bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human foodborne listeriosis in England and Wales, 1981 to 2015
Authors: McLauchlin J. , Grant K. A. , Amar C. F. L. 
Published: February 2020

Abstract
Almost all cases of human listeriosis are foodborne, however the proportion where specific exposures are identified is small. Between 1981 and 2015, 5252 human listeriosis cases were reported in England and Wales. The purpose of this study was to summarise data where consumption of specific foods was identified with transmission and these comprised 11 sporadic cases and 17 outbreaks. There was a single outbreak in the community of 378 cases (7% of the total) which was associated with pâté consumption and 112 cases (2% of the total) attributed to specific foods in all the other incidents. The proportion of food-attributed cases increased during this study with improvements in typing methods for Listeria monocytogenes. Ten incidents (one sporadic case and nine outbreaks of 2–9 cases over 4 days to 32 months) occurred in hospitals: all were associated with the consumption of pre-prepared sandwiches. The 18 community incidents comprised eight outbreaks (seven of between 3 and 17 cases) and 10 sporadic cases: food of animal origin was implicated in 16 of the incidents (sliced or potted meats, pork pies, pâté, liver, chicken, crab-meat, butter and soft cheese) and food of non-animal origin in the remaining two (olives and vegetable rennet).
Estimated dates of detectable infection (EDDIs) as an improvement upon Fiebig staging for HIV infection dating
Authors: Facente S. N. , Grebe E. , Pilcher C. D. , Busch M. P. , Murphy G. , Welte A. 
Published: February 2020

Abstract
Accurate methods for determining the duration of HIV infection at the individual level are valuable in many settings, including many critical research studies and in clinical practice (especially for acute infection). Since first published in 2003, the ‘Fiebig staging system’ has been used as the primary way of classifying early HIV infection into five sequential stages based on HIV test result patterns in newly diagnosed individuals. However, Fiebig stages can only be assigned to individuals who produce both a negative and a positive test result on the same day, on specific pairs of tests of varying ‘sensitivity’. Further, in the past 16 years HIV-testing technology has evolved substantially, and three of the five key assays used to define Fiebig stages are no longer widely used. To address these limitations, we developed an improved and more general framework for estimating the duration of HIV infection by interpreting any combination of diagnostic test results, whether obtained on single or multiple days, into an estimated date of detectable infection, or EDDI. A key advantage of the EDDI method over Fiebig staging is that it allows for the generation of a point estimate, as well as an associated credibility interval for the date of first detectable infection, for any person who has at least one positive and one negative HIV test of any kind. The tests do not have to be run on the same day; they do not have to be run during the acute phase of infection and the method does not rely on any special pairing of tests to define ‘stages’ of infection. The size of the interval surrounding the EDDI (and therefore the precision of the estimate itself) depends largely on the length of time between negative and positive tests. The EDDI approach is also flexible, seamlessly incorporating any assay for which there is a reasonable diagnostic delay estimate. An open-source, free online tool includes a user-updatable curated database of published diagnostic delays. HIV diagnostics have evolved tremendously since that original publication more than 15 years ago, and it is time to similarly evolve the methods used to estimate timing of infection. The EDDI method is a flexible and rigorous way to estimate the timing of HIV infection in a continuously evolving diagnostic landscape.
Applications of SAR Interferometric Coherence Time Series: Spatiotemporal Dynamics of Geomorphic Transitions in the South‐Central Andes
Authors: Olen Stephanie , Bookhagen Bodo 
Published: February 2020

AbstractSediment transport domains in mountain landscapes are characterized by fundamentally different processes and rates depending on several factors, including geology, climate, and biota. Accurately identifying where transitions between transport domains occur is an important step to quantify the past, present, and future contribution of varying erosion and sedimentation processes and enhance our predictive capabilities. We propose a new methodology based on time series of synthetic aperture radar (SAR) interferometric coherence images to map sediment transport regimes across arid and semiarid landscapes. Using 4 years of Sentinel‐1 data, we analyze sediment transport regimes for the south‐central Andes in northwestern Argentina characterized by steep topographic and climatic gradients. We observe seasonally low coherence during the regional wet season, particularly on hillslopes and in alluvial channels. The spatial distribution of coherence is compared to drainage areas extracted from digital topography to identify two distinct transitions within watersheds: (a) a hillslope‐to‐fluvial and (b) a fluvial‐to‐alluvial transition. While transitions within a given basin can be well‐constrained, the relative role of each sediment transport domain varies widely over the climatic and topographic gradients. In semiarid regions, we observe larger relative contributions from hillslopes compared to arid regions. Across regional gradients, the range of coherence within basins positively correlates to previously published millennial catchment‐wide erosion rates and to topographic metrics used to indicate long‐term uplift. Our study suggests that a dense time series of interferometric coherence can be used as a proxy for surface sediment movement and landscape stability in vegetation‐free settings at event to decadal timescales.
Effects of oral, smoked, and vaporized cannabis on endocrine pathways related to appetite and metabolism: a randomized, double-blind, placebo-controlled, human laboratory study
Authors: Farokhnia Mehdi , McDiarmid Gray R. , Newmeyer Matthew N. , Munjal Vikas , Abulseoud Osama A. , Huestis Marilyn A. , Leggio Lorenzo 
Published: February 2020

AbstractAs perspectives on cannabis continue to shift, understanding the physiological and behavioral effects of cannabis use is of paramount importance. Previous data suggest that cannabis use influences food intake, appetite, and metabolism, yet human research in this regard remains scant. The present study investigated the effects of cannabis administration, via different routes, on peripheral concentrations of appetitive and metabolic hormones in a sample of cannabis users. This was a randomized, crossover, double-blind, placebo-controlled study. Twenty participants underwent four experimental sessions during which oral cannabis, smoked cannabis, vaporized cannabis, or placebo was administered. Active compounds contained 6.9 ± 0.95% (~50.6 mg) ∆9-tetrahydrocannabinol (THC). Repeated blood samples were obtained, and the following endocrine markers were measured: total ghrelin, acyl-ghrelin, leptin, glucagon-like peptide-1 (GLP-1), and insulin. Results showed a significant drug main effect (p = 0.001), as well as a significant drug × time-point interaction effect (p = 0.01) on insulin. The spike in blood insulin concentrations observed under the placebo condition (probably due to the intake of brownie) was blunted by cannabis administration. A significant drug main effect (p = 0.001), as well as a trend-level drug × time-point interaction effect (p = 0.08) was also detected for GLP-1, suggesting that GLP-1 concentrations were lower under cannabis, compared to the placebo condition. Finally, a significant drug main effect (p = 0.01) was found for total ghrelin, suggesting that total ghrelin concentrations during the oral cannabis session were higher than the smoked and vaporized cannabis sessions. In conclusion, cannabis administration in this study modulated blood concentrations of some appetitive and metabolic hormones, chiefly insulin, in cannabis users. Understanding the mechanisms underpinning these effects may provide additional information on the cross-talk between cannabinoids and physiological pathways related to appetite and metabolism.
HHLA2 is expressed in pancreatic and ampullary cancers and increased expression is associated with better post-surgical prognosis
Authors: Boor Patrick P. C. , Sideras Kostandinos , Biermann Katharina , Hosein Aziz M. , Levink Iris J. M. , Mancham Shanta , Erler Nicole S. , Tang Xudong , van Eijck Casper H. , Bruno Marco J. , Sprengers Dave , Zang Xingxing , Kwekkeboom Jaap 
Published: February 2020

Abstract
Background
HHLA2 is a recently discovered member of the B7-family of immune checkpoint molecules with limited expression in normal tissues but overexpression in several types of cancer. The aim was to determine the expression, prevalence and biological relevance of HHLA2 protein expression in two closely related human cancer types, namely pancreatic cancer and ampullary cancer.

Methods
HHLA2 expression levels were retrospectively determined by immunohistochemistry in tissue micro-arrays of surgically resected tumours of 122 pancreatic cancer patients and 72 patients with ampullary cancer of the pancreato-biliary subtype.

Results
HHLA2 was expressed at variable levels by tumour cells in 67% of pancreatic tumours and 93% of ampullary tumours. In the combined cohort high tumoural HHLA2 expression levels were significantly associated with delayed cancer recurrence and improved post-operative cancer-specific survival. The association of HHLA2 expression with cancer-specific survival and recurrence was statistically significant for the pancreatic cancer subgroup while a similar trend was found for the ampullary cancer subgroup. In multivariable analysis together with clinicopathologic characteristics, higher HHLA2 expression was an independent predictor of cancer-specific survival.

Conclusion
The wide expression of HHLA2 in tumour cells and its association with cancer recurrence and patient survival suggest that HHLA2 represents a relevant immune checkpoint molecule in pancreatic and ampullary cancers.
Inhibition of keratinocyte necroptosis mediated by RIPK1/RIPK3/MLKL provides a protective effect against psoriatic inflammation
Authors: Duan Xiaoru , Liu Xinxin , Liu Nian , Huang Yuqiong , Jin Zilin , Zhang Song , Ming Zhangyin , Chen Hongxiang 
Published: February 2020

AbstractPsoriasis is a common autoimmune and chronic inflammatory skin disorder globally affecting 0.51–11.43% of adults. Inflammation-associated cell death in keratinocytes plays a key role in the process of integrate inflammatory cascade in psoriasis. Necroptosis is a regulated necrotic cell death mediated by receptor interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like pseudokinase (MLKL), which participates in many human inflammatory diseases. However, the mechanism and function of programmed necrosis in psoriasis is not well-illustrated. In the current study, we provide evidence for the involvement of necroptosis in psoriasis. RIPK1 and MLKL were significantly upregulated and localized in all layers of the epidermis in human psoriatic lesions, while RIPK3 and phosphorylated MLKL were mainly expressed in keratinocytes, which located in the upper layers. Increased tendency of necroptosis was also found in IMQ-induced psoriasiform skin of mice. Further, we discovered that both the inhibitor of RIPK1 R-7-Cl-O-Necrostatin-1 (Nec-1s) and MLKL-inhibitor necrosulfonamide (NSA) suppressed necroptosis in HaCaT cells and IMQ mouse models, powerfully blocked IMQ-induced inflammatory responses in vivo, and significantly downregulated the production of inflammatory factors like IL-1β, IL-6, IL-17A, IL-23a, CXCL1, and CCL20. These findings promote the development of new therapies for the treatment of necroptosis-activated pathologies for psoriasis.
A molecular gradient along the longitudinal axis of the human hippocampus informs large-scale behavioral systems
Authors: Vogel Jacob W. , La Joie Renaud , Grothe Michel J. , Diaz-Papkovich Alexandr , Doyle Andrew , Vachon-Presseau Etienne , Lepage Claude , Vos de Wael Reinder , Thomas Rhalena A. , Iturria-Medina Yasser , Bernhardt Boris , Rabinovici Gil D. , Evans Alan C. 
Published: February 2020

AbstractThe functional organization of the hippocampus is distributed as a gradient along its longitudinal axis that explains its differential interaction with diverse brain systems. We show that the location of human tissue samples extracted along the longitudinal axis of the adult human hippocampus can be predicted within 2mm using the expression pattern of less than 100 genes. Futhermore, this model generalizes to an external set of tissue samples from prenatal human hippocampi. We examine variation in this specific gene expression pattern across the whole brain, finding a distinct anterioventral-posteriodorsal gradient. We find frontal and anterior temporal regions involved in social and motivational behaviors, and more functionally connected to the anterior hippocampus, to be clearly differentiated from posterior parieto-occipital regions involved in visuospatial cognition and more functionally connected to the posterior hippocampus. These findings place the human hippocampus at the interface of two major brain systems defined by a single molecular gradient.
Global resource potential of seasonal pumped hydropower storage for energy and water storage
Authors: Hunt Julian D. , Byers Edward , Wada Yoshihide , Parkinson Simon , Gernaat David E. H. J. , Langan Simon , van Vuuren Detlef P. , Riahi Keywan 
Published: February 2020

AbstractSeasonal mismatches between electricity supply and demand is increasing due to expanded use of wind, solar and hydropower resources, which in turn raises the interest on low-cost seasonal energy storage options. Seasonal pumped hydropower storage (SPHS) can provide long-term energy storage at a relatively low-cost and co-benefits in the form of freshwater storage capacity. We present the first estimate of the global assessment of SPHS potential, using a novel plant-siting methodology based on high-resolution topographical and hydrological data. Here we show that SPHS costs vary from 0.007 to 0.2 US$ m−1 of water stored, 1.8 to 50 US$ MWh−1 of energy stored and 370 to 600 US$ kW−1 of installed power generation. This potential is unevenly distributed with mountainous regions demonstrating significantly more potential. The estimated world energy storage capacity below a cost of 50 US$ MWh−1 is 17.3 PWh, approximately 79% of the world electricity consumption in 2017.
Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants
Authors: Donovan Margaret K. R. , D’Antonio-Chronowska Agnieszka , D’Antonio Matteo , Frazer Kelly A. 
Published: February 2020

AbstractThe Genotype-Tissue Expression (GTEx) resource has provided insights into the regulatory impact of genetic variation on gene expression across human tissues; however, thus far has not considered how variation acts at the resolution of the different cell types. Here, using gene expression signatures obtained from mouse cell types, we deconvolute bulk RNA-seq samples from 28 GTEx tissues to quantify cellular composition, which reveals striking heterogeneity across these samples. Conducting eQTL analyses for GTEx liver and skin samples using cell composition estimates as interaction terms, we identify thousands of genetic associations that are cell-type-associated. The skin cell-type associated eQTLs colocalize with skin diseases, indicating that variants which influence gene expression in distinct skin cell types play important roles in traits and disease. Our study provides a framework to estimate the cellular composition of GTEx tissues enabling the functional characterization of human genetic variation that impacts gene expression in cell-type-specific manners.
Intrinsic neuronal properties represent song and error in zebra finch vocal learning
Authors: Daou Arij , Margoliash Daniel 
Published: February 2020

AbstractNeurons regulate their intrinsic physiological properties, which could influence network properties and contribute to behavioral plasticity. Recording from adult zebra finch brain slices we show that within each bird basal ganglia Area X–projecting (HVCX) neurons share similar spike waveform morphology and timing of spike trains, with modeling indicating similar magnitudes of five principal ion currents. These properties vary among birds in lawful relation to acoustic similarity of the birds’ songs, with adult sibling pairs (same songs) sharing similar waveforms and spiking characteristics. The properties are maintained dynamically: HVCX within juveniles learning to sing show variable properties, whereas the uniformity rapidly degrades within hours in adults singing while exposed to abnormal (delayed) auditory feedback. Thus, within individual birds the population of current magnitudes covary over the arc of development, while rapidly responding to changes in feedback (in adults). This identifies network interactions with intrinsic properties that affect information storage and processing of learned vocalizations.
Anomalous Fano Resonance in Double Quantum Dot System Coupled to Superconductor
Authors: Barański Jan , Zienkiewicz Tomasz , Barańska Magdalena , Kapcia Konrad Jerzy 
Published: February 2020

AbstractWe analyze the influence of a local pairing on the quantum interference in nanoscopic systems. As a model system we choose the double quantum dot coupled to one metallic and one superconducting electrode in the T-shape geometry. The analysis is particularly valuable for systems containing coupled objects with considerably different broadening of energy levels. In such systems, the scattering of itinerant electrons on a discrete (or narrow) energy level gives rise to the Fano-type interference. Systems with induced superconducting order, along well understood Fano resonances, exhibit also another features on the opposite side of the Fermi level. The lineshape of these resonances differs significantly from their reflection on the opposite side of the Fermi level, and their origin was not fully understood. Here, considering the spin-polarized tunneling model, we explain a microscopic mechanism of a formation of these resonances and discuss the nature of their uncommon lineshapes. We show that the anomalous Fano profiles originate solely from the pairing of nonscattered electrons with scattered ones. We investigate also the interplay of each type of resonances with the Kondo physics and discuss the resonant features in differential conductivity.
Mammalian cell-free protein expression promotes the functional characterization of the tripartite non-hemolytic enterotoxin from Bacillus cereus
Authors: Ramm Franziska , Dondapati Srujan Kumar , Thoring Lena , Zemella Anne , Wüstenhagen Doreen Anja , Frentzel Hendrik , Stech Marlitt , Kubick Stefan 
Published: February 2020

