bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-Overhead Trace Collection and Profiling on GPU Compute Kernels
Authors: Darche Sébastien , Dagenais Michel R. 
Published: February 2024

While GPUs can bring substantial speedup to compute-intensive tasks, their programming is notoriously hard. From their programming model, to microarchitectural particularities, the programmer may encounter many pitfalls which may hinder performance in obscure ways. Numerous performance analysis tools provide helpful data on the efficiency of the compute kernels, but few allow the programmer to efficiently gather runtime information directly on the device and pinpoint the sections to optimize.
We propose in this article an instrumentation method to collect traces while executing the compute kernel, with a reduced overhead compared with other approaches, by exploiting the inherently parallel behavior of GPUs and compartmentalizing tracing phases. The reference implementation is freely available and induces an average overhead of 1.6 × on a popular scientific computing benchmark and 1.5 × over the kernel execution time. This represents an improvement of an order of magnitude compared with similar work, and proves useful for timing-guided optimizations. The tool generates insightful execution traces and timestamps which can be analyzed to better understand performance issues in the kernel.
Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data
Authors: Darmofal Madison , Suman Shalabh , Atwal Gurnit , Toomey Michael , Chen Jie-Fu , Chang Jason C. , Vakiani Efsevia , Varghese Anna M. , Balakrishnan Rema Anoop , Syed Aijazuddin , Schultz Nikolaus , Berger Michael F. , Morris Quaid 
Published: February 2024

Abstract

Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor-type classifiers trained on genomic features have been explored, but the most accurate methods are not clinically feasible, relying on features derived from whole-genome sequencing (WGS), or predicting across limited cancer types. We use genomic features from a data set of 39,787 solid tumors sequenced using a clinically targeted cancer gene panel to develop Genome-Derived-Diagnosis Ensemble (GDD-ENS): a hyperparameter ensemble for classifying tumor type using deep neural networks. GDD-ENS achieves 93% accuracy for high-confidence predictions across 38 cancer types, rivaling the performance of WGS-based methods. GDD-ENS can also guide diagnoses of rare type and cancers of unknown primary and incorporate patient-specific clinical information for improved predictions. Overall, integrating GDD-ENS into prospective clinical sequencing workflows could provide clinically relevant tumor-type predictions to guide treatment decisions in real time.

Significance:
We describe a highly accurate tumor-type prediction model, designed specifically for clinical implementation. Our model relies only on widely used cancer gene panel sequencing data, predicts across 38 distinct cancer types, and supports integration of patient-specific nongenomic information for enhanced decision support in challenging diagnostic situations.
See related commentary by Garg, p. 906.
This article is featured in Selected Articles from This Issue, p. 897
Control System for Swerve Drive Wheeled Automated Guided Vehicle with Ultra-Wide Band Local Positioning System
Authors: Arifianto Mada Jimmy Fonda , Afianto  , Suhendra  
Published: February 2024

Control system for Automates Guided Vehicle (AGV) is used to control the motor movement so that the AGV can go to a position in certain speed and orientation. Discussion in this paper is about how to control 4-wheel swerve drive-based AGV. Mechanical structure of each wheel is built in such a way that the wheel can move forward / backward and the orientation can be adjusted while moving. Each wheel requires two BLDC motors to drive and to steer the AGV. In this project, the power each motor is 200W which is drove and controlled by Syntron LS20530G motor driver that connected to a computer via CAN-bus. An Ultra-Wide Band (UWB)-based Local Positioning System (LPS) is used to monitor the position of the AGV as well as a guide for non-physical paths so that AGV moves according to a given path virtually. The experimental results show that AGV can move in a straight line with a speed of 50m/min. Wheels can also be steered according to a certain angle so that the AGV can move towards the destination point. The steering angle of each wheel is between -135 degrees to 135 degrees.
SELECTION OF ZEELAND’S MUNICIPAL EFFLUENT REUSE TECHNOLOGY FOR AGRICULTURE: PERSPECTIVE FROM DEVELOPING COUNTRY
Authors: Disrinama Am Maisarah 
Published: February 2024

