bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast convolutional neural networks on FPGAs with hls4ml
Authors: Aarrestad Thea , Loncar Vladimir , Ghielmetti Nicolò , Pierini Maurizio , Summers Sioni , Ngadiuba Jennifer , Petersson Christoffer , Linander Hampus , Iiyama Yutaro , Di Guglielmo Giuseppe , Duarte Javier , Harris Philip , Rankin Dylan , Jindariani Sergo , Pedro Kevin , Tran Nhan , Liu Mia , Kreinar Edward , Wu Zhenbin , Hoang Duc 
Published: June 2021

Abstract
We introduce an automated tool for deploying ultra low-latency, low-power deep neural networks with convolutional layers on field-programmable gate arrays (FPGAs). By extending the hls4ml library, we demonstrate an inference latency of 5 µs using convolutional architectures, targeting microsecond latency applications like those at the CERN Large Hadron Collider. Considering benchmark models trained on the Street View House Numbers Dataset, we demonstrate various methods for model compression in order to fit the computational constraints of a typical FPGA device used in trigger and data acquisition systems of particle detectors. In particular, we discuss pruning and quantization-aware training, and demonstrate how resource utilization can be significantly reduced with little to no loss in model accuracy. We show that the FPGA critical resource consumption can be reduced by 97% with zero loss in model accuracy, and by 99% when tolerating a 6% accuracy degradation.
Using mixed-effects modeling to estimate decay kinetics of response to SARS-CoV-2 infection
Authors: Bottino Dean , Hather Greg , Yuan L , Stoddard Madison , White Lin , Chakravarty Arijit 
Published: June 2021

Abstract
The duration of natural immunity in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a matter of some debate in the literature at present. For example, in a recent publication characterizing SARS-CoV-2 immunity over time, the authors fit pooled longitudinal data, using fitted slopes to infer the duration of SARS-CoV-2 immunity. In fact, such approaches can lead to misleading conclusions as a result of statistical model-fitting artifacts. To exemplify this phenomenon, we reanalyzed one of the markers (pseudovirus neutralizing titer) in the publication, using mixed-effects modeling, a methodology better suited to longitudinal datasets like these. Our findings showed that the half-life was both longer and more variable than reported by the authors. The example selected by us here illustrates the utility of mixed-effects modeling in provide more accurate estimates of the duration and heterogeneity of half-lives of molecular and cellular biomarkers of SARS-CoV-2 immunity.
Next-generation cytokines for cancer immunotherapy
Authors: Xue Diyuan , Hsu Eric , Fu Yang-Xin , Peng Hua 
Published: June 2021

AbstractMost studies focus on the first and second signals of T cell activation. However, the roles of cytokines in immunotherapy are not fully understood, and cytokines have not been widely used in patient care. Clinical application of cytokines is limited due to their short half-life in vivo, severe toxicity at therapeutic doses, and overall lack of efficacy. Several modifications have been engineered to extend their half-life and increase tumor targeting, including polyethylene glycol conjugation, fusion to tumor-targeting antibodies, and alteration of cytokine/cell receptor-binding affinity. These modifications demonstrate an improvement in either increased antitumor efficacy or reduced toxicity. However, these cytokine engineering strategies may still be improved further, as each strategy poses advantages and disadvantages in the delicate balance of targeting tumor cells, tumor-infiltrating lymphocytes, and peripheral immune cells. This review focuses on selected cytokines, including interferon-α, interleukin (IL)-2, IL-15, IL-21, and IL-12, in both preclinical studies and clinical applications. We review next-generation designs of these cytokines that improve half-life, tumor targeting, and antitumor efficacy. We also present our perspectives on the development of new strategies to potentiate cytokine-based immunotherapy.
Behaviour change interventions to increase physical activity in hospitalised patients: a systematic review, meta-analysis and meta-regression
Authors: Taylor Nicholas F , Harding Katherine E , Dennett Amy M , Febrey Samantha , Warmoth Krystal , Hall Abi J , Prendergast Luke A , Goodwin Victoria A 
Published: June 2021

