Parameter-Efficient Methods for Metastases Detection from Clinical Notes

Understanding the progression of cancer is crucial for defining treatments for patients. The objective of this study is to automate the detection of metastatic liver disease from free-style computed tomography (CT) radiology reports. Our research demonstrates that transferring knowledge using three approaches can improve model performance. First, we utilize generic language models (LMs), pretrained in a self-supervised manner. Second, we use a semi-supervised approach to train our model by automatically annotating a large unlabeled dataset; this approach substantially enhances the model's performance. Finally, we transfer knowledge from related tasks by designing a multi-task transfer learning methodology. We leverage the recent advancement of parameter-efficient LM adaptation strategies to improve performance and training efficiency. Our dataset consists of CT reports collected at Memorial Sloan Kettering Cancer Center (MSKCC) over the course of 12 years. 2,641 reports were manually annotated by domain experts; among them, 841 reports have been annotated for the presence of liver metastases. Our best model achieved an F1-score of 73.8%, a precision of 84%, and a recall of 65.8%.Comment: 6 pages, 1 figure, The 36th Canadian Conference on Artificial Intelligenc

Seasonal variation in the response of arbuscular mycorrhizal fungi to grazing intensity

Despite existing evidence of pronounced seasonality in arbuscular mycorrhizal (AM) fungal communities, little is known about the ecology of AM fungi in response to grazing intensity in different seasons. Here, we assessed AM fungal abundance, represented by soil hyphal length density (HLD), mycorrhizal root colonization intensity (MI), and arbuscule intensity (AI) throughout three seasons (spring, summer, autumn) in a farm-scale field experiment in typical, grazed steppe vegetation in northern China. Seven levels of field-manipulated, grazing intensities had been maintained for over 13 years within two topographies, flat and slope. We also measured soil nutrients and carbon content throughout the growing season to investigate whether seasonal variation in AM fungal abundance was related to seasonal shifts in soil resource availability along the grazing gradient. We further examined the association between AM fungal metrics in the different grazing treatments through the growing season. Our results showed a pronounced seasonal shift in HLD but there was no clear seasonality in MI and AI. HLD was significantly negatively related to grazing intensity over the course of the growing season from spring to autumn. However, MI and AI were related negatively to grazing intensity only in spring. In addition, differential responses of AM fungal abundance to grazing intensity at the two topographical sites were detected. No strong evidence was found for associations between AM fungal abundance and soil resource availability. Moreover, AM fungal internal and external abundance were correlated positively under the different grazing intensities throughout the growing season. Overall, our study suggests that external AM fungal structures in soil were more responsive to seasonal variation and grazing than internal structures in roots. The findings also suggest that early grazing may be detrimental to AM fungal root colonization of newly emerged plants

Long-Term Grazing Intensity Impacts Belowground Carbon Allocation and Mycorrhizas Revealed by 13CO2 Pulse Labeling

Despite the importance of grasslands for carbon storage and climate regulation, there is uncertainty about the effect of livestock grazing intensity on aboveground carbon assimilation and belowground carbon partitioning. Furthermore, the relationship between belowground carbon allocation and arbuscular mycorrhizal fungi, which serve as a conduit for carbon movement through the plant and soil, is unclear. To investigate this, we used an in situ 13C stable isotope pulse-chase labeling approach in plots under seven rates of sheep grazing intensity in a steppe grassland in northern China. We quantified the allocation of carbon to plants, soil, and soil-respired CO2 along with measurements of mycorrhizal hyphal density in the soil. With increasing grazing intensity, carbon assimilation per unit shoot biomass increased significantly, whereas carbon allocation to roots marginally decreased. Soil-respired CO2 appeared to be independent of grazing intensity. Mycorrhizal hyphal density decreased with increasing grazing intensity and was correlated significantly with new carbon input to roots 2 d after labeling and marginally related to that of soil 1 d after the 13C-CO2 pulse. Our study suggests that grazing intensity alters the distribution of carbon among different carbon pools within the plant-soil system. The results also underscored the key role of mycorrhizas as a fast route for carbon transfer from plant to soil

The roles of personality and resilience in associations between combat experiences and posttraumatic stress disorder among Canadian Armed Forces Veterans

Canadian Armed Forces (CAF) Veterans encounter unique challenges associated with their service. Exposure to service-related traumatic events places them at risk for developing adverse mental health outcomes, including posttraumatic stress disorder (PTSD). Our research aimed to assess whether the HEXACO personality model and resilience impacted associations between combat experiences and PTSD symptomatology in CAF Veterans in the past month. We recruited a sample of 245 CAF Veterans (81 % men; Mage = 48.47, SDage = 10.34) to complete a battery of questionnaires. PTSD symptoms were significantly associated with more combat experience, lower resilience, lower extraversion, higher emotionality, and lower agreeableness. However, personality traits did not moderate the relationship between combat experiences and PTSD symptoms. Overall, this research can be used to enhance researchers\u27 and clinicians\u27 understanding of personality traits as risk and protective factors for PTSD symptoms

The response of grassland mycorrhizal fungal abundance to a range of long-term grazing intensities

