bluuebunny/crossref_metadata_2025_split huggingface dataset:
Paleoenvironmental context of the early Neanderthals of Poggetti Vecchi for the late middle Pleistocene of Central Italy
Authors: Benvenuti Marco , Bahain Jean-Jacques , Capalbo Chiara , Capretti Chiara , Ciani Francesco , D’Amico Carmine , Esu Daniela , Giachi GIanna , Giuliani Claudia , Gliozzi Elsa , Lazzeri Simona , Macchioni Nicola , Lippi Marta Mariotti , Masini Federico , Mazza Paul Peter A. , Pallecchi Pasquino , Revedin Anna , Savorelli Andrea , Spadi Marco , Sozzi Lorena , Vietti Amina , Voltaggio Mario , Aranguren Biancamaria 
Published: August 2017

AbstractWork on thermal pools at Poggetti Vecchi in Grosseto, Italy, exposed an up to 3-meter-thick succession of seven sedimentary units. Unit 2 in the lower portion of the succession contained vertebrate bones, mostly of the straight-tusked elephant,Palaeoloxodon antiquus, commingled with stone, bone, and wooden tools. Thermal carbonates overlying Unit 2 are radiometrically dated to the latter part of the middle Pleistocene. This time span indicates that early Neanderthals produced the human artifacts from Poggetti Vecchi. The elephant bones belong to seven individuals of different ages. Sedimentary facies analysis and paleoecological evidence suggest a narrow lacustrine-palustrine embayment affected by water-level fluctuations and, at times, by hydrothermal water. Cyclic lake-level variations were predominantly forced by the rapid climatic fluctuations that occurred at Marine Isotope Stage (MIS) 6–7 transition and throughout the MIS 6. Possibly an abrupt, intense, and protracted cold episode during the onset of MIS 6 led to the sudden death of the elephants, which formed an unexpected food resource for the humans of the area. The Poggetti Vecchi site adds new information on the behavioral plasticity and food procurement strategies that early Neanderthals were able to develop in Italy during the middle to the late Pleistocene transition.
Analysis of pathogenic variants from the ClinVar database in healthy people using next-generation sequencing
Authors: RANČELIS TAUTVYDAS , ARASIMAVIČIUS JUSTAS , AMBROZAITYTĖ LAIMA , KAVALIAUSKIENĖ INGRIDA , DOMARKIENĖ INGRIDA , KARČIAUSKAITĖ DOVILĖ , KUČINSKIENĖ ZITA AUŠRELĖ , KUČINSKAS VAIDUTIS 
Published: August 2017

SummaryNext-generation sequencing (NGS) became an effective approach for finding novel causative genomic variants of genetic disorders and is increasingly used for diagnostic purposes. Public variant databases that gather data of pathogenic variants are being relied upon as a source for clinical diagnosis. However, research of pathogenic variants using public databases data could be carried out not only in patients, but also in healthy people. This could provide insights into the most common recessive disorders in populations. The study aim was to use NGS and data from the ClinVar database for the identification of pathogenic variants in the exomes of healthy individuals from the Lithuanian population. To achieve this, 96 exomes were sequenced. An average of 42 139 single-nucleotide variants (SNVs) and 2306 short INDELs were found in each individual exome. Pooled data of study exomes provided a total of 243 192 unique SNVs and 31 623 unique short INDELs. Three hundred and twenty-one unique SNVs were classified as pathogenic. Comparison of the European data from the 1000 Genomes Project with our data revealed five pathogenic genomic variants that are inherited in an autosomal recessive pattern and that statistically significantly differ from the European population data.
Fair enumeration combinators
Authors: NEW MAX S. , FETSCHER BURKE , FINDLER ROBERT BRUCE , MCCARTHY JAY 
Published: August 2017

