bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sox2 promotes expression of the ST6Gal-I glycosyltransferase in ovarian cancer cells
Authors: Dorsett Kaitlyn A. , Jones Robert B. , Ankenbauer Katherine E. , Hjelmeland Anita B. , Bellis Susan L. 
Published: October 2019

AbstractBackgroundThe ST6Gal-I glycosyltransferase, which adds α2–6-linked sialic acids toN-glycosylated proteins is upregulated in a wide range of malignancies including ovarian cancer. Prior studies have shown that ST6Gal-I-mediated sialylation of select surface receptors remodels intracellular signaling to impart cancer stem cell (CSC) characteristics. However, the mechanisms that contribute to ST6Gal-I expression in stem-like cancer cells are poorly understood.ResultsHerein, we identify the master stem cell transcription factor, Sox2, as a novel regulator of ST6Gal-I expression. Interestingly,SOX2andST6GAL1are located within the same tumor-associated amplicon, 3q26, and these two genes exhibit coordinate gains in copy number across multiple cancers including ~ 25% of ovarian serious adenocarcinomas. In conjunction with genetic co-amplification, our studies suggest that Sox2 directly binds theST6GAL1promoter to drive transcription. ST6Gal-I expression is directed by at least four distinct promoters, and we identified the P3 promoter as the predominant promoter utilized by ovarian cancer cells. Chromatin Immunoprecipitation (ChIP) assays revealed that Sox2 binds regions proximal to the P3 promoter. To confirm that Sox2 regulates ST6Gal-I expression, Sox2 was either overexpressed or knocked-down in various ovarian cancer cell lines. Sox2 overexpression induced an increase in ST6Gal-I mRNA and protein, as well as surface α2–6 sialylation, whereas Sox2 knock-down suppressed levels of ST6Gal-I mRNA, protein and surface α2–6 sialylation.ConclusionsThese data suggest a process wherebySOX2andST6GAL1are coordinately amplified in cancer cells, with the Sox2 protein then binding theST6GAL1promoter to further augment ST6Gal-I expression. Our collective results provide new insight into mechanisms that upregulate ST6Gal-I expression in ovarian cancer cells, and also point to the possibility that some of the CSC characteristics commonly attributed to Sox2 may, in part, be mediated through the sialyltransferase activity of ST6Gal-I.
Survival by colon cancer stage and screening interval in Lynch syndrome: a prospective Lynch syndrome database report
Authors: Dominguez-Valentin Mev , Seppälä Toni T. , Sampson Julian R. , Macrae Finlay , Winship Ingrid , Evans D. Gareth , Scott Rodney J. , Burn John , Möslein Gabriela , Bernstein Inge , Pylvänäinen Kirsi , Renkonen-Sinisalo Laura , Lepistö Anna , Lindblom Annika , Plazzer John-Paul , Tjandra Douglas , Thomas Huw , Green Kate , Lalloo Fiona , Crosbie Emma J. , Hill James , Capella Gabriel , Pineda Marta , Navarro Matilde , Vidal Joan Brunet , Rønlund Karina , Nielsen Randi Thyregaard , Yilmaz Mette , Elvang Louise Laurberg , Katz Lior , Nielsen Maartje , ten Broeke Sanne W. , Nakken Sigve , Hovig Eivind , Sunde Lone , Kloor Matthias , Knebel Doeberitz Magnus v , Ahadova Aysel , Lindor Noralane , Steinke-Lange Verena , Holinski-Feder Elke , Mecklin Jukka-Pekka , Møller Pål 
Published: October 2019

Abstract

Background
We previously reported that in pathogenic mismatch repair (path_MMR) variant carriers, the incidence of colorectal cancer (CRC) was not reduced when colonoscopy was undertaken more frequently than once every 3 years, and that CRC stage and interval since last colonoscopy were not correlated.

Methods
The Prospective Lynch Syndrome Database (PLSD) that records outcomes of surveillance was examined to determine survival after colon cancer in relation to the time since previous colonoscopy and pathological stage. Only path_MMR variants scored by the InSiGHT variant database as class 4 or 5 (clinically actionable) were included in the analysis.

