bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Different Methodologies for Mapping Urban Heat Vulnerability for Milan, Italy
Authors: Bhattacharjee S , Gerasimova E , Imbert C , Tencar J , Rotondo F 
Published: June 2019

Abstract

Aims: To compare methodologies for calculating vulnerability index of Milan city and find correlation between the main components influencing vulnerability.

Methodology: At-satellite brightness temperatures were used to study exposure of city districts to Urban Heat Island. The distribution of vulnerable population (people younger than 14 and older than 65) was also taken into account by producing a map, which showed sensitivity indices for each city district. Adaptive capacity was represented as a complex set of subindicators such as health care accessibility, level of living conditions and vegetation cover. Exposure, sensitivity and adaptive capacity – main indicators of vulnerability – were used to obtain five different maps, which could identify districts more vulnerable to the Urban Heat Island. Collected data showed correlations between factors influencing vulnerability.

Results: All formulas except one show similar vulnerability index distributions. Correlation graphs showed direct proportionality with exposure, very low correlation with sensitivity and indirect proportionality with adaptive capacity (except one formula which is discussed in paper).
ENERGIS: Decision-Support Tool for the Implementation of Energy Policies at Urban and Regional Level
Authors: Hernández Moral G , Serna González V I , Massa G , Valmaseda Tranque C 
Published: June 2019

Abstract
The implementation of energy policies to reduce CO2 emissions poses specific challenges, especially to public authorities, who should define specific objectives, and evaluate the adequacy and impact of energy actions proposed. Nevertheless, an appropriate analysis is highly time-consuming due to the lack of tools. In this process, the first step is to establish the baseline energy status of the area of study. Only with this knowledge, in particular of the residential sector (main CO2 emissions contributor in cities), is it possible to plan for a low carbon economy. In this context, the ENERGIS tool will support energy planners by mapping energy demand of the residential sector at different scales, as a first step towards CO2 emissions calculation. To do so, a nationally validated Energy Performance Certification (EPC) tool has been automated, its results at building level mapped and aggregated at different scales. By basing the proposed platform on EPC calculation methodologies supported by the Energy Performance Directive of Buildings (EPBD 2010/31/EU), the ENERGIS platform achieves two main goals: it aids in the implementation of energy directives and energy actions by offering an easy to use tool to identify areas in need and, secondly, it promotes the EPBD, by making use of one of its main instruments to measure energy performance: the EPCs.
Developments and perspectives on the precision forming processes for ultra-large size integrated components
Authors: Yuan Shijian , Fan Xiaobo 
Published: June 2019

Abstract
In order to meet the requirements of high reliability, long-lifetime and lightweight in a new generation of aerospace, aviation, high-speed train, and energy power equipment, integrated components are urgently needed to replace traditional multi-piece, welded components. The applications of integrated components involve in a series of large-size, complex-shaped, high-performance components made of difficult-to-deform materials, which present a huge challenge for forming ultra-large size integrated components. In this paper, the developments and perspectives of several extreme forming technologies are reviewed, including the sheet hydroforming of ultra-large curved components, dieless hydroforming of ellipsoidal shells, radial-axial ring rolling of rings, in situ manufacturing process of flanges, and local isothermal forging of titanium alloy components. The principle and processes for controlling deformation are briefly illustrated. The forming of typical ultra-large size integrated components and industrial applications are introduced, such as the high strength aluminum alloy, 3 m in diameter, integrated tank dome first formed by using a sheet blank with a thickness the same as the final component, and a 16 m diameter, integrated steel ring rolled by using a single billet. The trends for extreme forming of ultra-large size integrated components are discussed with a goal of providing ideas and fundamental guidance for the further development of new forming processes for extreme-size integrated components in the future.
ATRX Mutations in Pineal Parenchymal Tumors of Intermediate Differentiation
Authors: Martínez Haydee , Nagurney Michelle , Wang Zi-Xuan , Eberhart Charles G , Heaphy Christopher M , Curtis Mark T , Rodriguez Fausto J 
Published: June 2019

