Miracle-dz/UniFAR-FTUs huggingface dataset:
Earlier colony arrival but no trend in hatching timing in two congeneric seabirds (Uria spp.) across the North Atlantic

A global analysis recently showed that seabird breeding phenology (as the timing of egg-laying and hatching) does not, on average, respond to temperature changes or advance with time (Keogan et al. 2018 Nat. Clim. Change 8, 313–318). This group, the most threatened of all birds, is therefore prone to spatio-temporal mismatches with their food resources. Yet, other aspects of the breeding phenology may also have a marked influence on breeding success, such as the arrival date of adults at the breeding site following winter migration. Here, we used a large tracking dataset of two congeneric seabirds breeding in 14 colonies across 18° latitudes, to show that arrival date at the colony was highly variable between colonies and species (ranging 80 days) and advanced 1.4 days/year while timing of egg-laying remained unchanged, resulting in an increasing pre-laying duration between 2009 and 2018. Thus, we demonstrate that potentially not all components of seabird breeding phenology are insensitive to changing environmental conditions.
Inhibition of lipopolysaccharide-stimulated TNF- (cid:1) promoter activity by S -adenosylmethionine and 5 (cid:2) -methylthioadenosine

Inhibition of lipopolysaccha-ride-stimulated TNF- (cid:1) promoter activity by S -adenosylmethionine and 5 (cid:2) -methylthioadenosine. Am J Physiol Gastrointest Liver Physiol 287: G352–G362, 2004. 2004; 10.1152/ ajpgi.00316. 2003. — S -adenosylmethionine (SAM) is the principal biological methyl donor and precursor for polyamines. SAM is known to be hepatoprotective in many liver disease models in which TNF- (cid:1) is implicated. The present study investigated whether and how SAM inhibited LPS-stimulated TNF- (cid:1) expression in Kupffer cells (hepatic macrophages). SAM downregulated TNF- (cid:1) expression in LPS-stim-ulated Kupffer cells at the transcriptional level as suggested by a transfection experiment with a TNF- (cid:1) promoter-reporter gene. This inhibition was not mediated through decreased NF- (cid:3) B binding to four putative (cid:3) B binding elements located within the promoter. The inhibited promoter activity was neither prevented by overexpression of p65 and/or its coactivator p300 nor enhanced by overexpression of coac-tivator-associated arginine methyltransferase-1, an enzyme that methylates p300 and inhibits a p65-p300 interaction. SAM did not lead to DNA methylation at the most common CpG target sites in the TNF- (cid:1) promoter. Moreover, 5 (cid:2) -methylthioadenosine (MTA), which is derived from SAM but does not serve as a methyl donor, recapitulated SAM’s effect with more potency. These data demonstrate that SAM inhibits TNF- (cid:1) expression at the level downstream of NF- (cid:3) B binding and at the level of the promoter activity via mechanisms that do not appear to involve the limited availability of p65 or p300. Furthermore, our study is the ﬁrst to demonstrate a potent inhibitory effect on NF- (cid:3) B promoter activity and TNF- (cid:1) expression by a SAM’s metabolite, MTA.
A Mutual Information Analysis of Neural Coding of Speech by Low 4 Frequency Meg Phase Information 5

23 24 Recent work has implicated low-frequency (<20 Hz) neuronal phase information as being 25 important for both auditory (< 10 Hz) and speech perception (theta ~ 4-8 Hz). Activity on the 26 timescale of theta corresponds linguistically to the average length of a syllable, suggesting that 27 the information within this range has consequences for the segmentation of meaningful units of 28 speech. Longer timescales that correspond to lower frequencies (delta 1-3 Hz) also reflect 29 important linguistic features – prosodic/suprasegmental – but it is unknown if the patterns of 30 activity in this range are similar to theta. We investigate low-frequency activity using 31 magnetoencephalography (MEG) and mutual information (MI), an analysis that has not yet been 32 applied to non-invasive electrophysiological recordings. We find that during speech perception, 33 each frequency sub-band examined (delta/1-3 Hz, theta low /3-5 Hz, and theta high /5-7 Hz) 34 processes independent information from the speech stream. This contrasts with hypotheses that 35 either delta and theta reflect their corresponding linguistic levels of analysis or that each band is 36 part of a single holistic onset response that tracks global acoustic transitions in the speech 37 stream. Single-trial template-based classifier results further validate this finding: information 38 from each sub-band can be used to classify individual sentences, and classifier results that utilize 39 the combination of frequency bands provide better results than single bands alone. Our results 40 suggest that during speech perception, low-frequency phase of the MEG signal corresponds 41 neither to abstract linguistic units nor holistic evoked potentials but rather tracks different 42 aspects of the input signal. This study also validates a new method of analysis for non-invasive 43 electrophysiological recordings that can be used to formally characterize the information content 44 of neural responses and the interactions between these responses. Furthermore, it bridges results 45 3 from different levels of neurophysiological study: small-scale multi unit recordings and local 46 field potentials and macroscopic magneto/electrophysiological non-invasive recordings.
Status and innovations in pre-treatment CT imaging for Proton therapy.

