24 research outputs found

    Topic Segmentation of Semi-Structured and Unstructured Conversational Datasets using Language Models

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    Breaking down a document or a conversation into multiple contiguous segments based on its semantic structure is an important and challenging problem in NLP, which can assist many downstream tasks. However, current works on topic segmentation often focus on segmentation of structured texts. In this paper, we comprehensively analyze the generalization capabilities of state-of-the-art topic segmentation models on unstructured texts. We find that: (a) Current strategies of pre-training on a large corpus of structured text such as Wiki-727K do not help in transferability to unstructured conversational data. (b) Training from scratch with only a relatively small-sized dataset of the target unstructured domain improves the segmentation results by a significant margin. We stress-test our proposed Topic Segmentation approach by experimenting with multiple loss functions, in order to mitigate effects of imbalance in unstructured conversational datasets. Our empirical evaluation indicates that Focal Loss function is a robust alternative to Cross-Entropy and re-weighted Cross-Entropy loss function when segmenting unstructured and semi-structured chats.Comment: Accepted to IntelliSys 2023. arXiv admin note: substantial text overlap with arXiv:2211.1495

    Molecular Recalibration of PD-1+ Antigen-Specific T Cells from Blood and Liver.

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    Checkpoint inhibitors and adoptive cell therapy provide promising options for treating solid cancers such as HBV-related HCC, but they have limitations. We tested the potential to combine advantages of each approach, genetically reprogramming T cells specific for viral tumor antigens to overcome exhaustion by down-modulating the co-inhibitory receptor PD-1. We developed a novel lentiviral transduction protocol to achieve preferential targeting of endogenous or TCR-redirected, antigen-specific CD8 T cells for shRNA knockdown of PD-1 and tested functional consequences for antitumor immunity. Antigen-specific and intrahepatic CD8 T cells transduced with lentiviral (LV)-shPD-1 consistently had a marked reduction in PD-1 compared to those transduced with a control lentiviral vector. PD-1 knockdown of human T cells rescued antitumor effector function and promoted killing of hepatoma cells in a 3D microdevice recapitulating the pro-inflammatory PD-L1hi liver microenvironment. However, upon repetitive stimulation, PD-1 knockdown drove T cell senescence and induction of other co-inhibitory pathways. We provide the proof of principle that T cells with endogenous or genetically engineered specificity for HBV-associated HCC viral antigens can be targeted for functional genetic editing. We show that PD-1 knockdown enhances immediate tumor killing but is limited by compensatory engagement of alternative co-inhibitory and senescence program upon repetitive stimulation

    Global burden and strength of evidence for 88 risk factors in 204 countries and 811 subnational locations, 1990–2021: a systematic analysis for the Global Burden of Disease Study 2021