The water demands for agricultural purposes are increasing along with the population growth. Unfortunately, the water source is not sufficiently available nowadays. Furthermore, the quality of available water is more deteriorated due to the contamination from many sources such as households, industrial areas and other activities. Water board Scheldestromen handles 16 wastewater treatment plants located in Province of Zeeland in The Netherlands. The total production of treated effluent water from 16 wastewater treatment plants is 50 million annually. Quality of the effluent is relatively good, however, some potential risks related to the number of pathogenic microorganism and some trace metals are still there. The treated effluent is mostly discharged to river near to the treatment plant. The high amount of effluent discharge would potentially to be re-used for fulfill the demand for agricultural water. Therefore, this study aims to evaluate the feasibility of treated effluent from one of Walcheren wastewater treatment plants located in Ritthem, Province of Zeeland. This study uses the method of Multi Criteria Analysis (MCA) for looking the best way to reuse the effluent for agricultural purposes. The MCA questionnaire was developed based on the thorough literature review of effluent reuse. There are 6 criteria that need to be weighted and 6 scenario alternatives that need to be scored for the MCA questionnaire. The result show that the effluent water contained pathogenic bacteria (E.Coli) and some trace metals (Ni and Cu) more than suggested by FAO standard. Hence the most preferred technology is combination between closed conduits and UV system, with weighted score 0.78 while others had less weighted score compared to the selected one.
Key words : Agriculture, Effluent, Environment, Water Treatment, Zeeland.
Acute Adenoviral Infection Elicits an Arrhythmogenic Substrate Prior to Myocarditis
Authors: Padget Rachel L. , Zeitz Michael J. , Blair Grace A. , Wu Xiaobo , North Michael D. , Tanenbaum Mira T. , Stanley Kari E. , Phillips Chelsea M. , King D. Ryan , Lamouille Samy , Gourdie Robert G. , Hoeker Gregory S. , Swanger Sharon A. , Poelzing Steven , Smyth James W. 
Published: February 2024

BACKGROUND:
Viral cardiac infection represents a significant clinical challenge encompassing several etiological agents, disease stages, complex presentation, and a resulting lack of mechanistic understanding. Myocarditis is a major cause of sudden cardiac death in young adults, where current knowledge in the field is dominated by later disease phases and pathological immune responses. However, little is known regarding how infection can acutely induce an arrhythmogenic substrate before significant immune responses. Adenovirus is a leading cause of myocarditis, but due to species specificity, models of infection are lacking, and it is not understood how adenoviral infection may underlie sudden cardiac arrest. Mouse adenovirus type-3 was previously reported as cardiotropic, yet it has not been utilized to understand the mechanisms of cardiac infection and pathology.

METHODS:
We have developed mouse adenovirus type-3 infection as a model to investigate acute cardiac infection and molecular alterations to the infected heart before an appreciable immune response or gross cardiomyopathy.

RESULTS:

Optical mapping of infected hearts exposes decreases in conduction velocity concomitant with increased Cx43
Ser368
phosphorylation, a residue known to regulate gap junction function. Hearts from animals harboring a phospho-null mutation at Cx43
Ser368
are protected against mouse adenovirus type-3–induced conduction velocity slowing. Additional to gap junction alterations, patch clamping of mouse adenovirus type-3–infected adult mouse ventricular cardiomyocytes reveals prolonged action potential duration as a result of decreased
I
K1
and
I
Ks
current density. Turning to human systems, we find human adenovirus type-5 increases phosphorylation of Cx43
Ser368
and disrupts synchrony in human induced pluripotent stem cell-derived cardiomyocytes, indicating common mechanisms with our mouse whole heart and adult cardiomyocyte data.

CONCLUSIONS:
Together, these findings demonstrate that adenoviral infection creates an arrhythmogenic substrate through direct targeting of gap junction and ion channel function in the heart. Such alterations are known to precipitate arrhythmias and likely contribute to sudden cardiac death in acutely infected patients.
Association of Cannabis Use With Cardiovascular Outcomes Among US Adults
Authors: Jeffers Abra M. , Glantz Stanton , Byers Amy L. , Keyhani Salomeh 
Published: February 2024

Background
We examined the association between cannabis use and cardiovascular outcomes among the general population, among never‐tobacco smokers, and among younger individuals.

Methods and Results
This is a population‐based, cross‐sectional study of 2016 to 2020 data from the Behavioral Risk Factor Surveillance Survey from 27 American states and 2 territories. We assessed the association of cannabis use (number of days of cannabis use in the past 30 days) with self‐reported cardiovascular outcomes (coronary heart disease, myocardial infarction, stroke, and a composite measure of all 3) in multivariable regression models, adjusting for tobacco use and other characteristics in adults 18 to 74 years old. We repeated this analysis among nontobacco smokers, and among men <55 years old and women <65 years old who are at risk of premature cardiovascular disease. Among the 434 104 respondents, the prevalence of daily and nondaily cannabis use was 4% and 7.1%, respectively. The adjusted odds ratio (aOR) for the association of daily cannabis use and coronary heart disease, myocardial infarction, stroke, and the composite outcome (coronary heart disease, myocardial infarction, and stroke) was 1.16 (95% CI, 0.98–1.38), 1.25 (95% CI, 1.07–1.46), 1.42 (95% CI, 1.20–1.68), and 1.28 (95% CI, 1.13–1.44), respectively, with proportionally lower log odds for days of use between 0 and 30 days per month. Among never‐tobacco smokers, daily cannabis use was also associated with myocardial infarction (aOR, 1.49 [95% CI, 1.03–2.15]), stroke (aOR, 2.16 [95% CI, 1.43–3.25]), and the composite of coronary heart disease, myocardial infarction, and stroke (aOR, 1.77 [95% CI, 1.31–2.40]). Relationships between cannabis use and cardiovascular outcomes were similar for men <55 years old and women <65 years old.

Conclusions
Cannabis use is associated with adverse cardiovascular outcomes, with heavier use (more days per month) associated with higher odds of adverse outcomes.
White matter microstructural plasticity associated with educational intervention in reading disability
Authors: Meisler Steven L. , Gabrieli John D. E. , Christodoulou Joanna A. 
Published: February 2024

AbstractChildren’s reading progress typically slows during extended breaks in formal education, such as summer vacations. This stagnation can be especially concerning for children with reading difficulties or disabilities, such as dyslexia, because of the potential to exacerbate the skills gap between them and their peers. Reading interventions can prevent skill loss and even lead to appreciable gains in reading ability during the summer. Longitudinal studies relating intervention response to brain changes can reveal educationally relevant insights into rapid learning-driven brain plasticity. The current work focused on reading outcomes and white matter connections, which enable communication among the brain regions required for proficient reading. We collected reading scores and diffusion-weighted images at the beginning and end of summer for 41 children with reading difficulties who had completed either 1st or 2nd grade. Children were randomly assigned to either receive an intensive reading intervention (n = 26; Seeing Stars from Lindamood-Bell which emphasizes orthographic fluency) or be deferred to a wait-list group (n = 15), enabling us to analyze how white matter properties varied across a wide spectrum of skill development and regression trajectories. On average, the intervention group had larger gains in reading compared to the non-intervention group, who declined in reading scores. Improvements on a proximal measure of orthographic processing (but not other more distal reading measures) were associated with decreases in mean diffusivity within core reading brain circuitry (left arcuate fasciculus and left inferior longitudinal fasciculus) and increases in fractional anisotropy in the left corticospinal tract. Our findings suggest that responses to intensive reading instruction are related predominantly to white matter plasticity in tracts most associated with reading.
Previous motor task performance impacts phase-based EEG resting-state connectivity states
Authors: Rosjat Nils , Hommelsen Maximilian , Fink Gereon R. , Daun Silvia 
Published: February 2024

