bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maternal Protection in Childhood is Associated with Amygdala Reactivity and Structural Connectivity in Adulthood
Authors: Farber Madeline J. , Kim M. Justin , Knodt Annchen R. , Hariri Ahmad R. 
Published: February 2019

ABSTRACTRecently, we reported that variability in early-life caregiving experiences maps onto individual differences in threat-related brain function. Specifically, we found that greater familial affective responsiveness is associated with increased amygdala reactivity to interpersonal threat, particularly in adolescents having experienced relatively low recent stress. Here, we conceptually replicate and extend on our previous work to provide further evidence that subtle variability in specific features of early caregiving shapes structural and functional connectivity between the amygdala and medial prefrontal cortex (mPFC) in a cohort of 312 young adult volunteers. Multiple regression analyses revealed that participants who reported higher maternal but not paternal protection exhibited increased amygdala reactivity to explicit signals of interpersonal threat (i.e., angry facial expressions) but not implicit signals of broad environmental threat (i.e., fearful facial expressions). While amygdala functional connectivity with regulatory regions of the mPFC was not significantly associated with maternal protection, participants who reported higher maternal protection exhibited relatively decreased structural integrity of the uncinate fasciculus (UF), a white matter tract connecting these same brain regions. The observed associations were independent of the potential confounding influences of participant sex, socioeconomic status, and self-reported childhood trauma. There were no significant associations between structural or functional brain measures and either maternal or paternal care ratings. These findings suggest that an over controlling parenting style in mothers during childhood is associated with functional and structural alterations of brain regions involved in generating and regulating responses to threat in young adulthood.
Addressing reverse inference in structural brain alterations
Authors: Cauda Franco , Nani Andrea , Liloia Donato , Manuello Jordi , Premi Enrico , Duca Sergio , Fox Peter T. , Costa Tommaso 
Published: February 2019

AbstractIn neuroimaging with reverse inferences we can infer the involvement of cognitive processes from certain patterns of brain activity. Still, the same reasoning holds if we substitute “brain activity” with “brain alteration” and “cognitive process” with “brain disorder”. To assess the involvement of a certain alteration pattern in a brain disorder we used the Bayes’ factor technique on voxel-based morphometry data of schizophrenia and Alzheimer’s disease. This technique allows to calculate the ratio between the likelihoods of two alternative hypotheses (in our case, that the alteration of the voxel is specific for the brain disorder under scrutiny or that the alteration is not specific). We then performed temporal simulations of the alteration spread associated with different pathologies. The Bayes’ factor values calculated on these simulated data were able to reveal that the areas which are more specific to a certain disease are also the ones to be early altered.
Coordinate-based mapping of tabular data enables fast and scalable queries
Authors: Piccolo Stephen R. , Ence Zachary E. , Hill Kimball , Tatlow PJ , Fry Brandon J. , Dayton Jonathan B. 
Published: February 2019

AbstractMotivationBiologists commonly store data in tabular form with observations as rows, attributes as columns, and measurements as values. Due to advances in high-throughput technologies, the sizes of tabular datasets are increasing. Some datasets contain millions of rows or columns. To work effectively with such data, researchers must be able to efficiently extract subsets of the data (using filters to select specific rows and retrieving specific columns). However, existing methodologies for querying tabular data do not scale adequately to large datasets or require specialized tools for processing. We sought a methodology that would overcome these challenges and that could be applied to an existing, text-based format.ResultsIn a systematic benchmark, we tested 10 techniques for querying simulated, tabular datasets. These techniques included a delimiter-splitting method, the Pythonpandasmodule, regular expressions, object serialization, theawkutility, and string-based indexing. We found that storing the data in fixed-width formats provided excellent performance for extracting data subsets. Because columns have the same width on every row, we could pre-calculate column and row coordinates and quickly extract relevant data from the files. Memory mapping led to additional performance gains. A limitation of fixed-width files is the increased storage requirement of buffer characters. Compression algorithms help to mitigate this limitation at a cost of reduced query speeds. Lastly, we used this methodology to transpose tabular files that were hundreds of gigabytes in size, without creating temporary files. We propose coordinate-based, fixed-width storage as a fast, scalable methodology for querying tabular biological data.Contactstephen_piccolo@byu.edu
A novel QTL conferring Fusarium crown rot resistance located on chromosome arm 6HL in barley
Authors: Gao Shang , Zheng Zhi , Hu Haiyan , Shi Haoran , Ma Jian , Liu Yaxi , Wei Yuming , Zheng You-Liang , Zhou Meixue , Liu Chunji 
Published: February 2019