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    Background: Understanding the health consequences associated with exposure to risk factors is necessary to inform public health policy and practice. To systematically quantify the contributions of risk factor exposures to specific health outcomes, the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 aims to provide comprehensive estimates of exposure levels, relative health risks, and attributable burden of disease for 88 risk factors in 204 countries and territories and 811 subnational locations, from 1990 to 2021. Methods: The GBD 2021 risk factor analysis used data from 54 561 total distinct sources to produce epidemiological estimates for 88 risk factors and their associated health outcomes for a total of 631 risk–outcome pairs. Pairs were included on the basis of data-driven determination of a risk–outcome association. Age-sex-location-year-specific estimates were generated at global, regional, and national levels. Our approach followed the comparative risk assessment framework predicated on a causal web of hierarchically organised, potentially combinative, modifiable risks. Relative risks (RRs) of a given outcome occurring as a function of risk factor exposure were estimated separately for each risk–outcome pair, and summary exposure values (SEVs), representing risk-weighted exposure prevalence, and theoretical minimum risk exposure levels (TMRELs) were estimated for each risk factor. These estimates were used to calculate the population attributable fraction (PAF; ie, the proportional change in health risk that would occur if exposure to a risk factor were reduced to the TMREL). The product of PAFs and disease burden associated with a given outcome, measured in disability-adjusted life-years (DALYs), yielded measures of attributable burden (ie, the proportion of total disease burden attributable to a particular risk factor or combination of risk factors). Adjustments for mediation were applied to account for relationships involving risk factors that act indirectly on outcomes via intermediate risks. Attributable burden estimates were stratified by Socio-demographic Index (SDI) quintile and presented as counts, age-standardised rates, and rankings. To complement estimates of RR and attributable burden, newly developed burden of proof risk function (BPRF) methods were applied to yield supplementary, conservative interpretations of risk–outcome associations based on the consistency of underlying evidence, accounting for unexplained heterogeneity between input data from different studies. Estimates reported represent the mean value across 500 draws from the estimate's distribution, with 95% uncertainty intervals (UIs) calculated as the 2·5th and 97·5th percentile values across the draws. Findings: Among the specific risk factors analysed for this study, particulate matter air pollution was the leading contributor to the global disease burden in 2021, contributing 8·0% (95% UI 6·7–9·4) of total DALYs, followed by high systolic blood pressure (SBP; 7·8% [6·4–9·2]), smoking (5·7% [4·7–6·8]), low birthweight and short gestation (5·6% [4·8–6·3]), and high fasting plasma glucose (FPG; 5·4% [4·8–6·0]). For younger demographics (ie, those aged 0–4 years and 5–14 years), risks such as low birthweight and short gestation and unsafe water, sanitation, and handwashing (WaSH) were among the leading risk factors, while for older age groups, metabolic risks such as high SBP, high body-mass index (BMI), high FPG, and high LDL cholesterol had a greater impact. From 2000 to 2021, there was an observable shift in global health challenges, marked by a decline in the number of all-age DALYs broadly attributable to behavioural risks (decrease of 20·7% [13·9–27·7]) and environmental and occupational risks (decrease of 22·0% [15·5–28·8]), coupled with a 49·4% (42·3–56·9) increase in DALYs attributable to metabolic risks, all reflecting ageing populations and changing lifestyles on a global scale. Age-standardised global DALY rates attributable to high BMI and high FPG rose considerably (15·7% [9·9–21·7] for high BMI and 7·9% [3·3–12·9] for high FPG) over this period, with exposure to these risks increasing annually at rates of 1·8% (1·6–1·9) for high BMI and 1·3% (1·1–1·5) for high FPG. By contrast, the global risk-attributable burden and exposure to many other risk factors declined, notably for risks such as child growth failure and unsafe water source, with age-standardised attributable DALYs decreasing by 71·5% (64·4–78·8) for child growth failure and 66·3% (60·2–72·0) for unsafe water source. We separated risk factors into three groups according to trajectory over time: those with a decreasing attributable burden, due largely to declining risk exposure (eg, diet high in trans-fat and household air pollution) but also to proportionally smaller child and youth populations (eg, child and maternal malnutrition); those for which the burden increased moderately in spite of declining risk exposure, due largely to population ageing (eg, smoking); and those for which the burden increased considerably due to both increasing risk exposure and population ageing (eg, ambient particulate matter air pollution, high BMI, high FPG, and high SBP). Interpretation: Substantial progress has been made in reducing the global disease burden attributable to a range of risk factors, particularly those related to maternal and child health, WaSH, and household air pollution. Maintaining efforts to minimise the impact of these risk factors, especially in low SDI locations, is necessary to sustain progress. Successes in moderating the smoking-related burden by reducing risk exposure highlight the need to advance policies that reduce exposure to other leading risk factors such as ambient particulate matter air pollution and high SBP. Troubling increases in high FPG, high BMI, and other risk factors related to obesity and metabolic syndrome indicate an urgent need to identify and implement interventions

    Global age-sex-specific mortality, life expectancy, and population estimates in 204 countries and territories and 811 subnational locations, 1950–2021, and the impact of the COVID-19 pandemic: a comprehensive demographic analysis for the Global Burden of Disease Study 2021

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    Background: Estimates of demographic metrics are crucial to assess levels and trends of population health outcomes. The profound impact of the COVID-19 pandemic on populations worldwide has underscored the need for timely estimates to understand this unprecedented event within the context of long-term population health trends. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2021 provides new demographic estimates for 204 countries and territories and 811 additional subnational locations from 1950 to 2021, with a particular emphasis on changes in mortality and life expectancy that occurred during the 2020–21 COVID-19 pandemic period. Methods: 22 223 data sources from vital registration, sample registration, surveys, censuses, and other sources were used to estimate mortality, with a subset of these sources used exclusively to estimate excess mortality due to the COVID-19 pandemic. 2026 data sources were used for population estimation. Additional sources were used to estimate migration; the effects of the HIV epidemic; and demographic discontinuities due to conflicts, famines, natural disasters, and pandemics, which are used as inputs for estimating mortality and population. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate under-5 mortality rates, which synthesised 30 763 location-years of vital registration and sample registration data, 1365 surveys and censuses, and 80 other sources. ST-GPR was also used to estimate adult mortality (between ages 15 and 59 years) based on information from 31 642 location-years of vital registration and sample registration data, 355 surveys and censuses, and 24 other sources. Estimates of child and adult mortality rates were then used to generate life tables with a relational model life table system. For countries with large HIV epidemics, life tables were adjusted using independent estimates of HIV-specific mortality generated via an epidemiological analysis of HIV prevalence surveys, antenatal clinic serosurveillance, and other data sources. Excess mortality due to the COVID-19 pandemic in 2020 and 2021 was determined by subtracting observed all-cause mortality (adjusted for late registration and mortality anomalies) from the mortality expected in the absence of the pandemic. Expected mortality was calculated based on historical trends using an ensemble of models. In location-years where all-cause mortality data were unavailable, we estimated excess mortality rates using a regression model with covariates pertaining to the pandemic. Population size was computed using a Bayesian hierarchical cohort component model. Life expectancy was calculated using age-specific mortality rates and standard demographic methods. Uncertainty intervals (UIs) were calculated for every metric using the 25th and 975th ordered values from a 1000-draw posterior distribution. Findings: Global all-cause mortality followed two distinct patterns over the study period: age-standardised mortality rates declined between 1950 and 2019 (a 62·8% [95% UI 60·5–65·1] decline), and increased during the COVID-19 pandemic period (2020–21; 5·1% [0·9–9·6] increase). In contrast with the overall reverse in mortality trends during the pandemic period, child mortality continued to decline, with 4·66 million (3·98–5·50) global deaths in children younger than 5 years in 2021 compared with 5·21 million (4·50–6·01) in 2019. An estimated 131 million (126–137) people died globally from all causes in 2020 and 2021 combined, of which 15·9 million (14·7–17·2) were due to the COVID-19 pandemic (measured by excess mortality, which includes deaths directly due to SARS-CoV-2 infection and those indirectly due to other social, economic, or behavioural changes associated with the pandemic). Excess mortality rates exceeded 150 deaths per 100 000 population during at least one year of the pandemic in 80 countries and territories, whereas 20 nations had a negative excess mortality rate in 2020 or 2021, indicating that all-cause mortality in these countries was lower during the pandemic than expected based on historical trends. Between 1950 and 2021, global life expectancy at birth increased by 22·7 years (20·8–24·8), from 49·0 years (46·7–51·3) to 71·7 years (70·9–72·5). Global life expectancy at birth declined by 1·6 years (1·0–2·2) between 2019 and 2021, reversing historical trends. An increase in life expectancy was only observed in 32 (15·7%) of 204 countries and territories between 2019 and 2021. The global population reached 7·89 billion (7·67–8·13) people in 2021, by which time 56 of 204 countries and territories had peaked and subsequently populations have declined. The largest proportion of population growth between 2020 and 2021 was in sub-Saharan Africa (39·5% [28·4–52·7]) and south Asia (26·3% [9·0–44·7]). From 2000 to 2021, the ratio of the population aged 65 years and older to the population aged younger than 15 years increased in 188 (92·2%) of 204 nations. Interpretation: Global adult mortality rates markedly increased during the COVID-19 pandemic in 2020 and 2021, reversing past decreasing trends, while child mortality rates continued to decline, albeit more slowly than in earlier years. Although COVID-19 had a substantial impact on many demographic indicators during the first 2 years of the pandemic, overall global health progress over the 72 years evaluated has been profound, with considerable improvements in mortality and life expectancy. Additionally, we observed a deceleration of global population growth since 2017, despite steady or increasing growth in lower-income countries, combined with a continued global shift of population age structures towards older ages. These demographic changes will likely present future challenges to health systems, economies, and societies. The comprehensive demographic estimates reported here will enable researchers, policy makers, health practitioners, and other key stakeholders to better understand and address the profound changes that have occurred in the global health landscape following the first 2 years of the COVID-19 pandemic, and longer-term trends beyond the pandemic