Abstract
Pineal parenchymal tumors are rare neoplasms, ranging from WHO Grade I to IV. There are few studies characterizing the molecular profiles of these tumors. ATRX alterations are strongly associated with the presence of the alternative lengthening of telomeres (ALT) phenotype, and within the central nervous system they tend to occur in subsets of gliomas, including those with IDH, NF1, or histone (H3 K27M or G34) mutations. Here, we identified ATRX frameshift mutations by next generation sequencing associated with corresponding protein loss in 2 cases of pineal parenchymal tumors of intermediate differentiation (PPTID) developing in a 21-year-old woman and a 64-year-old man. In contrast, we identified partial ATRX loss in 1 pineoblastoma, among 14 pineal parenchymal tumors of various grades (6 pineoblastomas, 4 pineocytomas, and 4 PPTID) using tissue microarrays; ALT was absent in these cases. Evaluating the cBioPortal database, an ATRX mutation was identified in one (of 3 total) PPTIDs analyzed. Thus, ATRX mutations associated with protein loss and ALT develop in a small subset of pineal parenchymal tumors and may be limited to those with intermediate differentiation. The clinical significance of these alterations requires further study.
Branched-chain amino acid interactions in growing pig diets1
Authors: Cemin Henrique S , Tokach Mike D , Woodworth Jason C , Dritz Steve S , DeRouchey Joel M , Goodband Robert D 
Published: June 2019

Abstract
The branched-chain amino acids (BCAA) Leu, Ile, and Val share the first steps of their catabolism due to similarities in their structure. The BCAA are reversibly transaminated in skeletal muscle through the activity of branched-chain aminotransferase and then transported to the liver. They undergo an irreversible decarboxylation catalyzed by the branched-chain α-keto acid dehydrogenase complex. Both enzymes are common to Leu, Ile, and Val and increased enzymatic activity stimulated by an excess of one of them will increase the catabolism of all BCAA, which can result in antagonisms. Leucine and its keto acid are the most potent stimulators of BCAA catabolic enzymes. Moreover, BCAA and large neutral amino acids (LNAA) share common brain transporters. Research has shown that high concentrations of BCAA, especially Leu, can decrease the absorption of LNAA, such as Trp, which is a precursor of serotonin and can have a significant impact in feed intake regulation. Finally, high Leu concentrations have the ability to overstimulate the mTOR signaling pathway, resulting in an inhibitory effect on feed intake. Most of the research conducted to evaluate the impact of BCAA on growth performance of pigs seems to agree that high levels of Leu decrease weight gain, mostly due to a reduction in feed intake. However, some studies, mostly with finishing pigs, observed no evidence for an impact on growth performance even with extremely high levels of Leu. It could be hypothesized that these inconsistencies are driven by the entire dietary amino acid profile as opposed to only considering the level of Leu. Grow-finish diets typically contain high levels of Leu, but the other BCAA are also well above the requirement and could potentially mitigate the negative impact of Leu on BCAA catabolism. Indeed, some studies suggest that when diets contain high levels of Leu, more Ile and Val are needed to optimize growth performance. However, the precise relationship between BCAA and their balance in swine diets is not fully understood. More research is needed to understand and quantify the relationship between LNAA and BCAA.
Long non-coding RNA Gm15441 attenuates hepatic inflammasome activation in response to metabolic stress
Authors: Brocker Chad N. , Kim Donghwan , Melia Tisha , Karri Kritika , Velenosi Thomas J. , Takahashi Shogo , Bonzo Jessica A. , Waxman David J. , Gonzalez Frank J. 
Published: June 2019