AbstractBackgroundLow physical activity levels are a major problem for people in hospital and are associated with adverse outcomes.ObjectiveThis systematic review, meta-analysis and meta-regression aimed to determine the effect of behaviour change interventions on physical activity levels in hospitalised patients.MethodsRandomised controlled trials of behaviour change interventions to increase physical activity in hospitalised patients were selected from a database search, supplemented by reference list checking and citation tracking. Data were synthesised with random-effects meta-analyses and meta-regression analyses, applying Grades of Recommendation, Assessment, Development and Evaluation criteria. The primary outcome was objectively measured physical activity. Secondary measures were patient-related outcomes (e.g. mobility), service level outcomes (e.g. length of stay), adverse events and patient satisfaction.ResultsTwenty randomised controlled trials of behaviour change interventions involving 2,568 participants (weighted mean age 67 years) included six trials with a high risk of bias. There was moderate-certainty evidence that behaviour change interventions increased physical activity levels (SMD 0.34, 95% CI 0.14–0.55). Findings in relation to mobility and length of stay were inconclusive. Adverse events were poorly reported. Meta-regression found behaviour change techniques of goal setting (SMD 0.29, 95% CI 0.05–0.53) and feedback (excluding high risk of bias trials) (SMD 0.35, 95% CI 0.11–0.60) were independently associated with increased physical activity.ConclusionsTargeted behaviour change interventions were associated with increases in physical activity in hospitalised patients. The trials in this review were inconclusive in relation to the patient-related or health service benefits of increasing physical activity in hospital.
Pragmatics of Democracy: A Political Theory of African American Literature before Emancipation
Authors: Jones Douglas A 
Published: June 2021

Abstract
“Pragmatics of Democracy: A Political Theory of African American Literature before Emancipation” reads scenes of embodied experience in early African American literary culture to theorize how persons come to regard democratic cultures as productive of the most excellent forms of life. The book proposes a typology of these iterative bodily events which dispose persons toward democratic subjectivity: ecstasy, violence, impersonality, respectability, and autonomy.
[E]arly African American narratives offer speculations, categories, and hermeneutics concerning democracy grounded in Black life amid new-world chattel slavery that sometimes contradict, sometimes complement those that prevailed in early US political thought.
Going Underground: Race, Space, and the Subterranean in the Nineteenth-Century US
Authors: Cohen Lara Langer 
Published: June 2021

Abstract
This essay examines the emergence of the underground as a figure for being in but not of a rotten world. First popularized by newspaper coverage of the Underground Railroad in the 1840s, the underground offered a metaphor for subversive activity that has remained central to our political vocabulary. My forthcoming book, Going Underground: Race, Space, and the Subterranean in the Nineteenth-Century US, excavates the long history of this now-familiar idea, but most of all, it seeks out versions of the underground that got left behind along the way. To do so, it traces images of the subterranean from David Walker’s Appeal (1829) to Pauline Hopkins’s Of One Blood (1902–03), and from anarchist periodicals and exposés of the urban underworld to the initiation rites of secret societies and manuals for sex magic. In this essay, an adaptation of the book’s introduction, I focus on how early visions of the underground were shaped by literal subterranean spaces and associations with racialized Blackness. I argue that nineteenth-century undergrounds can expand our thinking about political agitation outside the familiar framework of resistance and suggest some new—which is to say old—modes of world-making and world-breaking for a time when this world feels increasingly untenable.
At times going underground is an effect of subjugation, but at other times it is an act of refusal. Some undergrounds are sites to carve out other worlds … and some are sites to prepare the destruction of this one.
Deer exclusion unveils abiotic filtering in forest understorey plant assemblages
Authors: Chollet Simon , Baltzinger Christophe , Maillard Morgane , Martin Jean-Louis 
Published: June 2021

Abstract

Background and Aims
The role of deer (family Cervidae) in ecosystem functioning has traditionally been neglected by forest ecologists due to the animal’s scarcity in most parts of the northern hemisphere. However, the dramatic rebound in deer populations throughout the 20th century has brought deer browsing to the forefront of forest ecological questioning. Today there is ample evidence that deer affect tree regeneration, understorey plant and animal diversity, and even litter decomposition. However, the mechanisms underlying the effects of deer on forest ecosystems remain unclear. Among others, the relative role of abiotic factors versus biotic interactions (e.g. herbivory) in shaping plant assemblages remains largely unknown.

Methods
We used a large-scale experiment with exclosures distributed along abiotic gradients to understand the role of black-tailed deer (Odocoileus hemionus sitchensis) on the forest understorey on the Haida Gwaii archipelago (western Canada), a unique context where most of the key ecological effects of deer presence have already been intensively studied.

Key Results
Our results demonstrate that 20 years of deer exclusion resulted in a clear increase in vascular plant richness, diversity and cover, and caused a decline in bryophyte cover. Exclusion also unveiled abiotic (i.e. soil water availability and fertility) filtering of plant assemblages that would otherwise have been masked by the impact of abundant deer populations. However, deer exclusion did not lead to an increase in beta diversity, probably because some remnant species had a competitive advantage to regrow after decades of over browsing.

Conclusions
We demonstrated that long-term herbivory by deer can be a dominant factor structuring understorey plant communities that overwhelms abiotic factors. However, while exclosures prove useful to assess the overall effects of large herbivores, the results from our studies at broader scales on the Haida Gwaii archipelago suggest that exclosure experiments should be used cautiously when inferring the mechanisms at work.
EpitopeVec: linear epitope prediction using deep protein sequence embeddings
Authors: Bahai Akash , Asgari Ehsaneddin , Mofrad Mohammad R K , Kloetgen Andreas , McHardy Alice C 
Published: June 2021

Abstract

Motivation
B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%.