Results
Ninety-nine path_MMR carriers had no cancer prior to or at first colonoscopy, but subsequently developed colon cancer. Among these, 96 were 65 years of age or younger at diagnosis, and included 77 path_MLH1, 17 path_MSH2, and 2 path_MSH6 carriers. The number of cancers detected within < 1.5, 1.5–2.5, 2.5–3.5 and at > 3.5 years after previous colonoscopy were 9, 43, 31 and 13, respectively. Of these, 2, 8, 4 and 3 were stage III, respectively, and only one stage IV (interval 2.5–3.5 years) disease. Ten-year crude survival after colon cancer were 93, 94 and 82% for stage I, II and III disease, respectively (p < 0.001). Ten-year crude survival when the last colonoscopy had been < 1.5, 1.5–2.5, 2.5–3.5 or > 3.5 years before diagnosis, was 89, 90, 90 and 92%, respectively (p = 0.91).

Conclusions
In path_MLH1 and path_MSH2 carriers, more advanced colon cancer stage was associated with poorer survival, whereas time since previous colonoscopy was not. Although the numbers are limited, together with our previously reported findings, these results may be in conflict with the view that follow-up of path_MMR variant carriers with colonoscopy intervals of less than 3 years provides significant benefit.
Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome
Authors: Shi Wentao , Massaia Andrea , Louzada Sandra , Handsaker Juliet , Chow William , McCarthy Shane , Collins Joanna , Hallast Pille , Howe Kerstin , Church Deanna M. , Yang Fengtang , Xue Yali , Tyler-Smith Chris 
Published: October 2019

Abstract

Background
Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they underlie many genomic disorders. Maintenance of the palindromic structure by gene conversion between the arms has been documented, but over longer time periods, palindromes are remarkably labile. Mechanisms of origin and loss of palindromes have, however, received little attention.

Results
Here, we use fiber-FISH, 10x Genomics Linked-Read sequencing, and breakpoint PCR sequencing to characterize the structural variation of the P8 palindrome on the human Y chromosome, which contains two copies of the VCY (Variable Charge Y) gene. We find a deletion of almost an entire arm of the palindrome, leading to death of the palindrome, a size increase by recruitment of adjacent sequence, and other complex changes including the formation of an entire new palindrome nearby. Together, these changes are found in ~ 1% of men, and we can assign likely molecular mechanisms to these mutational events. As a result, healthy men can have 1–4 copies of VCY.

Conclusions
Gross changes, especially duplications, in palindrome structure can be relatively frequent and facilitate the evolution of sex chromosomes in humans, and potentially also in other mammalian species.
Global impact of somatic structural variation on the DNA methylome of human cancers
Authors: Zhang Yiqun , Yang Lixing , Kucherlapati Melanie , Hadjipanayis Angela , Pantazi Angeliki , Bristow Christopher A. , Lee Eunjung Alice , Mahadeshwar Harshad S. , Tang Jiabin , Zhang Jianhua , Seth Sahil , Lee Semin , Ren Xiaojia , Song Xingzhi , Sun Huandong , Seidman Jonathan , Luquette Lovelace J. , Xi Ruibin , Chin Lynda , Protopopov Alexei , Park Peter J. , Kucherlapati Raju , Creighton Chad J. 
Published: October 2019

Abstract

Background
Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by which we can assign global significance to a core set of genes, analogous to established methods that identify genes non-randomly targeted by somatic mutation or copy number alteration. While recent studies have defined broad patterns of association involving gene transcription and nearby SSV breakpoints, global alterations in DNA methylation in the context of SSVs remain largely unexplored.

Results
By data integration of whole genome sequencing, RNA sequencing, and DNA methylation arrays from more than 1400 human cancers, we identify hundreds of genes and associated CpG islands (CGIs) for which the nearby presence of a somatic structural variant (SSV) breakpoint is recurrently associated with altered expression or DNA methylation, respectively, independently of copy number alterations. CGIs with SSV-associated increased methylation are predominantly promoter-associated, while CGIs with SSV-associated decreased methylation are enriched for gene body CGIs. Rearrangement of genomic regions normally having higher or lower methylation is often involved in SSV-associated CGI methylation alterations. Across cancers, the overall structural variation burden is associated with a global decrease in methylation, increased expression in methyltransferase genes and DNA damage response genes, and decreased immune cell infiltration.