Pre-treatment CT imaging is a topic of growing importance in particle therapy. Improvements in the accuracy of stopping-power prediction are demanded to allow for a dose conformality that is not inferior to state-of-the-art image-guided photon therapy. Although range uncertainty has kept practically constant over the last decades, recent technological and methodological developments, like the clinical application of dual-energy CT, have been introduced or arise at least on the horizon to improve the accuracy and precision of range prediction. This review gives an overview of the current status, summarizes the innovations in dual-energy CT and its potential impact on the field as well as potential alternative technologies for SPR prediction.
Ion-channel function and cross-species determinants in viral assembly of nonprimate

Nonprimate hepacivirus (NPHV), the closest homolog of hepatitis C virus (HCV) described to 67 date, has recently been discovered in horses. Even though both viruses share a similar genomic 68 organization, conservation of the encoded hepaciviral proteins remains undetermined. The HCV 69 p7 protein is localized within endoplasmic reticulum (ER) membranes and is important for 70 production of infectious particles. In this study, we analyzed the structural and functional features 71 of NPHV p7 in addition to its role during virus assembly. Three-dimensional homology models 72 for NPHV p7 by using various NMR structures were generated highlighting conserved residues 73 important for ion-channel function. By applying a liposome permeability assay, we observed that 74 NPHV p7 exhibited similar liposome permeability features than HCV p7 indicative of similar 75 ion-channel activity. Next, we characterized the viral protein using a p7-based trans - 76 complementation approach. A similar sub-cellular localization pattern at the ER membrane was 77 observed, although production of infectious particles was likely hindered by genetic 78 incompatibilities with HCV proteins. To further characterize these cross-species constraints, 79 chimeric viruses were constructed by substituting different regions of HCV p7 with NPHV p7. 80 The N-terminus and transmembrane domains were non-exchangeable and therefore constitute a 81 cross-species barrier in hepaciviral assembly. In contrast, the basic loop and the C-terminus of 82 NPHV p7 were readily exchangeable allowing production of infectious trans -complemented viral 83 particles. In conclusion, comparison of NPHV and HCV p7 revealed structural and functional homology of these proteins including liposome permeability and broadly acting determinants were identified which modulate hepaciviral virion assembly and contribute to the host-species barrier. a fluorescence. Assays were carried out in black-walled, black-base 96-well plates at 37°C. Each contained 50 µM of liposomes from the rhodamine fluorescence) and 1 µl of peptide in DMSO in a total volume of with liposome assay buffer. 0.5 % v/v Triton TX-100, which lyses liposomes, a 90% The 96-well plate was kept on for 2- minutes after while the peptide +/- drug was release fluorescence as an peptide A of 30 the course of three repeats. point
Automated Pancreas Segmentation from Three-dimensional Contrast-enhanced Computed Tomography