    Current management of the gastrointestinal complications of systemic sclerosis.

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    Systemic sclerosis is a multisystem autoimmune disorder that involves the gastrointestinal tract in more than 90% of patients. This involvement can extend from the mouth to the anus, with the oesophagus and anorectum most frequently affected. Gut complications result in a plethora of presentations that impair oral intake and faecal continence and, consequently, have an adverse effect on patient quality of life, resulting in referral to gastroenterologists. The cornerstones of gastrointestinal symptom management are to optimize symptom relief and monitor for complications, in particular anaemia and malabsorption. Early intervention in patients who develop these complications is critical to minimize disease progression and improve prognosis. In the future, enhanced therapeutic strategies should be developed, based on an ever-improving understanding of the intestinal pathophysiology of systemic sclerosis. This Review describes the most commonly occurring clinical scenarios of gastrointestinal involvement in patients with systemic sclerosis as they present to the gastroenterologist, with recommendations for the suggested assessment protocol and therapy in each situation

    Energy and Moisture Transport in the Earth Climate System: Mean State and the Perturbation Response

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    Thesis (Ph.D.)--University of Washington, 2015Four studies are presented which investigate how energy and moisture transport define the mean state of the Earth Climate System and its response to perturbations. In the first study, we use a global climate model to study the effect of flattening the orography of the Antarctic Ice Sheet on climate. A general result is that the Antarctic continent and the atmosphere aloft warm, while there is modest cooling globally. The large local warming over Antarctica leads to increased outgoing longwave radiation, which drives anomalous southward energy transport towards the continent and cooling elsewhere. Atmosphere and ocean both anomalously transport energy southward in the Southern Hemisphere. Near Antarctica, poleward energy and momentum transport by baroclinic eddies strengthens. Anomalous southward cross-equatorial energy transport is associated with a northward shift of the inter-tropical convergence zone. In the ocean, anomalous southward energy transport arises from a slowdown of the upper cell of the oceanic meridional overturning circulation and a weakening of the horizontal ocean gyres, causing sea ice in the Northern Hemisphere to expand and the Arctic to cool. Comparison with a slab ocean simulation confirms the importance of ocean dynamics in determining the climate system response to Antarctic orography. We conclude this study by briefly discussing the relevance of these results to climates of the past and to future climate scenarios. The remaining studies consider atmospheric moisture transport. First, we develop a new mathematical framework for analyzing results from climate modeling studies that employ numerical water tracers (WTs). Data made available from WTs, which track the movement of water in the aerial hydrological cycle from evaporation to precipitation, are used to analyze the sources and transport of precipitable water in the climate system. The precipitation over a tagged region is subdivided into contributions from local evaporation and remote evaporation. The contribution from remote evaporation, the moisture convergence, can be further subdivided into zonal, meridional (north-to-south and south-to-north), intrabasin, and interbasin parts to yield additional insight into how the aerial hydrological cycle transports water. This theory is applied to the preindustrial mean state climate as simulated by a global climate model in which evaporated water has been tagged in 10-degree latitude bands in each of the major ocean basins, and in which each major land mass has been tagged separately. Findings from analysis of the mean state concur with findings from earlier studies of the hydrological cycle: water evaporated at the equator and in the high latitudes tends to precipitate locally, whereas water evaporated in the subtropics and midlatitudes tends to precipitate remotely; water evaporated in the subtropics precipitates