Keystone root symbiotic arbuscular mycorrhizal fungi play a major role in maintaining plant biodiversity, increasing plant productivity and enhancing storage of carbon in soil. AM fungi are ubiquitous and found in most ecosystems including grasslands currently experiencing increasing pressures form human activity. Grazing is known to impact AM fungi but very little is known about how AM fungi are affected by different levels of grazing intensity. Here we report on results from a long-term experimental site in a typical steppe in the north of China, containing seven levels of field-manipulated grazing intensities maintained for over 13 years. We assessed arbuscular mycorrhizal fungal abundance, represented by soil hyphal length density and mycorrhizal root colonization (mycorrhizal root frequency, intensity and arbuscule intensity) within the farm-scale field experiment. We also measured environmental variables to explain the responses of mycorrhizal fungi to grazing intensity. Our results showed that with an increase in grazing intensity, soil hyphal length density linearly decreased. There was, however, no significant trend for mycorrhizal root colonization variables in relation to grazing intensity. Mycorrhizal root frequency was negatively correlated with topographic-induced changes in soil nitrogen and phosphorus, while arbuscule intensity was marginally negatively correlated with soil available phosphorus. Further, we found a possible hump-shaped relationship between the ratio of external to internal AM fungal structures and grazing intensity. Our finding showed that external AM fungal structure was clearly impacted by grazing intensity but that this was not the case for internal mycorrhizal structures. This indicated that mycorrhizal functioning was impacted by the intensity of grazing as the mycorrhizal structures responded differently. Indeed the ratio of the foraging extra-radical mycorrhizal hyphae to intra-radical mycorrhizal structures was highest at moderate grazing intensity but strongly decreased by high grazing intensity. Our study suggests that the impacts of grazing intensity on the plant-AMF association could lead to further knock-on effects on the plant-soil system via the feedbacks that exist between plant and AMF communities

The upgraded cold neutron triple axis spectrometer FLEXX enhanced capabilities by new instrumental options

The upgrade of the cold neutron triple axis spectrometer FLEXX, a work-horse instrument for inelastic neutron scattering matching the sample environment capabilities at Helmholtz-Zentrum Berlin, has been successfully accomplished. Experiments confirmed an order of magnitude gain in flux now allowing for intensity demanding options to be fully exploited at FLEXX. In this article, we describe the layout and design of two newly available FLEXX instrument options in detail. The new Heusler analyzer gives an increase of the detected polarized neutron flux due to its superior focusing properties, significantly improving the feasibility of future polarized and neutron resonance spin echo experiments. The MultiFLEXX option provides simultaneous access to large regions in wavevector and energy space for inelastic excitations thus adding mapping capabilities to the spectrometer

Comparative Study Of The Antioxidant Defence Systems In The Erythrocytes Of Australian Marsupials And Monotremes

A comparison of the erythrocyte (RBC) antioxidant metabolites and enzymes in nine marsupial and two monotreme species was carried out. Reduced glutathione (GSH) concentrations were comparable with those reported for other marsupial and eutherian species. An important finding was that the erythrocytes of the southern hairy nosed wombat regenerated GSH faster than the erythrocytes from its close relative, the common wombat. The activities of glutathione-S-transferase, NADH methaemoglobin reductase, superoxide dismutase, and glutathione peroxidase (GSH-Px), showed similar levels and extents of variation as those observed in other marsupial and eutherian species. Catalase activities in the marsupials were lower than those measured in the two monotreme species and much lower than those reported in eutherian species. A negative correlation, significant at P < 0.05, was observed between GSH-PX and catalase activities in the RBC of the marsupials. Since both these enzymes "detoxify" H202, there appears to be a reciprocal relationship between the activities of these enzymes in marsupial RB

N-terminal amino acid sequences of chloroform/methanol-soluble proteins and albumins from endosperms of wheat, barley and related species: Homology with inhibitors of α-amylase and trypsin and with 2 S storage globulins

The N-terminal amino acid sequences of two chloroform/methanol soluble globulins from barley and one form wheat are reported. They are homologous with N-terminal sequences previously reported for α-amylase and trypsin inhibitors from cereals and 2 S storage proteins from castor bean and rape. Three albumins were also purified from Aegilops squarrosa and Triticum monococcum. These had N-terminal amino acid sequences most closely related to the α-amylase and trypsin inhibitors. The relationships of this superfamily of seed proteins are discussed

Advancing cross-national planning and partnership: proceedings from the International Multimorbidity Symposium 2019

The International Multimorbidity Symposium was held in November 2019 at Western University to achieve three main objectives: to discuss progress and findings from various jurisdictions; to facilitate collaboration through group discussion to identify strategies to move multimorbidity research forward; and to create concrete plans to ensure advances in multimorbidity research and knowledge can be achieved through cross-national partnership. This event included keynote presentations, elevator pitch presentations and breakout sessions and there was a total of 35 attendees from eight countries, representing diverse disciplines and training levels. The overall themes arising from the event were: the importance of integrating the study and management of multimorbidity from both the primary care and public health perspectives; meaningful engagement and collaboration with patients and caregivers to understand key dimensions of multimorbidity; the considerable benefit of collaborative international partnerships; and the need to spread and scale innovations for health care systems that can better respond to the complex needs of patients and caregivers who are living with multimorbidity. Finally, it was well-acknowledged among the attendees that expanding the collaboration and discussion among international colleagues via in-person and virtual events will be important to move multimorbidity research forward

Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD+ kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host' nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems