Miracle-dz/UniFAR-FTUs huggingface dataset:
Enzyme-Free Exponential Amplification via Growth and Scission of Crisscross Ribbons from Single-Stranded DNA Components

The self-assembly of DNA-based monomers into higher-order structures has significant potential for realizing various biomimetic behaviors including algorithmic assembly, ultrasensitive detection, and self-replication. For these behaviors, it is desirable to implement high energetic barriers to undesired spurious nucleation, where such barriers can be bypassed via seed-initiated assembly. Joint-neighbor capture is a mechanism enabling the construction of such barriers while allowing for algorithmic behaviors, such as bit-copying. Cycles of polymerization with division could accordingly be used for implementing exponential growth in self-replicating materials. Previously, we demonstrated crisscross polymerization, a strategy that attains robust seed-dependent self-assembly of single-stranded DNA and DNA-origami monomers via joint-neighbor capture. Here, we expand the crisscross assembly to achieve autonomous, isothermal exponential amplification of ribbons through their concurrent growth and scission via toehold-mediated strand displacement. We demonstrate how this crisscross chain reaction, or 3CR, can be used as a detection strategy through coupling to single- and double-stranded nucleic acid targets and introduce a rule-based stochastic modeling approach for simulating molecular self-assembly behaviors such as crisscross-ribbon scission.
Source appointment of nitrogen in PM2.5 based on bulk δ15N signatures and a Bayesian isotope mixing model

Abstract Nitrogen isotope (δ15N) has been employed to differentiate major sources of atmospheric N. However, it remains a challenge to quantify contributions of multiple sources based on δ15N values of the N mixture in atmospheric samples. This study measured δ15N of bulk N in PM2.5 at an urban site of Beijing during a severe haze episode of 22–30 January 2013 and a background site of Qinghai, north-western China from 6 September to 15 October 2013, then applied a Bayesian isotope mixing model (SIAR, Stable Isotope Analysis in R) to analyse the N sources. At Beijing site, δ15N values of PM2.5 (−4.1‰ to +13.5‰, +2.8 ± 6.4‰) were distributed within the range of major anthropogenic sources (including NH3 and NO2 from coal combustion, vehicle exhausts and domestic wastes/sewage). At Menyuan site, δ15N values of PM2.5 (+8.0‰ to +27.9‰, +18.5 ± 5.8‰) were significantly higher than that of potential sources (including NH3 and NO2 from biomass burning, animal wastes, soil N cycle, fertilizer application and dust N). High molar ratios of to and/or in PM2.5 at the background site suggested that the equilibrium of NH3 ↔ caused apparent 15N enrichments in ammonium. Results of the SIAR model showed that 39 and 32% of bulk N in PM2.5 of Beijing site were contributed from N emissions of coal combustion and vehicle exhausts, respectively, whereas N in PM2.5 at Menyuan site was derived mainly from N emissions of biomass burning (46%) and NH3 volatilization (34%). These results revealed that the stoichiometry between NH3 and acidic gases plays an important role in controlling the bulk δ15N signatures of PM2.5 and emissions of reactive N from coal combustion and urban transportation should be strictly controlled to advert the risk of haze episodes in Beijing.
EHR-HGCN: An Enhanced Hybrid Approach for Text Classification Using Heterogeneous Graph Convolutional Networks in Electronic Health Records

Text classification is a central part of natural language processing, with important applications in understanding the knowledge behind biomedical texts including electronic health records (EHR). In this article, we propose a novel heterogeneous graph convolutional network method for classifying EHR texts. Our method, called EHR-HGCN, is able to combine context-sensitive word and sentence embeddings with structural sentence-level and word-level relation information to perform text classification. EHR-HGCN reframes EHR text classification as a graph classification task to better capture structural information about the document using a heterogeneous graph. To mine contextual information from a document, EHR-HGCN first applies a bidirectional recurrent neural network (BiRNN) on word embeddings obtained via Global Vectors for word representation (GloVe) to obtain context-sensitive word-level and sentence-level embeddings. To mine structural relationships from the document, EHR-HGCN then constructs a heterogeneous graph over the word and sentence embeddings, where sentence-word and word-word relationships are represented by graph edges. Finally, a heterogeneous graph convolutional neural network is used to classify documents by their graph representation. We evaluate EHR-HGCN on a variety of standard text classification benchmarks and find that EHR-HGCN has higher accuracy and F1-score than other representative machine learning and deep learning methods. We also apply EHR-HGCN to the MedLit benchmark and find it performs with high accuracy and F1-score on the task of section classification in EHR texts. Our ablation experiments show that the heterogeneous graph construction and heterogeneous graph convolutional network are critical to the performance of EHR-HGCN.
Investigation of statistical methods used in prognostic prediction models for obstetric care: A 10 year‐span cross‐sectional study

Abstract Introduction Obstetric care is a highly active area in the development and application of prognostic prediction models. The development and validation of these models often require the utilization of advanced statistical techniques. However, failure to adhere to rigorous methodological standards could greatly undermine the reliability and trustworthiness of the resultant models. Consequently, the aim of our study was to examine the current statistical practices employed in obstetric care and offer recommendations to enhance the utilization of statistical methods in the development of prognostic prediction models. Material and methods We conducted a cross‐sectional survey using a sample of studies developing or validating prognostic prediction models for obstetric care published in a 10‐year span (2011–2020). A structured questionnaire was developed to investigate the statistical issues in five domains, including model derivation (predictor selection and algorithm development), model validation (internal and external), model performance, model presentation, and risk threshold setting. On the ground of survey results and existing guidelines, a list of recommendations for statistical methods in prognostic models was developed. Results A total of 112 eligible studies were included, with 107 reporting model development and five exclusively reporting external validation. During model development, 58.9% of the studies did not include any form of validation. Of these, 46.4% used stepwise regression in a crude manner for predictor selection, while two‐thirds made decisions on retaining or dropping candidate predictors solely based on p‐values. Additionally, 26.2% transformed continuous predictors into categorical variables, and 80.4% did not consider nonlinear relationships between predictors and outcomes. Surprisingly, 94.4% of the studies did not examine the correlation between predictors. Moreover, 47.1% of the studies did not compare population characteristics between the development and external validation datasets, and only one‐fifth evaluated both discrimination and calibration. Furthermore, 53.6% of the studies did not clearly present the model, and less than half established a risk threshold to define risk categories. In light of these findings, 10 recommendations were formulated to promote the appropriate use of statistical methods. Conclusions The use of statistical methods is not yet optimal. Ten recommendations were offered to assist the statistical methods of prognostic prediction models in obstetric care.
Bedaquiline for treatment of non-tuberculous mycobacteria (NTM): a systematic review and meta-analysis

Abstract Background Non-tuberculous mycobacteria (NTM) infections are increasing in incidence and associated mortality. NTM are naturally resistant to a variety of antibiotics, complicating treatment. We conducted a literature assessment on the efficacy of bedaquiline in treating NTM species in vitro and in vivo (animal models and humans); meta-analyses were performed where possible. Method Four databases were searched using specific terms. Publications were included according to predefined criteria. Bedaquiline’s impact on NTM in vitro, MICs and epidemiological cut-off (ECOFF) values were evaluated. A meta-analysis of bedaquiline efficacy against NTM infections in animal models was performed. Culture conversion, cure and/or relapse-free cure were used to evaluate the efficacy of bedaquiline in treating NTM infection in humans. Results Fifty studies met the inclusion criteria: 33 assessed bedaquiline’s impact on NTM in vitro, 9 in animal models and 8 in humans. Three studies assessed bedaquiline’s efficacy both in vitro and in vivo. Due to data paucity, an ECOFF value of 0.5 mg/mL was estimated for Mycobacterium abscessus only. Meta-analysis of animal studies showed a 1.86× reduction in bacterial load in bedaquiline-treated versus no treatment within 30 days. In humans, bedaquiline-including regimens were effective in treating NTM extrapulmonary infection but not pulmonary infection. Conclusions Bedaquiline demonstrated strong antibacterial activity against various NTM species and is a promising drug to treat NTM infections. However, data on the genomic mutations associated with bedaquiline resistance were scarce, preventing statistical analyses for most mutations and NTM species. Further studies are urgently needed to better inform treatment strategies.
Restricted life‐space mobility impacts physical but not mental quality of life in older cancer survivors

Abstract Background Older cancer survivors often value quality of life (QOL) over survival. Life‐space mobility (LSM), defined as the individual's spatial geographic mobility range, is an important QOL indicator in older adults with chronic illnesses; however, this relationship is unexplored in older cancer survivors. Methods We examined the longitudinal associations and causal relationships between LSM and QOL in 153 older cancer survivors (≥65 years) from the University of Alabama at Birmingham (UAB) Study of Aging. LSM was assessed using the UAB Life‐Space Assessment‐Composite score (LSA‐C), and QOL was assessed by the SF‐12 Mental Component Score (MCS12) and Physical Component Score (PCS12) at 0 (study entry), 6, 18, 36, 54, and 72 months. We examined the causal relationship between LSM and QOL using a cross‐lagged panel model (CLPM). Results The cohort (n = 153) was 76 years old on average and predominantly White (58%), female (58%), and married (55%). Longitudinal analyses found LSM decreased over time (p < 0.0001), and this decrease was associated with decreased QOL (PCS12, p < 0.0001, MCS12, p < 0.0001). In the CLPM causal analysis, lower LSM resulted in worse PCS12 (p < 0.001), but not worse MSC12. Conclusions Restricted LSM resulted in worse physical QOL over 72 months in a sample of 153 older cancer survivors. Developing and evaluating interventions to preserve greater LSM could be a promising approach to improving QOL.
An Inducible ESCRT-III Inhibition Tool to Control HIV-1 Budding

HIV-1 budding as well as many other cellular processes require the Endosomal Sorting Complex Required for Transport (ESCRT) machinery. Understanding the architecture of the native ESCRT-III complex at HIV-1 budding sites is limited due to spatial resolution and transient ESCRT-III recruitment. Here, we developed a drug-inducible transient HIV-1 budding inhibitory tool to enhance the ESCRT-III lifetime at budding sites. We generated autocleavable CHMP2A, CHMP3, and CHMP4B fusion proteins with the hepatitis C virus NS3 protease. We characterized the CHMP-NS3 fusion proteins in the absence and presence of protease inhibitor Glecaprevir with regard to expression, stability, localization, and HIV-1 Gag VLP budding. Immunoblotting experiments revealed rapid and stable accumulation of CHMP-NS3 fusion proteins. Notably, upon drug administration, CHMP2A-NS3 and CHMP4B-NS3 fusion proteins substantially decrease VLP release while CHMP3-NS3 exerted no effect but synergized with CHMP2A-NS3. Localization studies demonstrated the relocalization of CHMP-NS3 fusion proteins to the plasma membrane, endosomes, and Gag VLP budding sites. Through the combined use of transmission electron microscopy and video-microscopy, we unveiled drug-dependent accumulation of CHMP2A-NS3 and CHMP4B-NS3, causing a delay in HIV-1 Gag-VLP release. Our findings provide novel insight into the functional consequences of inhibiting ESCRT-III during HIV-1 budding and establish new tools to decipher the role of ESCRT-III at HIV-1 budding sites and other ESCRT-catalyzed cellular processes.
Glacier stagnant in central Karakorum during 2003 to 2008 derived from DEOS Mass Transport Model GRACE data and one monthly degree-day model

Glacier change in central Karakorum is known as ‘anomony’ in the late 1990s, where many glaciers expanded and numbers of glacier surged while most of glaciers in the Greater Himalaya rapidly retreated. However, the understanding of glacier change in this region is still poor. Glacier changes for the Hunza river basin (HRB) in central Karakorum during 2003 to 2008 were investigated from different data sources. The mass variation in HRB were estimated from the DEOS Mass Transport Model (DMT-1) GRACE data and the Variable Infiltration Capacity (VIC) model, and compared with the simulated glacier mass balance by one monthly degree-day model. The surface elevation difference of glaciers between ASTER DEM and SRTM were calculated. The mass variations from GRACE data suggest that the glacier mass balance in HRB during 2003-2007 has no clear trend. The cumulative mass balance is positive during 2003-2008. The average glacier surface elevation difference between SRTM DEM and ASTER DEM is 11.8±3.2 m. The average differences of glacier surface elevation of Batura glaciers in accumulation zones is increased with 0.88m. a-1, These results indicate that there is no significant glacier retreat during 1999 to 2008. The seasonal amplitude of simulated mass variation of the monthly degree-day model agreed well with that estimated from DMT-1 GRACE data, but the simulated glacier accumulation is less than that calculated from GRACE data. The main reason probably lies in that the precipitation of glaciers and ungalciated areas were underestimated, especially in alpine areas.
Stable isotopes in atmospheric water vapor and applications to the hydrologic cycle

The measurement and simulation of water vapor isotopic composition has matured rapidly over the last decade, with long‐term data sets and comprehensive modeling capabilities now available. Theories for water vapor isotopic composition have been developed by extending the theories that have been used for the isotopic composition of precipitation to include a more nuanced understanding of evaporation, large‐scale mixing, deep convection, and kinetic fractionation. The technologies for in situ and remote sensing measurements of water vapor isotopic composition have developed especially rapidly over the last decade, with discrete water vapor sampling methods, based on mass spectroscopy, giving way to laser spectroscopic methods and satellite‐ and ground‐based infrared absorption techniques. The simulation of water vapor isotopic composition has evolved from General Circulation Model (GCM) methods for simulating precipitation isotopic composition to sophisticated isotope‐enabled microphysics schemes using higher‐order moments for water and ice size distributions. The incorporation of isotopes into GCMs has enabled more detailed diagnostics of the water cycle and has led to improvements in its simulation. The combination of improved measurement and modeling of water vapor isotopic composition opens the door to new advances in our understanding of the atmospheric water cycle, in processes ranging from the marine boundary layer, through deep convection and tropospheric mixing, and into the water cycle of the stratosphere. Finally, studies of the processes governing modern water vapor isotopic composition provide an improved framework for the interpretation of paleoclimate proxy records of the hydrological cycle.
The Visual Design and Control of Trellis Display