SummaryFasting paradigms elicit a wide-range of health benefits including suppressing inflammation. Exploring the molecular mechanisms that prevent inflammation during caloric restriction may yield promising new therapeutic targets. During fasting, activation of the nuclear receptor peroxisome proliferator-activated receptor alpha (PPARA) promotes the utilization of lipids as an energy source. Herein, we show that ligand activation of PPARA directly upregulates the long non-coding RNA geneGm15441through binding sites within its promoter.Gm15441expression suppresses its antisense transcript, encoding thioredoxin interacting protein (TXNIP). This, in turn, decreases TXNIP-stimulated NLRP3 inflammasome activation, caspase-1 (CASP1) cleavage, and proinflammatory interleukin 1 beta (IL1B) maturation.Gm15441-null mice were developed and shown to be more susceptible to NLRP3 inflammasome activation and to exhibit elevated CASP1 and IL1B cleavage in response to metabolic and inflammatory stimuli. These findings provide evidence for a novel mechanism by which PPARA attenuates hepatic inflammasome activation in response to metabolic stress through lncRNAGm15441induction.Graphical abstract
A new family of Type VI secretion system-delivered effector proteins displays ion-selective pore-forming activity
Authors: Mariano Giuseppina , Trunk Katharina , Williams David J. , Monlezun Laura , Strahl Henrik , Pitt Samantha J. , Coulthurst Sarah J. 
Published: June 2019

AbstractType VI secretion systems (T6SSs) are nanomachines widely used by bacteria to compete with rivals. T6SSs deliver multiple toxic effector proteins directly into neighbouring cells and play key roles in shaping diverse polymicrobial communities. A number of families of T6SS-dependent anti-bacterial effectors have been characterised, however the mode of action of others remains unknown. Here we report that Ssp6, an anti-bacterial effector delivered by theSerratia marcescensT6SS, is an ion-selective pore-forming toxin.In vivo, Ssp6 inhibits growth by causing depolarisation of the inner membrane of intoxicated cells and also leads to increased outer membrane permeability, whilst reconstruction of Ssp6 activityin vitrodemonstrated that it forms cation-selective pores. A survey of bacterial genomes revealed that Ssp6-like effectors are widespread in Enterobacteriaceae and often linked with T6SS genes. We conclude that Ssp6 represents a new family of T6SS-delivered anti-bacterial effectors, further diversifying the portfolio of weapons available for deployment during inter-bacterial conflict.
Intragenic recruitment of NF-κB drives alternative splicing modifications upon activation by the viral oncogene TAX of HTLV-1
Authors: Ameur Lamya Ben , Thenoz Morgan , Giraud Guillaume , Combe Emmanuel , Claude Jean-Baptiste , Lemaire Sebastien , Fontrodona Nicolas , Polveche Hélène , Bastien Marine , Gessain Antoine , Wattel Eric , Bourgeois Cyril F. , Auboeuf Didier , Mortreux Franck 
Published: June 2019

SummaryThe chronic NF-κB activation in inflammation and cancer has long been linked to persistent activation of NF-κB responsive gene promoters. However, NF-κB factors such as RELA also massively bind to gene bodies. Here, we demonstrate that the recruitment of RELA to intragenic regions regulates alternative splicing upon activation of NF-κB by the viral oncogene TAX of HTLV-1. Integrative analysis of RNA splicing and chromatin occupancy, combined with chromatin tethering assays, demonstrate that DNA-bound RELA interacts with and recruits the splicing regulator DDX17 in a NF-kB activation-dependent manner, leading to alternative splicing of target exons thanks to DDX17 RNA helicase activity. This NF-kB/DDX17 axis accounts for a major part of the TAX-induced alternative splicing landscape that mainly affects genes involved in oncogenic pathways. Collectively, our results demonstrate a physical and direct involvement of NF-κB in alternative splicing regulation, which significantly revisits our knowledge of HTLV-1 pathogenesis and other NF-κB-related diseases.
Ramified rolling circle amplification for efficient and flexible synthesis of nucleosomal DNA sequences
Authors: van Emmerik Clara L. , Gachulincova Ivana , Lobbia Vincenzo R. , Daniëls Mark A. , Heus Hans A. , Soufi Abdenour , Nelissen Frank H.T. , van Ingen Hugo 
Published: June 2019