AbstractFusarium crown rot (FCR), caused primarily by Fusarium pseudograminearum, is a devastating disease for cereal production in semi-arid regions worldwide. To identify and characterize loci conferring FCR resistance, we assessed a landrace AWCS799 which is among the top lines identified from a screening. Genetic control of its resistance was investigated by generating and analysing two populations of recombinant inbred lines. One of the populations was used for QTL detection and the other for validation. A novel QTL, located on the long arm of chromosome 6H (designated as Qcrs.caf-6H), was consistently detected in each of the four trials conducted against the mapping population. The QTL explained up to 29.1% of the phenotypic variance and its effect was confirmed in the validation population. Significant interactions between this resistance locus and either plant height or heading date were not detected, further facilitating its manipulation in breeding programs.Key MessageThis study identified and validated a novel and large-effect QTL conferring Fusarium crown rot resistance on the long arm of chromosome 6HL in barley.
Antibiotic Treatment Drives the Diversification of the Human Gut Resistome
Authors: Li Jun , Rettedal Elizabeth A. , van der Helm Eric , Ellabaan Mostafa , Panagiotou Gianni , Sommer Morten O.A. 
Published: February 2019

AbstractDespite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.
Saffron (Crocus sativus) is an autotriploid that evolved in Attica (Greece) from wildCrocus cartwrightianus
Authors: Nemati Zahra , Harpke Dörte , Gemicioglu Almila , Kerndorff Helmut , Blattner Frank R. 
Published: February 2019

AbstractCrocus sativusis the source of saffron, which is made from dried stigmas of the plant. It is a male-sterile triploid that ever since its origin has been propagated vegetatively. The mode of evolution and area of origin of saffron are matters of long-lasting debates. Here we analyzed chloroplast genomes, genotyping-by-sequencing (GBS) data, nuclear single-copy genes, and genome sizes to solve these controversial issues. We could place 99.3% of saffron GBS alleles inCrocus cartwrightianus, a species occurring in southern mainland Greece and on Aegean islands, identifying it as the sole progenitor of saffron. Phylogenetic and population assignment analyses together with chloroplast polymorphisms indicated the wildC. cartwrightianuspopulation south of Athens as most similar toC. sativus. We conclude that the crop is an autotriploid that evolved in Attica by combining two different genotypes ofC. cartwrightianus. Vegetative propagation prevented afterwards segregation of the favorable traits of saffron.
Pannexin-1 Channels govern the Generation of Necroptotic small Extracellular Vesicles
Authors: Douanne Tiphaine , André-Grégoire Gwennan , Feyeux Magalie , Hulin Philippe , Gavard Julie , Bidère Nicolas 
Published: February 2019

ABSTRACTThe activation of mixed lineage kinase-like (MLKL) by receptor-interacting protein kinase-3 (RIPK3) controls the execution of necroptosis, a regulated form of necrosis that occurs in apoptosis-deficient conditions. Active oligomerized MLKL triggers the exposure of phosphatidylserine residues on the cell surface and disrupts the plasma membrane integrity by forming lytic pores. MLKL also governs the biogenesis and shedding of proinflammatory small extracellular vesicles (EVs) during the early steps of necroptosis, however the molecular basis is unknown. Here, we find that MLKL oligomers activate plasma membrane Pannexin-1 (PANX1) channels, concomitantly to the loss of phosphatidylserine asymmetry. This plasma membrane “leakiness” requires the Rab GTPase Rab27 isoforms, which usher the small EVs to their release. Conversely, PANX1 knockdown disorganized the small EVs machinery and precludes vesicles extrusion. These data identify a novel signaling nexus between MLKL, Rab27, and PANX1, and propose ways to interfere with small EV generation.
The coiled coil domain of DEF6 facilitates formation of large vesicle-like, cytoplasmic aggregates that trap the P-body marker DCP1 and exhibit prion-like features
Authors: Cheng Huaitao , Sablitzky Fred 
Published: February 2019