AbstractBacillus cereus is increasingly recognized as an opportunistic pathogen causing local and systemic infections. The causative strains typically produce three pore-forming enterotoxins. This study focusses on the tripartite non-hemolytic enterotoxin (Nhe). Until today, studies have tried to elucidate the structure, complex formation and cell binding mechanisms of the tripartite Nhe toxin. Here, we demonstrate the synthesis of the functional tripartite Nhe toxin using eukaryotic cell-free systems. Single subunits, combinations of two Nhe subunits as well as the complete tripartite toxin were tested. Functional activity was determined by hemolytic activity on sheep blood agar plates, planar lipid bilayer measurements as well as cell viability assessment using the MTT assay. Our results demonstrate that cell-free protein synthesis based on translationally active eukaryotic lysates is a platform technology for the fast and efficient synthesis of functionally active, multicomponent toxins.
Impact of water deficit stress in maize: Phenology and yield components
Authors: Sah R. P. , Chakraborty M. , Prasad K. , Pandit M. , Tudu V. K. , Chakravarty M. K. , Narayan S. C. , Rana M. , Moharana D. 
Published: February 2020

AbstractFifteen million farmers in India engaged in Maize cultivation. India would require 45 MMT of Maize by 2022. But, only 15% of cultivated area of maize is under irrigation and water shortage has been a challenge for sustainability of maize production. Water deficit stress (WDS) during pre-flowering and grain filling stages massively affects the plant performance due to imprecise traits function. Thus, the effect of WDS on non-drought tolerant (NDT) and drought tolerant (DT) maize lines were investigated. WDS increased the flowering days, days to maturity, anthesis silk interval, decreased the leaf number, abnormal expression of secondary stress responsive traits, loss of normal root architecture which overall lead to a reduction in GY/ha. WDS at flowering and grain filling stage leads to significant yield penalty especially in NDT lines than DT lines. The yield penalty was ranged from 34.28 to 66.15% in NDT and 38.48 to 55.95% in DT lines due to WDS. Using multiple statistics, traits which improve WDS tolerance in maize were identified viz; number of leaves, number of stomata on lower surface of leaf, leaf angle at ear forming node internodal length between 3rd and 4th leaf from top, flag leaf length, flag leaf width, ear per plants, leaf senescence, pollen stainability, root fresh weight and root length. These traits would help in trait specific breeding in maize for WDS tolerance.
A High Throughput Approach to Reconstruct Partial-Body and Neutron Radiation Exposures on an Individual Basis
Authors: Shuryak Igor , Turner Helen C. , Perrier Jay R. , Cunha Lydia , Canadell Monica Pujol , Durrani Mohammad H. , Harken Andrew , Bertucci Antonella , Taveras Maria , Garty Guy , Brenner David J. 
Published: February 2020

AbstractBiodosimetry-based individualized reconstruction of complex irradiation scenarios (partial-body shielding and/or neutron + photon mixtures) can improve treatment decisions after mass-casualty radiation-related incidents. We used a high-throughput micronucleus assay with automated scanning and imaging software on ex-vivo irradiated human lymphocytes to: a) reconstruct partial-body and/or neutron exposure, and b) estimate separately the photon and neutron doses in a mixed exposure. The mechanistic background is that, compared with total-body photon irradiations, neutrons produce more heavily-damaged lymphocytes with multiple micronuclei/binucleated cell, whereas partial-body exposures produce fewer such lymphocytes. To utilize these differences for biodosimetry, we developed metrics that describe micronuclei distributions in binucleated cells and serve as predictors in machine learning or parametric analyses of the following scenarios: (A) Homogeneous gamma-irradiation, mimicking total-body exposures, vs. mixtures of irradiated blood with unirradiated blood, mimicking partial-body exposures. (B) X rays vs. various neutron + photon mixtures. The results showed high accuracies of scenario and dose reconstructions. Specifically, receiver operating characteristic curve areas (AUC) for sample classification by exposure type reached 0.931 and 0.916 in scenarios A and B, respectively. R2 for actual vs. reconstructed doses in these scenarios reached 0.87 and 0.77, respectively. These encouraging findings demonstrate a proof-of-principle for the proposed approach of high-throughput reconstruction of clinically-relevant complex radiation exposure scenarios.