Results
We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

Availability and implementation
The software is available at https://github.com/hzi-bifo/epitope-prediction.

Supplementary information
Supplementary data are available at Bioinformatics online.
Identifying driver genes for individual patients through inductive matrix completion
Authors: Zhang Tong , Zhang Shao-Wu , Li Yan 
Published: June 2021

Abstract

Motivation
The driver genes play a key role in the evolutionary process of cancer. Effectively identifying these driver genes is crucial to cancer diagnosis and treatment. However, due to the high heterogeneity of cancers, it remains challenging to identify the driver genes for individual patients. Although some computational methods have been proposed to tackle this problem, they seldom consider the fact that the genes functionally similar to the well-established driver genes may likely play similar roles in cancer process, which potentially promotes the driver gene identification. Thus, here we developed a novel approach of IMCDriver to promote the driver gene identification both for cohorts and individual patients.

Results
IMCDriver first considers the well-established driver genes as prior information, and adopts the using multi-omics data (e.g. somatic mutation, gene expression and protein–protein interaction) to compute the similarity between patients/genes. Then, IMCDriver prioritizes the personalized mutated genes according to their functional similarity to the well-established driver genes via Inductive Matrix Completion. Finally, IMCDriver identifies the highly rank-ordered genes as the personalized driver genes. The results on five cancer datasets from the Cancer Genome Consortium show that our IMCDriver outperforms other existing state-of-the-art methods both in the cohort and patient-specific driver gene identification. IMCDriver also reveals some novel driver genes that potentially drive cancer development. In addition, even for the driver genes rarely mutated among a population, IMCDriver can still identify them and prioritize them with high priorities.

Availability and implementation
Code available at https://github.com/NWPU-903PR/IMCDriver.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ancestral smoking and developmental outcomes: a review of publications from a population birth cohort
Authors: Golding Jean , Pembrey Marcus , Iles-Caven Yasmin , Watkins Sarah , Suderman Matthew , Northstone Kate 
Published: June 2021

AbstractThe adverse effects on the child of maternal smoking in pregnancy is well-recognized, but little research has been carried out on the possible non-genetic effects of ancestral smoking prior to the pregnancy including parental initiation of cigarette smoking in their own childhoods or a grandmother smoking during pregnancy. Here, we summarize the studies that have been published mainly using data from the Avon Longitudinal Study of Parents and Children. We demonstrate evidence that ancestral smoking prior to or during pregnancy can often be beneficial for offspring health and both ancestor- and sex-specific. More specifically, we report evidence of (i) adverse effects of the father starting to smoke pre-puberty on his son’s development; (ii) beneficial effects on the grandson if his maternal grandmother had smoked in pregnancy; and (iii) mainly adverse effects on the granddaughter when the paternal grandmother had smoked in pregnancy. The ancestor- and sex-specificity of these results are consistent with earlier studies reporting associations of health and mortality with ancestral food supply in their parents’ and grandparents’ pre-pubertal childhoods.
Bayesian adaptive model selection design for optimal biological dose finding in phase I/II clinical trials
Authors: Lin Ruitao , Yin Guosheng , Shi Haolun 
Published: June 2021

SummaryIdentification of the optimal dose presents a major challenge in drug development with molecularly targeted agents, immunotherapy, as well as chimeric antigen receptor T-cell treatments. By casting dose finding as a Bayesian model selection problem, we propose an adaptive design by simultaneously incorporating the toxicity and efficacy outcomes to select the optimal biological dose (OBD) in phase I/II clinical trials. Without imposing any parametric assumption or shape constraint on the underlying dose–response curves, we specify curve-free models for both the toxicity and efficacy endpoints to determine the OBD. By integrating the observed data across all dose levels, the proposed design is coherent in dose assignment and thus greatly enhances efficiency and accuracy in pinning down the right dose. Not only does our design possess a completely new yet flexible dose-finding framework, but it also has satisfactory and robust performance as demonstrated by extensive simulation studies. In addition, we show that our design enjoys desirable coherence properties, while most of existing phase I/II designs do not. We further extend the design to accommodate late-onset outcomes which are common in immunotherapy. The proposed design is exemplified with a phase I/II clinical trial in chronic lymphocytic leukemia.
Policing’s New Vulnerability Re-Envisioning Local Accountability in an Era of Global Outrage
Authors: Goldsmith Andrew , McLaughlin Eugene 
Published: June 2021