ABSTRACTDEF6, also known as SLAT and IBP, is critical for the development of autoimmune disease and cancer. In T cells, DEF6 participates in TCR-mediated signalling determining T helper cell-mediated immune responses. In addition, DEF6 acts as a guanine nucleotide exchange factor for Rho GTPases facilitating F-actin assembly and stabilisation of the immunological synapse. However, DEF6 is also a component of mRNA processing bodies (P-bodies) linking it to mRNA metabolism. DEF6 can adopt multiple conformations that result in different cellular localisations and functions. Post translational modifications such as phosphorylation result in conformational change liberating functional domains that are masked in the native stage of DEF6. ITK phosphorylation of Try210/222 liberates the N-terminal end and to a certain extend also the C-terminal coiled coil domain of DEF6 resulting in P-body colocalisation. In fact, the N-terminal 45 amino acids of DEF6 that encode a Ca2+-binding EF hand are sufficient to target P-bodies. Mutant proteins that unleashed the C-terminal coiled coil domain of DEF6 spontaneously aggregated forming large vesicle-like, cytoplasmic structures. These aggregates trapped proteins such as the P-body component DCP1 altering its cytoplasmic localisation. However, cellular stress reversed aggregate formation in mutant DEF6 proteins that contained ITAM and PH domain in conjunction with the coiled coil domain resulting in colocalisation with DCP1. Furthermore, coiled coil-mediated aggregates appeared to function like prions enforcing conformational change onto wild type DEF6 protein.
A Retrospective Study of Intentional Body Dismemberment in New York City: 1996–2017
Authors: Adams Bradley J. , Rainwater Christopher W. , Yim An‐Di , Alesbury Helen S. 
Published: February 2019

AbstractA review of New York City dismemberment cases occurring between 1996 and 2017 was conducted, which resulted in a total of 55 dismembered decedents in a 22‐year period. Annual trends indicate an average of 2.5 dismembered decedents. Additional results show that 53% of cases involved transection only, 35% involved disarticulation only, and 13% involved a combination of both. When the entire body could be accounted for, the average number of body portions per case was 5.5. Frequent locations for dismemberment were the neck, shoulders, hips, and knees. Dismemberment locations showed a general trend of anatomical symmetry. Seventy‐eight percent of the dismemberments involve disposal of body parts in an outside location. Eighty‐four percent were concealed from view with some type of covering. The findings from New York City are compared with other studies.
Pits, mounds, and vernal ponds in a Tasmanian subalpine grassland
Authors: Harrison‐Day Violet , Kirkpatrick James 
Published: February 2019

AbstractFalling trees commonly turbate soils in primary forest, creating characteristic edaphic patterns related to pit and mound topography. Vernal ponds with associated mounds were observed in mineral soils on a treeless plain in subalpine Tasmania, Australia. The hypothesis that paired ponds and mounds on the plain originated as pit and mound features in forests that were later destroyed by fire was tested by comparing the soils and landforms caused by recent tree falls in adjacent forest with those on the plain. The soil characteristics, orientations, and dimensions of the ponds and mounds were consistent with a tree fall origin, although rare secondary ponds on the tops of mounds may derive from the burrowing activities of the medium‐sized marsupial, Vombatus ursinus (common wombat). The characteristics of pond and mound soils suggested that most were hundreds to thousands of years old, with the ponds persisting because of differences in deflation, deposition, and organic matter formation between themselves and adjacent persistently dry land.
A Population‐wide study of electrocardiographic (ECG) norms and the effect of demographic and anthropometric factors on selected ECG characteristics in young, Southeast Asian males—results from the Singapore Armed Forces ECG (SAFE) study
Authors: Sia Ching‐Hui , Dalakoti Mayank , Tan Benjamin Y. Q. , Lee Edward C. Y. , Shen Xiayan , Wang Kangjie , Lee Joshua S. , Arulanandam Shalini , Chow Weien , Yeo Tee Joo , Yeo Khung Keong , Chua Terrance S. J. , Tan Ru San , Lam Carolyn S. P. , Chong Daniel T. T. 
Published: February 2019