ABSTRACTNucleosomes are a crucial platform for the recruitment and assembly of protein complexes that process the DNA. Mechanistic and structuralin vitrostudies typically rely on recombinant nucleosomes that are reconstituted using artificial, strong-positioning DNA sequences. To facilitate such studies on native, genomic nucleosomes, there is a need for methods to produce any desired DNA sequence in an efficient manner. The current methods either do not offer much flexibility in choice of sequence or are less efficient in yield and labor. Here, we show that using ramified rolling circle amplification (RCA) milligram amounts of a genomic nucleosomal DNA fragment can be produced in a scalable, one-pot reaction overnight. The ramified RCA reaction is more efficient than the existing methods, is flexible in DNA sequence and shows a 10-fold increase in yield compared to PCR, rivalling the production using plasmids. We demonstrate the method by producing the genomic DNA from the human LIN28B locus and show that it forms functional nucleosomes capable of binding pioneer transcription factor Oct4.
Characterization of consensus operator site for Streptococcus pneumoniae copper repressor, CopY
Authors: O’Brien Henrik , Alvin Joseph W. , Menghani Sanjay V. , Van Doorslaer Koenraad , Johnson Michael D. L. 
Published: June 2019

ABSTRACTCopper is broadly toxic to bacteria. As such, bacteria have evolved specialized copper export systems (cop operons) often consisting of a DNA-binding/copper-responsive regulator (which can be a repressor or activator), a copper chaperone, and a copper exporter. For those bacteria using DNA-binding copper repressors, few studies have examined the regulation of this operon regarding the operator DNA sequence needed for repression. In Streptococcus pneumoniae (the pneumococcus), CopY is the copper repressor for the cop operon. Previously, these homologs have been characterized to bind a 10-base consensus sequence T/GACAnnTGTA. Here, we bioinformatically and empirically characterize these operator sites across species using S. pneumoniae CopY as a guide for binding. By examining the 21-base repeat operators for the pneumococcal cop operon and comparing binding of recombinant CopY to this, and the operator sites found in Enterococcus hirae, we show using biolayer interferometry that the T/GACAnnTGTA sequence is essential to binding, but it is not sufficient. We determine a more comprehensive S. pneumoniae CopY operator sequence to be RnYKACAAATGTARnY (where “R” is purine, “Y” is pyrimidine, and “K” is either G or T) binding with an affinity of 28 nM. We further propose that the cop operon operator consensus site of pneumococcal homologs be RnYKACAnnYGTARnY. This study illustrates the necessity to explore bacterial operator sites further to better understand bacterial gene regulation.
Sampling strategies to assess microbial diversity of Antarctic cryptoendolithic communities
Authors: Coleine Claudia , Stajich Jason E. , Pombubpa Nuttapon , Zucconi Laura , Onofri Silvano , Selbmann Laura 
Published: June 2019

AbstractDescribing the total biodiversity of an environmental metacommunity is challenging due to the presence of cryptic and rare species and incompletely described taxonomy. How many samples to collect is a common issue faces ecologists when designing fieldwork sampling: collecting many samples may indeed capture the whole metacommunity structure, but can be prohibitively costly and lead to an enormous amount of data to analyse. Conversely, too few samples may yield inadequate and incomplete data which can prohibit complete assessment of community diversity. High-throughput sequencing allows examination of large numbers of samples enabling comprehensive biodiversity assessments. In this study, we sought to estimate how the scale of sampling affects accuracy of community diversity description in order to develop strategies to exhaustively describe the microbial diversity of cryptoendolithic communities in the McMurdo Dry Valleys in Antarctica accounted as the closest Martian analogue on Earth, exhibiting extreme conditions such as low temperatures, wide thermal fluctuations, low nutrient availability and high UV radiation. We found that sampling effort, based on accumulation curves analysis, had a considerable impact on assessing species richness and composition in these ecosystems, confirming that a sampling as large as nine rock specimens was necessary to detect almost all fungal species present, but was not sufficient to capture whole bacterial assemblage.
Emergence timing and voltinism of phantom midges, Chaoborus spp., in the UK
Authors: Cockroft R. , Jenkins W.R. , Irwin A. , Norman S. , Brown K.C. 
Published: June 2019