Conclusion
Genomic rearrangement appears to have a major role in shaping the cancer DNA methylome, to be considered alongside commonly accepted mechanisms including histone modifications and disruption of DNA methyltransferases.
French national survey of dog and cat owners on the deworming behaviour and lifestyle of pets associated with the risk of endoparasites
Authors: Roussel Clarisse , Drake Jason , Ariza Juan Manuel 
Published: October 2019

Abstract

Background
Endoparasites in dogs and cats are a concern related to pet health and zoonotic risks. Several determinants may affect the endoparasite transmission and infection of dogs and cats such as pet’s lifestyle or regional parasite distribution. Although different zoonotic endoparasites, such as Toxocara spp. and Echinococcus spp., have been identified in France, little information exists about the deworming behaviors of owners or the frequency of occurrence of risk factors associated with endoparasite infection or transmission. Deworming guidelines, such as those created by the European Scientific Counsel Companion Animal Parasites (ESCCAP), recommend a deworming frequency according to the risk of infection of every pet and the potential risk for zoonotic transmission. The objectives of this study were to explore how lifestyles of dogs and cats from France were related to a particular risk of endoparasites and assess whether deworming frequencies complied with ESCCAP recommendations.

Methods
French data were extracted from a database created during a recent European pet owner survey regarding endoparasitic infection risk. Dogs and cats were grouped into risk categories based upon the ESCCAP guidelines. The compliance between the actual and recommended deworming frequencies were explored among the regions surveyed.

Results
The majority of dogs and cats were older than 6 months, had outdoor access, had contact with children or elderly people, and lived in rural and town areas. Most of the dogs were in contact with other dogs, snails or prey (83%), and ate slugs, snails, grass or dug in the garden (68%). Likewise, most of the cats hunted outside (57%) and caught prey animals (52%). Consequently, most of the dogs (89%) and cats (53%) were considered to be in the highest-risk category (D). However, independent of the region, the average deworming compliance for dogs was poor (6%). While deworming compliance for cats in category A (low-risk) was excellent (94%), for cats in category D it was poor (6%).

Conclusions
Deworming compliance is needed to enhance pet health and reduce zoonotic risks. Future studies are warranted to thoroughly investigate the compliance and effectiveness of deworming protocols, and the risk factors associated with endoparasites in France.
A field-based modeling study on ecological characterization of hourly host-seeking behavior and its associated climatic variables in Aedes albopictus
Authors: Yin Qingqing , Li Li , Guo Xiang , Wu Rangke , Shi Benyun , Wang Yuji , Liu Yingjie , Wu Shang , Pan Yicheng , Wang Qi , Xie Tian , Hu Tian , Xia Dan , Xia Shang , Kambalame Dzinkambani Moffat , Li Wanyu , Song Zhangyao , Zhou Siyun , Deng Ye , Xie Yu , Zhou Xiao-Nong , Wang Chunmei , Chen Xiao-Guang , Zhou Xiaohong 
Published: October 2019

Abstract

Background
The global spread of mosquito-borne diseases (MBD) has presented increasing challenges to public health. The transmission of MBD is mainly attributable to the biting behaviors of female mosquitoes. However, the ecological pattern of hourly host-seeking behavior in Aedes albopictus and its association with climatic variables are still not well understood, especially for a precise requirement for establishing an effective risk prediction system of MBD transmission.

Methods
Mosquito samples and data on mosquito hourly density and site-specific climatic variables, including temperature, relative humidity, illuminance and wind speed, were collected simultaneously in urban outdoor environments in Guangzhou during 2016–2018. Kernel regression models were used to assess the temporal patterns of hourly host-seeking behavior in mosquito populations, and negative binomial regression models in the Bayesian framework were used to investigate the associations of host-seeking behavior with climatic variables.

Results
Aedes albopictus was abundant, constituting 82% (5569/6790) of the total collected mosquitoes. Host-seeking behavior in Ae. albopictus varied across time and was significantly influenced by climatic variables. The predicted hourly mosquito densities showed non-linear relationships with temperature and illuminance, whereas density increased with relative humidity but generally decreased with wind speed. The range of temperature estimates for female biting was 16.4–37.1 °C, peaking at 26.5 °C (95% credible interval: 25.3–28.1). During the favorable periods, biting behavior of female Ae. albopictus was estimated to occur frequently all day long, presenting a bimodal distribution with peaks within 2–3 h around both dawn and dusk (05:00–08:00 h and 16:00–19:00 h). Moreover, a short-term association in hourly density between the females and males was found.

Conclusions
Our field-based modeling study reveals that hourly host-seeking behavior of Ae. albopictus exhibits a complex pattern, with hourly variation constrained significantly by climatic variables. These findings lay a foundation for improving MBD risk assessments as well as practical strategies for vector control. For instances of all-day-long frequent female biting during the favorable periods in Guangzhou, effective integrated mosquito control measures must be taken throughout the day and night.
First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep
Authors: Uelze Laura , Borowiak Maria , Deneke Carlus , Jacobs Cécile , Szabó István , Tausch Simon H. , Malorny Burkhard 
Published: October 2019

Abstract

Background
The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s).

Results
We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation.

Conclusions
With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.
A path to next-generation reproducibility in cheminformatics
Authors: Clark Robert D. 
Published: October 2019

Abstract
Currently, the submission guidelines for the Journal of Cheminformatics say it will “only publish research or software that is entirely reproducible by third parties.” They go on to specify that being reproducible means that anything essential to the conclusion of the paper be freely accessible and states that source code must be provided. I submit that this definition of reproducibility is too narrow—that a cheminformatics method can only truly be replicated by reimplementing it from a detailed, step-by-step high-level description to determine how reliably the algorithm per se does what it is intended to do.
Blood lactate, pH, base excess and pCO2 as prognostic indicators in caesarean-born kids from goats with pregnancy toxaemia
Authors: Andrade I. M. , Simões P. B. A. , Lamas L. P. , Carolino N. , Lima M. S. 
Published: October 2019

AbstractThe objective of this study was to identify the prognostic value for survival of blood parameters in the immediate post-caesarean surgery period in kids born from pregnancy toxaemia (PT) goats. This study involved 10 PT goats, in which a caesarean surgery was performed. Twenty-five kids were born after caesarean surgery of which 16 survived. A blood sample was collected from the jugular vein of the 10 goats and from the kids immediately after caesarean surgery (within 15 min). There were differences between the kids that survived and the kids that did not survive concerning the blood levels of pH (7.22 vs 7.00), base excess (− 9 vs − 18 mmol/L), pCO2(46 vs 62 mmHg) and L-lactate (5.6 vs 16 mmol/L). Maternal ketoacidosis due to PT has a negative impact on the survival rate of the offspring. This appears to be associated to a metabolic acidosis of the offspring. However, the only blood parameter in which there was a strong association between the maternal and newborn kids was blood urea nitrogen (r = 0.97).
The UDWT image denoising method based on the PDE model of a convexity-preserving diffusion function
Authors: Wang Xianghai , Zhang Wenya , Li Rui , Song Ruoxi 
Published: October 2019