Abstract
The resting human brain cycles through distinct states that can be analyzed using microstate analysis and electroencephalography (EEG) data. This approach classifies multichannel EEG data into spontaneously interchanging microstates based on topographic features. These microstates may be valuable biomarkers in neurodegenerative diseases since they reflect the resting brain’s state. However, microstates do not provide information about the active neural networks during the resting state. This article presents an alternative and complementary method for analyzing resting-state EEG data and demonstrates its reproducibility and reliability. This method considers cerebral connectivity states defined by phase synchronization and measured using the corrected imaginary phase-locking value (ciPLV) based on source-reconstructed EEG recordings. We analyzed resting-state EEG data from young, healthy participants acquired on five consecutive days before and after a motor task. We show that our data reproduce microstates previously reported. Further, we reveal four stable topographic patterns over the multiple recording sessions in the source connectivity space. While the classical microstates were unaffected by a preceding motor task, the connectivity states were altered, reflecting the suppression of frontal activity in the post-movement resting state.
Looking Back: An Account of How Ice Nucleation by Bacteria Was Discovered (1963 to about Mid-1980s). Part I: The Basics
Authors: Vali Gabor , Schnell Russell C. 
Published: February 2024

Abstract
An overview is given of the path of research that led from asking how hailstones originate to the discovery that ice nucleation can be initiated by bacteria and other microorganisms at temperatures as high as −2°C. The major steps along that path were finding exceptionally effective ice nucleators in soils with a high content of decayed vegetative matter, then in decaying tree leaves, and then in plankton-laden ocean water. Eventually, it was shown that Pseudomonas syringae bacteria were responsible for most of the observed activity. That identification coincided with the demonstration that the same bacteria cause frost damage on plants. Ice nucleation by bacteria meant an unexpected turn in the understanding of ice nucleation and of ice formation in the atmosphere. Subsequent research confirmed the unique effectiveness of ice nucleating particles (INP) of biological origin, referred to as bio-INPs, so that bio-INPs are now considered to be important elements of lower-tropospheric cloud processes. Nonetheless, some of the questions which originally motivated the research are still unresolved, so that revisiting the early work may be helpful to current endeavors. Part I of this manuscript summarizes how the discovery progressed. Part II (Schnell and Vali) shows the relationship between bio-INPs in soils and in precipitation with climate and other findings. The online supplemental material contains a bibliography of recent work about bio-INPs.
The Energetics of the Lagrangian Evolution of Tropical Convective Systems
Authors: Masunaga Hirohiko , Takahashi Hanii 
Published: February 2024

Abstract
The convective life cycle is often conceptualized to progress from congestus to deep convection and develop further to stratiform anvil clouds, accompanied by a systematic change in the vertical structure of vertical motion. This archetype scenario has been developed largely from the Eulerian viewpoint, and it has yet to be explored whether the same life cycle emerges itself in a moving system tracked in the Lagrangian manner. To address this question, Lagrangian tracking is applied to tropical convective systems in combination with a thermodynamic budget analysis forced by satellite-retrieved precipitation and radiation. A new method is devised to characterize the vertical motion profiles in terms of the column import or export of moisture and moist static energy (MSE). The bottom-heavy, midheavy, and top-heavy regimes are identified for every 1° × 1° grid pixel accompanying tracked precipitation systems, making use of the diagnosed column export/import of moisture and MSE. The major findings are as follows. The Lagrangian evolution of convective systems is dominated by a state of dynamic equilibrium among different convective regimes rather than a monotonic progress from one regime to the next. The transition from the bottom-heavy to midheavy regimes is fed with intensifying precipitation presumably owing to a negative gross moist stability (GMS) of the bottom-heavy regime, whereas the transition from the midheavy to top-heavy regimes dissipates the system. The bottom-heavy to midheavy transition takes a relaxation time of about 5 h in the equilibrating processes, whereas the relaxation time is estimated as roughly 20 h concerning the midheavy to top-heavy transition.
Assessment of the Decadal Prediction Skill of Sahel Rainfall in CMIP5 and CMIP6
Authors: He Yujun , Wang Bin , Liu Juanjuan , Wang Yong , Li Lijuan , Liu Li , Xu Shiming , Huang Wenyu , Lu Hui 
Published: February 2024