either equatorward or poleward of its source region, while water evaporated in the midlatitudes mostly precipitates poleward. New insights from the method reveal fundamental differences between the major ocean basins in locally-sourced precipitation, remotely-sourced precipitation and their relative partitioning. Per unit area, the subtropical Atlantic is the largest global moisture source, providing precipitable water to adjacent land areas and to the eastern Pacific ITCZ while retaining the least for in situ precipitation. Subtropical moisture is least divergent over the Pacific basin, which is the smallest moisture source (per unit area) for global land areas. Basins also differ in how subtropical moisture sources are partitioned between tropical, midlatitude, and land regions. Next, we use the same matrix operator framework to study the aerial hydrological cycle response to quasi-equilibrium CO2-doubling. The total change in precipitation is separated into contributions from changes in moisture transport and changes in evaporation, and these, in turn, are further separated into changes due to local moisture divergence and remote moisture convergence. While increased surface evaporation increases precipitation everywhere, changes in moisture transport are necessary to create a spatial pattern where precipitation decreases in the subtropics and increases substantially at the equator. This finding agrees broadly with other findings that have emphasized the role of both surface thermodynamics and transport in determining precipitation changes. Overall, changes in the convergence of remotely-evaporated moisture are more important to the overall precipitation change than changes in the amount of locally-evaporated moisture that precipitates in situ. Further decompositions show that CO2-doubling increases the fraction of locally-evaporated moisture that is exported, enhances moisture exchange between ocean basins, and shifts moisture convergence within a given basin towards greater distances between moisture source (evaporation) and sink (precipitation) regions. These changes can be understood in terms of the increased residence timescale of water in the atmosphere with CO2-doubling, which correspond to an increase in the advective length scale of moisture transport. As a result, the distance between where moisture evaporates and where it precipitates increases. Analyses of several heuristic models further support this finding. We conclude by discussing implications of our findings, including effects of changing atmospheric moisture transport on ocean circulation and interpretation of water isotope proxy records. Finally, we consider the role of atmospheric moisture transport in maintaining the high salinity of surface waters in the tropical Atlantic basin. Two independent observational estimates show a 0.5 Sv freshwater deficit over the Atlantic drainage basin, and moisture flux calculations from the ERA interim observational reanalysis shows that at least half of this deficit is due to moisture export from the subtropical Atlantic basin, over the Panama Isthmus, into the tropical Pacific. GCM experiments with water tracers show that most moisture exported from the Atlantic to the Pacific originates between the equator and 30N, with a significant maximum in the 10N to 20N latitude band. Analysis of the CMIP5 abrupt CO2-quadrupling experiment shows striking intermodel agreement between decreased Atlantic drainage basin freshwater input (approximately 0.1 Sv in the multimodel mean) and increased tropical Atlantic sea surface salinity. GCM water tracer experiments reveal that enhanced Atlantic-to-Pacific moisture transport in a quasi-equilibrium CO2-doubling experiment is responsible for approximately one-quarter of the precipitation increase over the equatorial Pacific, resulting in freshening of the Pacific basin and salinizing of the Atlantic. Most of this increased Atlantic-to-Pacific moisture export originates between the equator and 30N in the Atlantic. This intensification of the interbasin moisture flux is due to altered transport attributable to increased atmospheric specific humidity; this results in increased moisture residence time scales and advective length scales, favoring longer distances between moisture source and sink regions. Implications of these findings are discussed
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