Purpose We propose an automated pancreas segmentation algorithm from contrast-enhanced multiphase computed tomography (CT) and verify its effectiveness in segmenta-tion. Methods The algorithm is characterized by three unique ideas. First, a two-stage segmentation strategy with spatial standardization of pancreas was employed to reduce variations in the pancreas shape and location. Second, patient-specific probabilistic atlas guided segmentation was developed to cope with the remaining variability in shape and location. Finally, a classifier ensemble was incorporated to refine the rough segmentation results. Results The effectiveness of the proposed algorithm was validated with 20 unknown CT volumes, as well as three on-site CT volumes distributed in a competition of pancreas segmentation algorithms. The experimental results indicated that the segmentation performance was enhanced by the proposed algorithm, and the Jaccard index between an extracted pancreas and a true one was 57.9%. Conclusions This study verified the effectiveness of two-stage segmentation with spatial standardization of pancreas in delineating the pancreas region, patient-specific probabi-listic atlas guided segmentation in reducing false negatives, and a classifier ensemble in boosting segmentation performance .
The trace fossil Nummipera eocenica from the Tatra Mountains, Poland: morphology and palaeoenvironmental implications

Jach, R. , Machaniec, E. & Uchman, A. 2011: The trace fossil Nummipera eocenica fromthe Tatra Mountains, Poland: morphology and palaeoenvironmental implications.Lethaia, Vol. 45, pp. 342–355.The tubular trace fossil Nummipera eocenica Ho¨lder 1989 occurs in a single stratigraphi-cal horizon in Eocene nummulitic limestones of the Tatra Mountains, Poland. The wallof N. eocenica is built of Discocyclina and Nummulities (larger foraminifera) tests, veryrarely of the Ditrupa (Polychaeta) tube fragments, bivalve shell fragments, echinoidspines and coralline algae. Morphotype are distinguished on the basis of wall composi-tion and structure. Morphotype A is dominated by fusiform Discocyclina tests, whichwere preferentially selected by the trace makers for construction of a well-constructedand resistant wall. Morphotype B contains more robust tests of Nummulites,whilemorphotype C is dominated by saddle-shaped tests of Discocyclina. Nummipera eocenicawas produced during a period of seaﬂoor stabilization caused by a deepening. The suc-cession of the morphotypes B, A reﬂects diminishing energy and increasing water depth.Probably morphotype C represents even lower energy environment than morphotype A.The trace fossil is interpreted as a domichnion, which wall was constructed for protec-tion. The trace maker can be considered between polychaetes and crustaceans; however,comparisons to the closest recent analogues, the polychaete Diopatra cuprea or alpheidshrimps, are not satisfactory. h Bartonian, burrow, Carpathians, large foraminifera, tracefossils.Renata Jach [renata.jach@uj.edu. pl], Elzbieta Machaniec [elzbieta.machaniec@uj.edu. pl],_Alfred Uchman [alfred.uchman@uj.edu. pl], Institute of Geological Science, JagiellonianUniversity, Oleandry 2a, 30-063 Krako´w, Poland; manuscript received on 04⁄04 ⁄2011;manuscript accepted on 09⁄06 ⁄2011.
The future of death: cryonics and the telos of liberal individualism

This paper is addressed to four questions: First, what is trajectory of Western liberal ethics and politics in defining life, rights and citizenship? Second, how will neuroremediation and other technologies change the definition of death for the brain injured and the cryonically suspended? Third, will people always have to be dead to be cryonically suspended? Fourth, how will changing technologies and definitions of identity effect the status of people revived from brain injury and cryonic suspension? I propose that Western liberal thought is working towards a natural end, a “telos:” the association of the ethical value of a life with its level of consciousness. Just as human rights have been made independent of race, gender and property, in the future rights will be made independent of being a breathing human being. I discuss the way that technology will force three clarifications about the value of consciousness, at the beginning, the end and boundaries of human life. Sentience and personhood will be seen as the basis of moral concern, regardless of its media. But even as we make this transition, the cryonically preserved are still likely to be considered dead for pragmatic reasons, albeit with gradually increasing rights as technology makes their reanimation increasingly possible. I next propose that having the frozen be defined as dead may be acceptable for cryonicists if assisted suicide can be legalized. Under a liberal assisted suicide policy cryonicists might be allowed to carry out a suspension before a declaration of death, preserving the maximum amount of neural information. The gradual redefinition of life and personal identity in terms of psychological continuity will also have consequences for the legal status of the reanimated. If, due to information loss, the reanimated do not meet a threshold of psychological continuity, they may be considered new persons. Cryonicists may therefore wish to specify whether they are still interested in being reanimated if pre-animation assessment suggests that the result will not meet the threshold. Finally, I touch on the truly unpredictable, the bioethical, moral and legal Singularity: the fundamental problematizing of the self. The Future of Death J. Hughes 07/14/00 3 The Future of Death: Cryonics and the Telos of Liberal Individualism
New phenotypes for new breeding goals in pigs

An essential step in any genetic improvement program is the definition of the overall breeding objective or breeding goal. This includes traits of interest, relative significance of each trait and the direction of improvement. The traits included in the breeding goal depend upon the expected market requirements of the end product. In pig breeding, this means consumer expectations when the pork from genetically improved breeding stock will be sold. It can take several years depending upon the generation interval and genetic lag. Therefore a good prediction of the future trends is required. Further, like any successful enterprise, the breeding goals should also be specific, measurable, attainable, realistic and timely (SMART). The specific traits included in the breeding goals should also be chosen carefully as the amount of genetic progress for each trait is inversely proportional to the number of traits. Further, technology should be available to record the associated trait phenotypes in a cost effective manner. In spite of these challenges, pig breeders have successfully selected and adapted their breeding stock to changing market requirements over the past centuries and decades, and should be able to do so even if the requirements are changing more rapidly and the times are more challenging. In this paper, the trends and factors that influence pig breeding goals and the desired phenotypes are presented and discussed.
Modification of Hyaluronan by Heavy Chains of Inter-Alpha-Inhibitor in Idiopathic Pulmonary Arterial Hypertension *

Background: Hyaluronan metabolism is altered in idiopathic pulmonary arterial hypertension lung tissue. Result: This hyaluronan is of a pathological form covalently modified by heavy chains from inter-alpha-inhibitor. Conclusion: The distribution of this matrix in regions of abnormal vascular remodeling implies a mechanistic role. Significance: Pathological hyaluronan matrices may direct inflammatory events and vascular changes in this disease.
Large‐scale circulation anomalies associated with ‘tropical night’ weather in Beijing, China

On the basis of the homogenized daily temperature data of China and daily mean National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis data during July and August 1979–2008, we analysed the large‐scale circulation anomalies associated with tropical night (TN; minimum temperature ≥25 °C) in Beijing, and compared these anomalies with those associated with extreme heat (EH; maximum temperature ≥35 °C). Composite analyses revealed that, for TN days, there is an upper‐tropospheric anticyclonic anomaly to the northwest of Beijing and a lower‐tropospheric anticyclonic anomaly to the southeast of Beijing. Associated with the lower‐tropospheric anticyclonic anomaly, a significant southerly anomaly occurs to the south of Beijing and leads to stronger northward water vapour flux, overlapping the climatological southerlies. Correspondingly, there is a belt of higher humidity over North China, Northeast Asia and northern Japan, which reduces longwave radiation cooling around Beijing and favours the occurrence of TN. The EH‐related anomalies, however, are distinct from the TN‐related ones. There is a significant cyclonic anomaly located to the northeast of North China in both the upper and lower troposphere. Associated with this cyclonic anomaly, an obvious northerly anomaly occurs over Beijing and reduces the northward water vapour flux. Hence, there is significant lower humidity over Beijing, which is also due to the significant descending anomaly over Beijing, favouring the occurrence of EH through enhancing solar radiation at the surface.
Economic Research Initiative on the Uninsured CONFERENCE DRAFT The Impact of the Medicaid Expansions of the Late 1990s on the Insurance Coverage of Poor Adolescents

This paper examines the effects of the Medicaid expansions of the late 1990s on the insurance coverage of poor adolescents. To control for the potentially confounding influences of competing trends, I use a difference-in-differences strategy that employs a comparison group of poor younger children who gained public insurance eligibility several years prior to their older peers. Results suggest that the introduction of Medicaid eligibility had a large impact on the insurance coverage of poor adolescents. The probability of being publicly insured at the time of survey rose substantially as a result of the expansions; both the probability of being privately insured and the probability of being uninsured decreased as a result of the expansions. The baseline specification implies that approximately 40% of the increase in public coverage came from those who were previously privately insured. The expansions also reduced the probability of spending any part of the past year without coverage and the probability of spending at least six months of the past year without coverage. Results from various robustness exercises, including a triple-difference specification, yield similar conclusions.
Biofuels: is the cure worse than the disease?