Abstract Trellis display is a framework for the visualization of data. Its most prominent aspect is an overall visual design, reminiscent of a garden trelliswork, in which panels are laid out into rows, columns, and pages. On each panel of the trellis, a subset of the data is graphed by a display method such as a scatterplot, curve plot, boxplot, 3-D wireframe, normal quantile plot, or dot plot. Each panel shows the relationship of certain variables conditional on the values of other variables. A number of display methods employed in the visual design of Trellis display enable it to succeed in uncovering the structure of data even when the structure is quite complicated. For example, Trellis display provides a powerful mechanism for understanding interactions in studies of how a response depends on explanatory variables. Three examples demonstrate this; in each case, we make important discoveries not appreciated in the original analyses. Several control methods are also essential to Trellis display. A con.
Semantic Completion and Filtration for Image-Text Retrieval

SONG YANG, Tianjin University; China and also with the Institute of Artiicial Intelligence, Hefei Comprehensive National Science Center, China QIANG LI, Tianjin University, China WENHUI LI, Tianjin University, China XUANYA LI*, Baidu Inc., China, Xuanya Li is the corresponding author RAN JIN, Zhejiang Wanli University, China BO LV, The 30th Research Institute of China Electronics Technology Group Corporation, China RUI WANG, The 30th Research Institute of China Electronics Technology Group Corporation, China AN-AN LIU, Tianjin University; China and also with the Institute of Artiicial Intelligence, Hefei Comprehensive National Science Center, China
Is group therapy democratic? Enduring consequences of Outward Is group therapy democratic? Enduring consequences of Outward Bound’s alignment with the Human Potential Movement Bound’s alignment with the Human Potential Movement

Franklin Vernon provided an example of how programs viewing themselves as “cultural islands” are in fact embedded within historical capitalist relations, through the discourses of self that they promote. In this response, I expand on Vernon’s argument to situate the quasi-therapeutic practices he identified in the history of the human potential movement, which effectively merged with Outward Bound starting in the 1960s and continues to define outdoor experiential education. Where Vernon sought the structural referents to different models of self, this response seeks their historical origins. The response concludes by linking Vernon’s argument with existing critiques and parallel efforts in the literature on youth development and identity formation
A general framework for coloring problems : old results , new results , and open problems ?

In this survey paper we present a general framework for coloring problems that was introduced in a joint paper which the author presented at WG2003. We show how a number of different types of coloring problems, most of which have been motivated from frequency assignment, fit into this framework. We give a survey of the existing results, mainly based on and strongly biased by joint work of the author with several different groups of coauthors, include some new results, and discuss several open problems for each of the variants.
Delay in the Air or Detour on the Ground?—A Case Study in Guangzhou Baiyun International Airport

Collaboration between terminal airspace and airport surface operation shows an increasing significance for the best efficiency of both parts of the air traffic management domain. Runways play a critical role in connecting the two parts for departure and arrival aircraft. Suppose the gate and the entry fix of an aircraft are predetermined according to the flight plan, and they are on the opposite side of the airport terminal. The aircraft will either spend more time (i.e., delay in the air) landing on a runway close to its gate or take a longer distance (i.e., detour on the ground) taxiing to its gate if a runway close to its entry fix is assigned. This paper proposes a runway assignment model considering terminal airspace operation and airport surface movement simultaneously to discover how runway assignments can affect integrated operations. Four different runway assignment schemes are applied in this model. Subsequently, a metaheuristic method is proposed to solve the model. Furthermore, the historical taxiing and flight time data are analyzed to demonstrate the potential benefits of runway reassignment. Finally, the results show that the free assignment of the runway stands out among the four schemes, not only in the performance of terminal airspace operation (lower flight time) but also in airport surface movement (lower pushback delay, taxi time).
Packed Memory Arrays for Dynamic Graphs in the Distributed Memory Setting

Sparse dynamic graph workloads are common for many modern database problems. Thus, it is necessary to have graph data structures that have high update and query throughput while also operating in a distributed manner, where many machines can access a shared structure. Furthermore, such a data structure should be cache-optimal in the face of locality-exploiting algorithms like Breadth-first search. The cache-friendly Packed Compact Sparse Row (PCSR) has already seen great use in the shared memory setting. We propose an extension of the PCSR, the DistPCSR, which uses ideas from the serial one-machine Packed Memory Array (PMA) to build a routing layer between many PCSRs on different machines. This allows us to take queries while updates are still being resolved, and to share load between servers to stop any one from using too much memory. We provide some guarantees for this data structure, allowing one to be confident in its answers in a distributed setting. We also describe how to use the UPC++ framework’s primitives to implement a DistPCSR. Finally, we test our implemented DistPCSR on realistic graph workloads with algorithms that are friendly with PCSRs and share our results.