AbstractBackgroundRoutine use of pre‐participation electrocardiograms (ECGs) has been used by the Singapore Armed Forces, targeting early detection of significant cardiac diseases. We aim to describe the impact of demographic and anthropometric factors on ECG variables and establish a set of electrocardiographic reference ranges specific to a young male multiethnic Southeast Asian cohort.Methods and resultsBetween November 1, 2009, and December 31, 2014, 144,346 young male conscripts underwent pre‐participation screening that included a 12‐lead ECG, demographic and anthropometric measurements. The Chinese population had the longest PR interval (146.7 ± 19.7 vs. 145.21 ± 19.2 in Malays vs. 141.2 ± 18.8 ms in Indians), QRS duration (94.5 ± 9.8 vs. 92.6 ± 9.7 in Malays vs. 92.5 ± 9.4 ms in Indians) and QTcB interval (408.3 ± 21.3 vs. 403.5 ± 21.6 in Malays vs. 401.2 ± 21.4 ms in Indians) (all p < 0.001). Body mass index (BMI) >25 kg/m2 and body fat >25% were independently associated with lower prevalence of increased QRS voltage on ECG. Systolic blood pressure of >140 mmHg or diastolic blood pressure of >90 mmHg independently increased the prevalence of increased QRS voltage on ECG.ConclusionsElectrocardiographic parameters vary across different ethnicities and in comparison with international norms. In our population, diagnosis of increased QRS voltage by ECG is less prevalent with obesity and increased body fat. Further analysis of gold standard measurements for the diagnosis of LVH in our population is ongoing, to improve the accuracy of the ECG screening process.
Providing clarity around ethical discussion: development of a neonatal intervention score
Authors: Prentice Trisha M. , Janvier Annie , Gillam Lynn , Donath Susan , Davis Peter G. 
Published: February 2019

AbstractAimTo develop a Neonatal Intervention Score (NIS) to describe the clinical trajectory of a neonate throughout their neonatal intensive care unit (NICU) admission.MethodsThe NIS was developed by modifying the Neonatal Therapeutic Intervention Scoring System (NTISS) to reflect illness severity, dependency on life‐sustaining interventions and overall life trajectory on a longitudinal basis, rather than illness burden. Validity for longitudinal use within the NICU was tested by calculating the score for 99 preterm babies born less than 28 weeks at predetermined time points throughout their admission to tertiary level care at two institutions.ResultsA total of 1333 NISs were analysed, ranging from 0 to 32.5 (mean 9.77, SD 5.4). Internal consistency (Cronbach alpha) reached 0.8. NIS moderately correlated to both SNAPPE‐II and SNAP‐II (Spearman's rho = 0.47, p =< 0.001) within the first 24 hours.ConclusionThe NIS is a useful and reliable descriptive tool of relative illness severity and degree of medical interventions throughout a baby's admission. Integrating a longitudinal description of medical dependency of a patient may assist both clinical and ethical decision‐making and empirical research by providing an objective account of a baby's clinical trajectory. Establishment of validity within individual institutions is required.
Developments beyond blood group serology in the genomics era
Authors: Hyland Catherine A. , Roulis Eileen V. , Schoeman Elizna M. 
Published: February 2019

SummaryBlood group serology and single nucleotide polymorphism‐based genotyping platforms are accurate but do not provide a comprehensive cover for all 36 blood group systems and do not cover the antigen diversity observed among population groups. This review examines the extent to which genomics is shaping blood group serology. Resources for genomics include the Human Reference Genome Sequence assembly; curated blood group tables listing variants; public databases providing information on genetic variants from world‐wide studies; and massively parallel sequencing technologies. Blood group genomic studies span the spectrum, from bioinformatic data mining of huge data sets containing whole genome and whole exome information to laboratory investigations utilising targeted sequencing approaches. Blood group predictions based on genome sequencing and genomic studies are proving accurate, and have shown utility in both research and reference settings. Overall, studies confirm the potential for blood group genomics to reshape donor and patient transfusion management strategies to provide more compatible blood transfusions.
Mature (non‐anaplastic, non‐cutaneous) T‐/NK‐cell lymphomas in children, adolescents and young adults: state of the science
Authors: Flower Allyson , Xavier Ana C. , Cairo Mitchell S. 
Published: February 2019

