclear how to treat duplicate reads.Here, we generate and analyse RNA-seq datasets prepared using three different protocols (Smart-Seq, TruSeq and UMI-seq). We find that a large fraction of computationally identified read duplicates can be explained by sampling and fragmentation bias. Consequently, the computational removal of duplicates does not improve accuracy, power or FDR, but can actually worsen them. Even when duplicates are experimentally identified by unique molecular identifiers (UMIs), power and FDR are only mildly improved. However, the pooling of samples as made possible by the early barcoding of the UMI-protocol leads to an appreciable increase in the power to detect differentially expressed genes.
Hilbert-Schmidt and Sobol sensitivity indices for static and time series Wnt signaling measurements in colorectal cancer - Part A
Authors: sinha shriprakash 
Published: December 2015

AbstractEver since the accidental discovery of Wingless [Sharma R.P., Drosophila information service, 1973, 50, p 134], research in the field of Wnt signaling pathway has taken significant strides in wet lab experiments and various cancer clinical trials, augmented by recent developments in advanced computational modeling of the pathway. Information rich gene expression profiles reveal various aspects of the signaling pathway and help in studying different issues simultaneously. Hitherto, not many computational studies exist which incorporate the simultaneous study of these issues. This manuscript • explores the strength of contributing factors in the signaling pathway, • analyzes the existing causal relations among the inter/extracellular factors effecting the pathway based on prior biological knowledge and • investigates the deviations in fold changes in the recently found prevalence of psychophysical laws working in the pathway. To achieve this goal, local and global sensitivity analysis is conducted on the (non)linear responses between the factors obtained from static and time series expression profiles using the density (Hilbert-Schmidt Information Criterion) and variance (Sobol) based sensitivity indices. The results show the advantage of using density based indices over variance based indices mainly due to the former’s employment of distance measures & the kernel trick via Reproducing kernel Hilbert space (RKHS) that capture nonlinear relations among various intra/extracellular factors of the pathway in a higher dimensional space. In time series data, using these indices it is now possible to observe where in time, which factors get influenced & contribute to the pathway, as changes in concentration of the other factors are made. This synergy of prior biological knowledge, sensitivity analysis & representations in higher dimensional spaces can facilitate in time based administration of target therapeutic drugs & reveal hidden biological information within colorectal cancer samples. Code has been made available at Google drive onhttps://drive.google.com/folderview?id=0B7Kkv8wlhPU-Q2NBZGt1ZERrSVE&usp=sharing