AbstractEnumerations represented as bijections between the natural numbers and elements of some given type have recently garnered interest in property-based testing because of their efficiency and flexibility. There are, however, many ways of defining these bijections, some of which are better than others. This paper offers a new property of enumeration combinators calledfairnessthat identifies enumeration combinators that are better suited to property-based testing. Intuitively, the result of a fair combinator indexes into its argument enumerations equally when constructing its result. For example, extracting thenth element from our enumeration of three-tuples indexes about$\sqrt[3]{n}$elements into each of its components instead of, say, indexing$\sqrt[2]{n}$into one and$\sqrt[4]{n}$into the other two, as you would if a three-tuple were built out of nested pairs. Similarly, extracting thenth element from our enumeration of a three-way union returns an element that is$\frac{n}{3}$into one of the argument enumerators. The paper presents a semantics of enumeration combinators, a theory of fairness, proofs establishing fairness of our new combinators and that some combinations of fair combinators are not fair. We also report on an evaluation of fairness for the purpose of finding bugs in programming-language models. We show that fair enumeration combinators have complementary strengths to an existing, well-tuned ad hoc random generator (better on short time scales and worse on long time scales) and that using unfair combinators is worse across the board.
Household income is associated with food and nutrient intake in Japanese schoolchildren, especially on days without school lunch
Authors: Murayama Nobuko , Ishida Hiromi , Yamamoto Taeko , Hazano Sayaka , Nakanishi Akemi , Arai Yumi , Nozue Miho , Yoshioka Yukiko , Saito Saori , Abe Aya 
Published: August 2017

AbstractObjectiveThe present study aimed to examine the association between household income and the intake of foods and nutrients by Japanese schoolchildren, and any differences between days with and without school lunch.DesignThis was a cross-sectional study. Children, with the support of their parents, kept dietary records with photographs for 4 d (2 d with school lunch and 2 d without). The socio-economic status of each family was obtained from a questionnaire completed by the parents.SettingJapan.SubjectsAll students in 5th grade (10–11 years old) at nineteen schools in four prefectures and their parents (1447 pairs of students and parents) were invited to take part in the study; 836 pairs of complete data sets were analysed.ResultsThe average results of four days of dietary records showed that lower income level was associated with a lower intake of fish/shellfish, green vegetables and sugar at the food group level, a lower intake of protein and several micronutrients, and a higher energy intake from carbohydrates at the nutrient level among the children. These associations between income and food/nutrient intake were not significant on days with school lunches, but were significant on days without school lunch.ConclusionsOur study confirmed an association between household income and the amount of foods and nutrients consumed by Japanese schoolchildren, and suggested that school lunches play a role in reducing disparities in the diets of children from households with various incomes.
Quality of food choices of Brazilian adolescents according to individual earnings
Authors: Araujo Marina Campos , Cunha Diana Barbosa , Bezerra Ilana Nogueira , de Castro Maria Beatriz Trindade , Sichieri Rosely 
Published: August 2017

AbstractObjectiveTo evaluate the quality of food choices according to adolescent individual earnings in Brazil.DesignAdolescents were classified according to their individual earnings as having or not having spending power for their own expenses. Food records from two non-consecutive days of the Brazilian National Dietary Survey (NDS 2008–2009) were used to estimate food intake. Quality of food choices was based on two approaches: (i) the NOVA classification, which classifies processed and ultra-processed foods and drinks as unhealthy food groups; and (ii) traditional classification, with beans, milk, fruits and vegetables as healthy food groups, and soft drinks, sweets, snacks and crackers classified as unhealthy. We compared mean food intake (g/kJ or ml/kJ) according to per capita household income (tertiles) and adolescent individual earnings, with adolescent earnings adjusted for household income, using multiple linear regression.SettingBrazilian households (n 13 569).SubjectsAdolescents aged 14–18 years (n 3673).ResultsMales without individual earnings had higher per capita household income than those with individual earnings. Household income was associated with all three food groups of the NOVA classification and seven of the eight groups of the traditional classification. However, only beans and snacks were consumed in significantly greater quantities by adolescents with individual earnings compared with those without earnings.ConclusionsAdolescent individual earnings were not the main driver of food choices; however, per capita household income was associated with food choices. The consumption of both healthy and unhealthy items increased with increasing household income.
Achievements in answer set programming
Authors: LIFSCHITZ VLADIMIR 
Published: August 2017