Biofuels have been championed as an energy source that can increase security of supply, reduce vehicle emissions and provide a new income stream for farmers. These claims are contested, however. Critics assert that biofuels will increase energy-price volatility, food prices and even life-cycle emissions of greenhouse gases. This paper presents salient facts and figures to shed light on these controversial issues and asks whether biofuels offer a cure that is worse than the disease they seek to heal.
Inferring Tumor Proliferative Organization from Phylogenetic Tree Measures in a Computational Model

—We use a computational modeling approach to explore whether it is possible to infer a solid tumor’s cellular proliferative hierarchy under the assumptions of the cancer stem cell hypothesis and neutral evolution. We work towards inferring the symmetric division probability for cancer stem cells, since this is believed to be a key driver of progression and therapeutic response. Motivated by the advent of multiregion sampling and resulting opportunities to infer tumor evolutionaryhistory,wefocusonasuiteofstatisticalmeasuresofthephylogenetictreesresultingfromthetumor’sevolutionindifferentregionsofparameterspaceandthroughtime. Weﬁndstrikinglydifferentpatternsinthesemeasuresforchanging symmetricdivisionprobabilitywhichhingeontheinclusionofspatialconstraints.Theseresultsgiveusastartingpointtobeginstratifyingtumorsbythisbiologicalparameterandalsogenerateanumberofactionableclinicalandbiological hypothesesregardingchangesduringtherapy,andthroughtumorevolutionarytime. [Cancer;evolution;phylogenetics. ]
Self‐healing of cement fractures under dynamic flow of CO2‐rich brine

Fractures and defects in wellbore cement can lead to increased possibilities of CO2 leakage from abandoned wells during geological carbon sequestration. To investigate the physicochemical response of defective wellbore cement to CO2‐rich brine, we carried out a reactive flow‐through experiment using an artificially fractured cement sample at a length of 224.8 mm. A brine solution with dissolved CO2 at a pH of approximately 3.9 was injected through the sample at a constant rate of 0.0083 cm3/s. Surface optical profilometry analysis and 3‐D X‐ray microtomography imaging confirmed fracture closure and self‐healing behavior consistent with the measured permeability decrease. Visual inspection of the reacted fracture surface showed the development of reactive patterns mapping the flow velocity field inside the fracture, as well as restricted flow toward the sample outlet. The postexperiment permeability of the core sample was measured at half of its initial permeability. A reactive transport model was developed with parameters derived from the experiment to further examine property evolution of fractured cement under dynamic flow of CO2‐rich brine. Sensitivity analysis showed that residence time and the size of initial fracture aperture are the key factors controlling the tendency to self‐healing or fracture opening behavior and therefore determine the long‐term integrity of the wellbore cement. Longer residence time and small apertures promote mineral precipitation, fracture closure, and therefore flow restriction. This work also suggests a narrow threshold separating the fracture opening and self‐sealing behavior.
Dynamic modelling of nitrous oxide emissions from three Swedish sludge liquor treatment systems

: The objective of this paper is to model the dynamics and validate the results of nitrous oxide (N 2 O) emissions from three Swedish full-scale nitrifying/denitrifying, nitritation and anammox systems treating anaerobic digester sludge liquor. The Activated Sludge Model No. 1 is extended in order to describe N 2 O production by both heterotrophic and autotrophic bacteria. In addition, mass transfer equations are implemented to characterize the dynamics of N 2 O in the water and the gas phases. The biochemical model is simulated for two hydraulic patterns: 1) a sequencing batch reactor (SBR); and, 2) a moving-bed biofilm reactor (MBBR). Preliminary results show that the calibrated model is partly capable of reproducing the behaviour of N 2 O as well as the nitritation/nitrification/denitrification dynamics. However, the results emphasize that more work is required before N 2 O emissions from sludge liquor treatment plants can be generally predicted with certainty by simulations. Continued efforts should focus on determining the switching conditions for different N 2 O formation pathways and, if full-scale data is used, modelling of the measurement devices might improve the conclusions that can be drawn.