AbstractIt is a great challenge to maintain details while suppressing and eliminating noise of the image. Considering the nonconvexity property of the diffusion function and the hypersensitivity of the Laplace operator to noise in the Y-K model, a fourth-order PDE image denoising model (Con_G&L model) is proposed in this paper. This model is constructed by a new convexity-preserving diffusion function which guarantees the corresponding energy functional has a globally unique minimum solution. At the same time, the Gaussian filter is combined with the Laplace operator in this model, and as a result, the noisy image is smoothed before the diffusion process, which improves the ability of capturing the details and edges of the noisy image greatly. Furthermore, by analyzing the statistical properties of the undecimated discrete wavelet transform (UDWT) coefficients of noisy image, we observe that the noise information is mainly distributed in the high-frequency sub-bands, and based on this, the proposed Con_G&L model is applied in the high-frequency sub-bands of the UDWT to get the denoising method. The proposed method removes the image noise effectively with the image texture and other details of the image being maintained. Meanwhile, the generation of false edges and the staircase effect can be suppressed. A large number of simulation experiments verify the effectiveness of the proposed method.
Qualitative and quantitative characterization of municipal solid waste and the unexploited potential of green energy in Tunisia
Authors: Wafi Taieb , Ben Othman Afef , Besbes Mongi 
Published: October 2019

Abstract
Municipal solid waste management (MSWM) is one of the major environmental issues in Tunisian cities. Rapid growth in urbanization and population rates and the changes in people’s lifestyle have prompted a dramatic increase quantity and a significant shift in the composition of municipal solid waste. There is insufficient data concerning the quantities and the composition of waste streams along with the absence of a comprehensive complete overview and a wider perspective of MSWM potential that provides detailed information at region and city level. As a result, it is still impossible for the scientific community and the authorities to provide synergetic schemes to tie the problems of MSWM with how to integrate economically feasible and environmentally sustainable practices holistically. In the present study, an attempt has been made to provide a comprehensive overview of MSW, through a qualitative (compositional) and quantitative (parametric) characterization of the generated total waste generated in Tunisian cities. A 1-year research survey was conducted in seven regions in Tunisia (Great Tunis, Northeast, Northwest, Midwest, Mideast, Southwest, and Southeast) that cover the 24 provinces of the country. Collected samples revealed that the distribution of waste by region was defined by the region’s demographic, economic, and industrial status. Approaches of possibly more efficient procedures that can be undertaken to improve MSW collection are discussed. At a final stage and based on the potential of biogas calculated in the seven regions, we suggest that the scientific community and the authorities should introduce applicable schemes to valorize MSW through generating biogas as a renewable energy.
Optimal diet strategy of a large-bodied psittacine: food resource abundance and nutritional content enable facultative dietary specialization by the Military Macaw
Authors: de la Parra-Martínez Sylvia Margarita , Muñoz-Lacy Luis Guillermo , Salinas-Melgoza Alejandro , Renton Katherine 
Published: October 2019

AbstractBackgroundDietary specialization should arise when there is a relatively high abundance of a particular resource, where animals may select food items to obtain an optimal diet that maximizes energy intake. Large-bodied psittacines frequently exhibit a narrow dietary niche with specific habitat use, but few studies have determined whether psittacines select food resources, and how this influences habitat use.MethodsWe established fruiting phenology transects to evaluate food resource availability for the large-bodied Military Macaw (Ara militaris) in semi-deciduous, deciduous, and pine-oak forest at two sites along the coast of Jalisco, during the dry season when macaws are nesting. We also determined Military Macaw diet by observations of foraging macaws along transect routes, and conducted bromatological analysis of the nutritional content of the most consumed resource.ResultsMilitary Macaws used six plant species as food items during the dry season, and had a narrow dietary niche (Levins’B = 0.28), with 56% of foraging macaws consuming the seeds ofHura polyandra. No food resources were recorded in pine-oak forest during the dry season, with food resources and foraging by macaws concentrated in tropical deciduous and semi-deciduous forest, whereH. polyandrawas the most abundant fruiting tree species. When considering the proportional availability of food resources, we determined a broad Hurlbert dietary niche breadth ofH = 0.67, indicating that Military Macaws consumed food resources according to their availability. Furthermore, the seeds ofH. polyandrawere an important source of protein, carbohydrates, minerals and moisture, and the hard fruit-casing means that these seeds are exclusively available for macaws.ConclusionsBy concentrating their diet on the most abundant resources, Military Macaws may increase foraging efficiency in the dry season. The high nutrient content also means that concentrating the diet on seeds ofH. polyandramay be an optimal foraging strategy for Military Macaws to meet their energy requirements during the breeding season.