AbstractThis paper describes an approach to the methodology of answer set programming that can facilitate the design of encodings that are easy to understand and provably correct. Under this approach, after appending a rule or a small group of rules to the emerging program, we include a comment that states what has been “achieved” so far. This strategy allows us to set out our understanding of the design of the program by describing the roles of small parts of the program in a mathematically precise way.
KEYBOARD-DUO ARRANGEMENTS IN EIGHTEENTH-CENTURY MUSICAL LIFE
Authors: CYPESS REBECCA 
Published: August 2017

ABSTRACTIt is well known that the instrumentation of eighteenth-century chamber music was highly flexible; composers frequently adapted their own works for a variety of instruments, and players often used whatever combinations they had available. One type of arrangement little used today but attested to in both verbal description and musical manuscripts of the period is that of trios and other chamber works adapted for two keyboard instruments. Players often executed such keyboard-duo arrangements on instruments with different mechanisms and timbres – for example, harpsichord and piano together – thus capturing something of the variety of timbres available in a mixed chamber ensemble.Keyboard duos were often played by members of a single family, or by teachers and students together, a practice that allowed for the construction of a sense of ‘sympathy’ – mutual understanding through shared experience and sentiment – between the players. These players shared common physical gestures at the instruments, which reinforced the emotional content of the music; this fostered the formation of a sympathetic connection even as players retained their individual identities.
Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants
Authors: Krishnan Michelle L. , Van Steenwinckel Juliette , Schang Anne-Laure , Yan Jun , Arnadottir Johanna , Le Charpentier Tifenn , Csaba Zsolt , Dournaud Pascal , Cipriani Sara , Auvynet Constance , Titomanlio Luigi , Pansiot Julien , Ball Gareth , Boardman James P. , Walley Andrew J. , Saxena Alka , Mirza Ghazala , Fleiss Bobbi , Edwards A. David , Petretto Enrico , Gressens Pierre 
Published: August 2017

AbstractPreterm birth places infants in an adverse environment that leads to abnormal brain development and cerebral injury through a poorly understood mechanism known to involve neuroinflammation. In this study, we integrate human and mouse molecular and neuroimaging data to investigate the role of microglia in preterm white matter damage. Using a mouse model where encephalopathy of prematurity is induced by systemic interleukin-1β administration, we undertake gene network analysis of the microglial transcriptomic response to injury, extend this by analysis of protein-protein interactions, transcription factors and human brain gene expression, and translate findings to living infants using imaging genomics. We show that DLG4 (PSD95) protein is synthesised by microglia in immature mouse and human, developmentally regulated, and modulated by inflammation; DLG4 is a hub protein in the microglial inflammatory response; and genetic variation in DLG4 is associated with structural differences in the preterm infant brain. DLG4 is thus apparently involved in brain development and impacts inter-individual susceptibility to injury after preterm birth.
Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ
Authors: Ding Wei , Ji Wenjuan , Wu Yujie , Wu Runze , Liu Wan-Qiu , Mo Tianlu , Zhao Junfeng , Ma Xiaoyan , Zhang Wei , Xu Ping , Deng Zixin , Tang Boping , Yu Yi , Zhang Qi 
Published: August 2017

AbstractNosiheptide is a prototypal thiopeptide antibiotic, containing an indole side ring in addition to its thiopeptide-characteristic macrocylic scaffold. This indole ring is derived from 3-methyl-2-indolic acid (MIA), a product of the radical S-adenosylmethionine enzyme NosL, but how MIA is incorporated into nosiheptide biosynthesis remains to be investigated. Here we report functional dissection of a series of enzymes involved in nosiheptide biosynthesis. We show NosI activates MIA and transfers it to the phosphopantetheinyl arm of a carrier protein NosJ. NosN then acts on the NosJ-bound MIA and installs a methyl group on the indole C4, and the resulting dimethylindolyl moiety is released from NosJ by a hydrolase-like enzyme NosK. Surface plasmon resonance analysis show that the molecular complex of NosJ with NosN is much more stable than those with other enzymes, revealing an elegant biosynthetic strategy in which the reaction flux is controlled by protein–protein interactions with different binding affinities.
Emergence of native peptide sequences in prebiotic replication networks
Authors: Nanda Jayanta , Rubinov Boris , Ivnitski Denis , Mukherjee Rakesh , Shtelman Elina , Motro Yair , Miller Yifat , Wagner Nathaniel , Cohen-Luria Rivka , Ashkenasy Gonen 
Published: August 2017

AbstractBiopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in β-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication. Remarkably, we find that the formation of several products in a mixture is not critically harmful, since efficient and selective template-assisted reactions serve as a backbone correction mechanism, namely, for keeping the concentration of the peptide containing the native backbone equal to, or even higher than, the concentrations of the other products. We suggest that these findings may shed light on molecular evolution processes that led to current biology.
RETRACTED ARTICLE: Liver X receptors constrain tumor development and metastasis dissemination in PTEN-deficient prostate cancer
Authors: Alioui Anthony , Dufour Julie , Leoni Valerio , Loregger Anke , Moeton Martina , Iuliano Luigi , Zerbinati Chiara , Septier Amandine , Val Pierre , Fouache Allan , Russo Vincenzo , Volle David H. , Lobaccaro Jean-Marc A. , Zelcer Noam , Baron Silvère 
Published: August 2017

AbstractAdvanced prostate cancer (PCa) is a clinical challenge as no curative therapeutic is available. In this context, a better understanding of metastasis and resistance mechanisms in PCa is an important issue. As phosphatase and tensin homolog (PTEN) loss is the most common genetic lesion in such cancer, we investigate human data sets for mechanisms that can constrain cancer evolution in this setting. Here we report a liver X receptor (LXR) signature, which tightly correlates with PTEN loss, in PCa. Accordingly, the LXR pathway is deregulated in prostate carcinomas in Pten-null mice. Genetic ablation of LXRs in Pten-null mice, exacerbates PCa invasiveness and metastatic dissemination, which involves mesenchymal transition and accumulation of matrix metalloproteinases. Mechanistically, PTEN deletion governed LXR transcriptional activity through deregulation of cholesterol de novo synthesis, resulting in accumulation of endogenous LXR ligands. Our study therefore reveals a functional circuit linking PTEN and LXR, and highlights LXRs as metabolic gatekeepers that are able to constrain PCa progression.
Land-locked mammalian Golgi reveals cargo transport between stable cisternae
Authors: Dunlop Myun Hwa , Ernst Andreas M. , Schroeder Lena K. , Toomre Derek K. , Lavieu Grégory , Rothman James E. 
Published: August 2017

AbstractThe Golgi is composed of a stack of cis, medial, trans cisternae that are biochemically distinct. The stable compartments model postulates that permanent cisternae communicate through bi-directional vesicles, while the cisternal maturation model postulates that transient cisternae biochemically mature to ensure anterograde transport. Testing either model has been constrained by the diffraction limit of light microscopy, as the cisternae are only 10–20 nm thick and closely stacked in mammalian cells. We previously described the unstacking of Golgi by the ectopic adhesion of Golgi cisternae to mitochondria. Here, we show that cargo processing and transport continue—even when individual Golgi cisternae are separated and “land-locked” between mitochondria. With the increased spatial separation of cisternae, we show using three-dimensional live imaging that cis-Golgi and trans-Golgi remain stable in their composition and size. Hence, we provide new evidence in support of the stable compartments model in mammalian cells.
Lineage overwhelms environmental conditions in determining rhizosphere bacterial community structure in a cosmopolitan invasive plant
Authors: Bowen Jennifer L. , Kearns Patrick J. , Byrnes Jarrett E. K. , Wigginton Sara , Allen Warwick J. , Greenwood Michael , Tran Khang , Yu Jennifer , Cronin James T. , Meyerson Laura A. 
Published: August 2017