AbstractAfter introduction of overwintered fourth instar larvae (2027 in total), emergence timing of adult Chaoborus spp. (Diptera: Chaoboridae) was investigated in four outdoor freshwater microcosms in the UK in 2017. Adults started emerging on 13 April and emergence reached a peak on 2 May. The majority of emergence was completed by 3 June. Emergence rates for each microcosm ranged from 51.4% to 66.2% with a mean of 60.9%. The great majority of emerged adults were C. obscuripes (99.68%). Males appeared to emerge slightly earlier than females. The results indicated that for overwintered C. obscuripes larvae, the adults emerged en masse in spring (rather than emerging gradually over the course of spring and summer). In a separate experiment at the same location, the number of Chaoborus spp. life-cycles occurring per year was determined using six replicate groups of microcosms, each group containing four microcosms. Each microcosm contained 200 L of water and was enclosed within a ‘pop-up’ frame covered with ‘insect-proof’ mesh (1 mm2 aperture). The first microcosm in each group was ‘seeded’ with egg rafts (first generation) of Chaoborus spp. Following adult emergence, as soon as the first egg rafts were laid in each microcosm these were removed and transferred to the second microcosm in that group, and so on. The larvae sampled from the second and subsequent generations in the microcosms were all C. crystallinus. C. crystallinus produced up to four discrete generations within the experimental period, and life-cycle times from egg-to-egg ranged from 14 days (replicate group 5, first generation) to 56 days (replicate 3, second generation). These two experiments, indicated that i) adult C. obscuripes arising from overwintered larvae emerged en masse in the spring, and ii) up to four generations of C. crystallinus occurred; i.e. C. crystallinus exhibited a multi-voltine life history under the temperate conditions of this UK study.
Down-regulatedGDF9andBMP15mRNAs are the important determining factors for the unexplained female infertility cases advised for assisted reproductive technology
Authors: Gupta Sumita Dutta , Kundu Sharbadeb , Dhar Bishal , Das Nabarun , Choudhury Arun Paul , Deb Monica , Das Abhijit , Das Amrita , Das Nayanika , Choudhury Biswadeep , Varghese Alex C , Kar Kushal Kumar , Choudhury Yashmin , Ghosh Sankar Kumar 
Published: June 2019

DISCLAIMERThe authors have withdrawn this manuscript because they intend to revise this version of pre-print substantially in response to comments received from the reviewers and other peers on some analytical parts along with the interpretation of corresponding results, in order to make a fresh submission to an impacted reputed journal. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Intracellular cyclic AMP levels modulate differential adaptive responses on epimastigotes and cell culture trypomastigotes of Trypanosoma cruzi
Authors: Sternlieb Tamara , Schoijet Alejandra C. , Alonso Guillermo D. 
Published: June 2019

ABSTRACTAmong the many environmental challenges the parasite Trypanosoma cruzi has to overcome to complete its life cycle through different hosts, oxidative stress plays a central role. Different stages of this parasite encounter distinct sources of oxidative stress, such as the oxidative burst of the immune system, or the Heme released from hemoglobin degradation in the triatomine’s midgut. Also, the redox status of the surroundings functions as a signal to the parasite, triggering processes coupled to differentiation or proliferation. Intracellular second messengers, like cAMP, are responsible for the transduction of environmental queues and initiating cellular processes accordingly. In trypanosomatids cAMP is involved in a variety of processes, including proliferation, differentiation, osmoregulation and quorum sensing. Trypanosomatid phosphodiesterases (PDE) show atypical pharmacological properties and some have been involved in key processes for the survival of the parasites, which validates them as attractive therapeutic targets. Our work here shows that cAMP modulates different processes according to parasite stage. Epimastigotes become more resistant to oxidative stress when pre-treated with cAMP analogs, while trypomastigotes do not alter their response to oxidative stress under the same treatment. However, cAMP analogs do increase trypomastigotes infectivity in vitro. Also, we show that TcrPDEA1, a functionally enigmatic phosphodiesterase with very high Km, is involved in the epimastigotes response to oxidative stress.