Abstract
In this paper, we argue that globally networked activism such as that triggered by the murder of George Floyd has dramatically amplified, and consequently rendered processes of police reform and accountability more vulnerable to exogenous influences. Recently witnessed activism in this sphere derives much of its significance from the ability to leverage the latest audio-visual technologies and social media platforms. The Black Lives Matter protests demonstrate how these technologies and platforms make flashpoint images of violent policing visible to diverse, global audiences in an extraordinary manner. Using the examples of Australia and the United Kingdom, we argue that these viral images have the capacity to ‘collapse contexts’ and radically disrupt policing in the places to which they migrate. The complicated impact of migrating flashpoint images of violent policing from ‘over there’ to ‘over here’ necessitates urgent analysis and debate.
Transmitted Drug Resistance Among Human Immunodeficiency Virus (HIV)-1 Diagnoses in the United States, 2014–2018
Authors: McClung R Paul , Oster Alexandra M , Ocfemia M Cheryl Bañez , Saduvala Neeraja , Heneine Walid , Johnson Jeffrey A , Hernandez Angela L 
Published: June 2021

Abstract

Background
Transmitted human immunodeficiency virus (HIV) drug resistance can threaten the efficacy of antiretroviral therapy and pre-exposure prophylaxis (PrEP). Drug-resistance testing is recommended at entry to HIV care in the United States and provides valuable insight for clinical decision making and population-level monitoring.

Methods
We assessed transmitted drug-resistance–associated mutation (TDRM) prevalence and predicted susceptibility to common HIV drugs among US persons with HIV diagnosed during 2014–2018 who had a drug resistance test performed ≤3 months after HIV diagnosis and reported to the National HIV Surveillance System and who resided in 28 jurisdictions where ≥20% of HIV diagnoses had an eligible sequence during this period.

Results
Of 50 747 persons in the analysis, 9616 (18.9%) had ≥1 TDRM. TDRM prevalence was 0.8% for integrase strand transfer inhibitors (INSTIs), 4.2% for protease inhibitors, 6.9% for nucleoside reverse transcriptase inhibitors (NRTIs), and 12.0% for non-NRTIs. Most individual mutations had a prevalence &lt;1.0% including M184V (0.9%) and K65R (0.1%); K103N was most prevalent (8.6%). TDRM prevalence did not increase or decrease significantly during 2014–2018 overall, for individual drug classes, or for key individual mutations except for M184V (12.9% increase per year; 95% confidence interval, 5.6–20.6%).

Conclusions
TDRM prevalence overall and for individual drug classes remained stable during 2014–2018; transmitted INSTI resistance was uncommon. Continued population-level monitoring of INSTI and NRTI mutations, especially M184V and K65R, is warranted amidst expanding use of second-generation INSTIs and PrEP.
Open or endovascular treatment of downstream thoracic or thoraco-abdominal aortic pathology after frozen elephant trunk: perioperative and mid-term outcomes
Authors: Loschi Diletta , Melloni Andrea , Grandi Alessandro , Baccellieri Domenico , Monaco Fabrizio , Melissano Germano , Chiesa Roberto , Bertoglio Luca 
Published: June 2021

Abstract

OBJECTIVES
The aim of this study was to evaluate the outcomes of open and endovascular treatment of downstream thoracic or thoraco-abdominal aortic pathology in patients who underwent previous frozen elephant trunk (FET).

METHODS
Data were retrieved to evaluate mortality, cardiac, pulmonary, cerebrovascular, renal and spinal cord major adverse events, early- and mid-term reintervention and survival rates. The Society for Vascular Surgery endovascular reporting standards were used.

RESULTS
From 2011 to 2020, 48 patients (36 males, median age 60 years) underwent downstream aortic repair at a median of 18 months (interquartile range: 6–57) after the initial FET. Twenty-eight patients (58.3%) received open and 20 (41.7%) endovascular repair. The overall 30-day mortality was 6.3% and the initial clinical success was 88%, with no inter-group differences (P = 0.22 and 0.66 respectively). Six spinal cord deficits were recorded (13%): 3 (6.3%) were permanent. The major adverse events incidence was lower in the endovascular cohort [4 (20%) vs 14 (50%); P = 0.047], mainly due to a lower rate of grade ≥2 respiratory complications (5% vs 42.9%; P = 0.004). Assisted primary clinical success at 5 years was higher in the endovascular group (95% vs 68%, P = 0.022); freedom from reintervention at competing risk analysis (P = 0.3) and overall survival at Kaplan–Meier curves (log-rank P = 0.29) were similar.

CONCLUSIONS
Downstream aortic repair after FET is feasible with both open and endovascular repair with acceptable mortality and permanent paraplegia rates. The endovascular approach has potential perioperative and mid-term advantages, but long-term durability has to be further investigated in larger cohorts.