AbstractPlant–microbe interactions play crucial roles in species invasions but are rarely investigated at the intraspecific level. Here, we study these interactions in three lineages of a globally distributed plant, Phragmites australis. We use field surveys and a common garden experiment to analyze bacterial communities in the rhizosphere of P. australis stands from native, introduced, and Gulf lineages to determine lineage-specific controls on rhizosphere bacteria. We show that within-lineage bacterial communities are similar, but are distinct among lineages, which is consistent with our results in a complementary common garden experiment. Introduced P. australis rhizosphere bacterial communities have lower abundances of pathways involved in antimicrobial biosynthesis and degradation, suggesting a lower exposure to enemy attack than native and Gulf lineages. However, lineage and not rhizosphere bacterial communities dictate individual plant growth in the common garden experiment. We conclude that lineage is crucial for determination of both rhizosphere bacterial communities and plant fitness.
Parkinson’s disease associated with pure ATXN10 repeat expansion
Authors: Schüle Birgitt , McFarland Karen N. , Lee Kelsey , Tsai Yu-Chih , Nguyen Khanh-Dung , Sun Chao , Liu Mei , Byrne Christie , Gopi Ramesh , Huang Neng , Langston J. William , Clark Tyson , Gil Francisco Javier Jiménez , Ashizawa Tetsudo 
Published: August 2017

AbstractLarge, non-coding pentanucleotide repeat expansions of ATTCT in intron 9 of the ATXN10 gene typically cause progressive spinocerebellar ataxia with or without seizures and present neuropathologically with Purkinje cell loss resulting in symmetrical cerebellar atrophy. These ATXN10 repeat expansions can be interrupted by sequence motifs which have been attributed to seizures and are likely to act as genetic modifiers. We identified a Mexican kindred with multiple affected family members with ATXN10 expansions. Four affected family members showed clinical features of spinocerebellar ataxia type 10 (SCA10). However, one affected individual presented with early-onset levodopa-responsive parkinsonism, and one family member carried a large repeat ATXN10 expansion, but was clinically unaffected. To characterize the ATXN10 repeat, we used a novel technology of single-molecule real-time (SMRT) sequencing and CRISPR/Cas9-based capture. We sequenced the entire span of ~5.3–7.0 kb repeat expansions. The Parkinson’s patient carried an ATXN10 expansion with no repeat interruption motifs as well as an unaffected sister. In the siblings with typical SCA10, we found a repeat pattern of ATTCC repeat motifs that have not been associated with seizures previously. Our data suggest that the absence of repeat interruptions is likely a genetic modifier for the clinical presentation of l-Dopa responsive parkinsonism, whereas repeat interruption motifs contribute clinically to epilepsy. Repeat interruptions are important genetic modifiers of the clinical phenotype in SCA10. Advanced sequencing techniques now allow to better characterize the underlying genetic architecture for determining accurate phenotype–genotype correlations.
Rotigotine transdermal patch and sleep in Parkinson’s disease: where are we now?
Authors: Rosa-Grilo Miguel , Qamar Mubasher A. , Taddei Raquel N. , Pagonabarraga Javier , Kulisevsky Jaime , Sauerbier Anna , Chaudhuri K. Ray 
Published: August 2017

AbstractA wide range of sleep dysfunction complicates Parkinson’s disease during its course from prodromal to palliative stage. It is now increasingly acknowledged that sleep disturbances are thus integral to the disease and pose a significant burden impacting on quality of life of patients. Sleep fragmentation, restless legs syndrome, nocturia, and nocturnal pain are regarded as one of the main components of night-time sleep dysfunction with possible secondary impact on cognition and well-being. The role of dopaminergic therapies, particularly using a continuous drug delivery strategy in managing some of these sleep issues, have been reported but the overall concept remains unclear. This review provides an overview of several aspects of night-time sleep dysfunction in Parkinson’s disease and describes all available published open-label and blinded studies that investigated the use of rotigotine transdermal patch targeting sleep. Blinded studies have suggested beneficial effects of rotigotine transdermal patch on maintenance insomnia and restless legs syndrome in Parkinson’s disease patients. Open-label studies support these observations and also suggest beneficial effects on nocturia and nocturnal pain.