SummaryMature (non‐anaplastic) T‐cell and natural killer (NK)‐lymphomas rarely occur in children or adolescents. Due to the low incidence and heterogeneity, information regarding the aetiology, physiopathology and genetics of paediatric mature (non‐anaplastic) T/NK‐cell lymphoma is lacking. In addition, standard treatments have not yet been established. In the absence of randomised clinical trials, anthracycline‐containing regimens are usually considered as the first treatment option, but with discouraging outcomes, especially in patients with advanced disease. The implementation of autologous or allogeneic stem cell transplantation as upfront consolidation therapy or for chemotherapy‐sensitive relapsed disease have resulted in improved survival for some patient subsets. The recent use of novel targeted molecular and immunotherapeutic agents has also been shown to be promising in small numbers of patients. In this context, we will review the current state of the scientific knowledge on the most common mature (non‐anaplastic, non‐cutaneous) T/NK‐cell lymphomas occurring in children, adolescent and young adults.
Treatment and prognosis of mature (non‐anaplastic) T‐ and NK‐cell lymphomas in childhood, adolescents, and young adults
Authors: Xavier Ana C. , Suzuki Ritsuro 
Published: February 2019

SummaryPaediatric non‐Hodgkin lymphomas (pNHL) are a diverse group of malignancies characterised by nodal and/or extranodal involvement. Less common pNHL forms include those derived from mature T‐ and natural killer (NK) cells. Much of our current understanding of paediatric mature (non‐anaplastic) T/NK‐cell lymphomas with respect to pathogenesis, diagnosis and treatment is extrapolated from adult literature. At the Sixth International Symposium on Childhood, Adolescent and Young Adult Non‐Hodgkin Lymphoma, convened September 26–29, 2018 in Rotterdam, The Netherlands, some important aspects on diagnosis and outcomes of mature (non‐anaplastic) T/NK‐cell lymphoma in children and adolescents were discussed and will be reviewed in here.
Second primary cancers in patients with acute lymphoblastic, chronic lymphocytic and hairy cell leukaemia
Authors: Zheng Guoqiao , Chattopadhyay Subhayan , Sud Amit , Sundquist Kristina , Sundquist Jan , Försti Asta , Houlston Richard , Hemminki Akseli , Hemminki Kari 
Published: February 2019

SummaryImprovement of survival in lymphocytic leukaemia has been accompanied by the occurrence of second primary cancer (SPCs). Based on Swedish Family Cancer Database, we applied bi‐directional analyses in which relative risks (RRs) were calculated for any SPCs in patients with chronic lymphocytic leukaemia (CLL), acute lymphoblastic leukaemia (ALL) and hairy cell leukaemia (HCL) and the risks of these leukaemias as SPCs. After CLL, RRs were significant for 20 SPCs, and high for skin squamous cell cancer (24·58 for in situ and 7·63 for invasive), Merkel cell carcinoma (14·36), Hodgkin lymphoma (7·16) and Kaposi sarcoma (6·76). Conversely, 15 CLL cancer pairs were reciprocally increased. The increased risks were reciprocal for ALL and four cancers. RR for ALL was 15·35 after myeloid neoplasia. HCL showed reciprocally increased RRs with non‐Hodgkin lymphoma and melanoma. The concordance between RRs for bi‐directional associations between CLL and different cancers, and HCL and different cancers was highly significant. For CLL (also for HCL), the bi‐directional risks with skin cancers and other immune‐related cancers suggest the probable involvement of immune dysfunction. For ALL, treatment may contribute to risks of multiple SPCs. Increased risk of ALL after haematological neoplasms may indicate bone marrow dysfunction. These findings may help guide treatment decisions and prognostic assessment.