Abstract
Accurately predicting the decadal variations in Sahel rainfall has important implications for the lives and economy in the Sahel. Previous studies found that the decadal variations in sea surface temperature (SST) in the Atlantic, Mediterranean Sea, Indian Ocean, and Pacific contribute to those in Sahel rainfall. This study evaluates the decadal prediction skills of Sahel rainfall from all the available hindcasts contributing to phases 5 and 6 of the Coupled Model Intercomparison Project (CMIP5 and CMIP6), in comparison with the related uninitialized simulations. A majority of the prediction systems show high skill with regard to Sahel rainfall. The high skill may be partly attributed to external forcings, which are reflected in good performance of the respective uninitialized simulations. The decadal prediction skills of the key SST drivers and their relationships with the Sahel rainfall are also assessed. Both the hindcasts and the uninitialized simulations generally present high skill for the Atlantic multidecadal variability (AMV) and Mediterranean Sea SST indices and low skill for the Indian Ocean basin mode (IOBM) and interdecadal Pacific variability (IPV) indices. The relationship between the Sahel rainfall and the AMV or Mediterranean Sea SST index is reasonably captured by most prediction systems and their uninitialized simulations, while that between the Sahel rainfall and the IOBM or IPV index is captured by only a few systems and their uninitialized simulations. The high skill of the AMV and Mediterranean Sea SST indices as well as the reasonable representations of their relationships with the Sahel rainfall by both the hindcasts and uninitialized simulations probably plays an important role in predicting the Sahel rainfall successfully.

Significance Statement
Predicting Sahel rainfall on the decadal time scale is of great importance. This study provides a thorough evaluation of the decadal prediction skills of Sahel rainfall in the current decadal prediction systems participating in phases 5 and 6 of the Coupled Model Intercomparison Project (CMIP5 and CMIP6). A majority of the systems achieve high prediction skill of Sahel rainfall, which probably results from the high prediction skill of some key sea surface temperature (SST) drivers, especially in the Atlantic and Mediterranean Sea SST, and their relationships with Sahel rainfall. This study provides a reference for better understanding the predictability of Sahel rainfall.
Quantification of Contributions from Different Dust Sources to the Distribution and the Variation of Spring Dust over the Tibetan Plateau and Corresponding Mechanisms since 2000
Authors: Zhu Qingzhe , Liu Yuzhi , Xiao Na 
Published: February 2024

Abstract
Dust is the predominant type of aerosol over the Tibetan Plateau (TP) due to the existence of surrounding significant dust sources. However, the contributions of different dust sources to the distribution and variation of dust over the TP and corresponding mechanisms are still being explored. By separating emissions from different dust sources in a numerical model, this study detected that dust originating from East Asia, the Middle East, and North Africa are the main contributors to spring dust over the TP, accounting for 42%–68%, 13%–27%, and 9%–25% of the total dust concentration, respectively. East Asian dust primarily affects the dust over the central and northern parts of the TP, whereas Middle Eastern and North African dust mainly contributes to the dust over the western and southern parts of the TP. Additionally, the variation in dust over the TP is related to East Asian and North African dust, which contribute 58% and 35% of the total variation, respectively. The mechanism underlying this association is attributable to the SST over the northern North Atlantic and updrafts over the northern slope of the TP: the increased SST enhances westerlies from North Africa to East Asia and northwesterly winds over the northern slope of the TP and combines with the stronger westerlies to promote the transport of East Asian and North African dust to the TP. Consequently, it is necessary to focus on the impact of multiple dust sources on the dust over the TP.
Foreign Interference and the Incremental Chilling of Free Speech
Authors: Sorial Sarah , Morris Shireen , Greste Peter 
Published: February 2024

AbstractForeign interference is a growing threat to all liberal democracies, including Australia. To respond to this growing threat, the Department of Home Affairs has developed a complex ‘Counter-Foreign Interference Strategy’ (CFIS). At the heart of the strategy lies a suite of interlocking and overlapping legislation, including the Foreign Influence Transparency Scheme Act 2018 (FITS Act), the National Security Legislation Amendment (Espionage and Foreign Interference) Act 2018 and the Electoral Legislation Amendment (Electoral Funding and Disclosure Reform) Act 2018 (Electoral Funding Act). The aim of this paper is to explain and clarify the legislation and the free speech burdens it imposes, and determine whether the laws are suitably targeted at foreign interference without unduly limiting legitimate communication activity. We argue that the current criminal law regime is ineffective in addressing the problem because foreign interference is a complex and pervasive phenomenon taking many different forms — from espionage on university campuses to anonymous and targeted social media campaigns. The legislative scheme is not properly tailored to tackle foreign interference as it actually occurs.