bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salivary biomarkers associated with the progression of disease in people living with HIV: A scoping review protocol
Authors: Prasad Priyanka , D’Souza Viola , Mithra Prasanna , Radhakrishnan Raghu 
Published: September 2021

Background: Biomarkers are measurable indicators of normal biological processes, which provide an objective assessment of the physiologic state of living systems. Saliva contains several biomarkers that serve as a diagnostic tool in health and disease. Evaluation of a multitude of salivary components could potentially predict the clinical outcome. This is especially critical in a chronic, potentially life-threatening condition like human immunodeficiency virus (HIV) infection. Scrupulous evaluation of relevant biomarkers could facilitate the early detection of HIV, determine the stage of infection and monitor the disease progression. Currently, there is a paucity of validated biomarkers in saliva predicting the disease progression in people living with HIV. In this scoping review, we aim to provide an overview of the available evidence on salivary markers associated with the progression of disease in people living with HIV. Methods: The authors shall develop a tailored search strategy for each database using relevant keywords. We will search for eligible studies indexed in the following databases: MEDLINE, EMBASE, and the Cochrane Library, Cumulative Index to Nursing and Allied Health Literature (CINAHL) and gray literature. We will restrict the search to studies published in the English language. Following deduplication, all search results will be exported to the EPPI reviewer web, where two independent reviewers using a data extraction tool developed and pretested by the review authors will screen eligible studies. The result of this review will be reported using the Preferred Reporting Items for Systematic Review and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) checklist and reporting guidelines. Discussion: The proposed scoping review protocol will enable the identification and assessment of salivary biomarkers, which can predict disease progression in patients with HIV infection. The synthesis of evidence from this review will assist in improving our current understanding of biomarkers used to evaluate the progression of HIV infection.
A hybrid recommender system based on data enrichment on the ontology modelling
Authors: Chew Lit-Jie , Haw Su-Cheng , Subramaniam Samini 
Published: September 2021

Background: A recommender system captures the user preferences and behaviour to provide a relevant recommendation to the user. In a hybrid model-based recommender system, it requires a pre-trained data model to generate recommendations for a user. Ontology helps to represent the semantic information and relationships to model the expressivity and linkage among the data. Methods: We enhanced the matrix factorization model accuracy by utilizing ontology to enrich the information of the user-item matrix by integrating the item-based and user-based collaborative filtering techniques. In particular, the combination of enriched data, which consists of semantic similarity together with rating pattern, will help to reduce the cold start problem in the model-based recommender system. When the new user or item first coming into the system, we have the user demographic or item profile that linked to our ontology. Thus, semantic similarity can be calculated during the item-based and user-based collaborating filtering process. The item-based and user-based filtering process are used to predict the unknown rating of the original matrix. Results: Experimental evaluations have been carried out on the MovieLens 100k dataset to demonstrate the accuracy rate of our proposed approach as compared to the baseline method using (i) Singular Value Decomposition (SVD) and (ii) combination of item-based collaborative filtering technique with SVD. Experimental results demonstrated that our proposed method has reduced the data sparsity from 0.9542% to 0.8435%. In addition, it also indicated that our proposed method has achieved better accuracy with Root Mean Square Error (RMSE) of 0.9298, as compared to the baseline method (RMSE: 0.9642) and the existing method (RMSE: 0.9492). Conclusions: Our proposed method enhanced the dataset information by integrating user-based and item-based collaborative filtering techniques. The experiment results shows that our system has reduced the data sparsity and has better accuracy as compared to baseline method and existing method.
Combined Global and Local Search for Optimization with Gaussian Process Models
Authors: Meng Qun , Wang Songhao , Ng Szu Hui 
Published: September 2021

Gaussian process (GP) model based optimization is widely applied in simulation and machine learning. In general, it first estimates a GP model based on a few observations from the true response and then uses this model to guide the search, aiming to quickly locate the global optimum. Despite its successful applications, it has several limitations that may hinder its broader use. First, building an accurate GP model can be difficult and computationally expensive, especially when the response function is multimodal or varies significantly over the design space. Second, even with an appropriate model, the search process can be trapped in suboptimal regions before moving to the global optimum because of the excessive effort spent around the current best solution. In this work, we adopt the additive global and local GP (AGLGP) model in the optimization framework. The model is rooted in the inducing points based GP sparse approximations and is combined with independent local models in different regions. With these properties, the AGLGP model is suitable for multimodal responses with relatively large data sizes. Based on this AGLGP model, we propose a combined global and local search for optimization (CGLO) algorithm. It first divides the whole design space into disjoint local regions and identifies a promising region with the global model. Next, a local model in the selected region is fit to guide detailed search within this region. The algorithm then switches back to the global step when a good local solution is found. The global and local natures of CGLO enable it to enjoy the benefits of both global and local search to efficiently locate the global optimum. Summary of Contribution: This work proposes a new Gaussian process based algorithm for stochastic simulation optimization, which is an important area in operations research. This type of algorithm is also regarded as one of the state-of-the-art optimization algorithms for black-box functions in computer science. The aim of this work is to provide a computationally efficient optimization algorithm when the baseline functions are highly nonstationary (the function values change dramatically across the design space). Such nonstationary surfaces are very common in reality, such as the case in the maritime traffic safety problem considered here. In this problem, agent-based simulation is used to simulate the probability of collision of one vessel with the others on a given trajectory, and the decision maker needs to choose the trajectory with the minimum probability of collision quickly. Typically, in a high-congestion region, a small turn of the vessel can result in a very different conflict environment, and thus the response is highly nonstationary. Through our study, we find that the proposed algorithm can provide safer choices within a limited time compared with other methods. We believe the proposed algorithm is very computationally efficient and has large potential in such operational problems.
CO2-based hollow-core fiber Raman laser with high-pulse energy at 1.95  µm
Authors: Wang Yazhou , Schiess Olav Thorbjørn Sandberg , Amezcua-Correa Rodrigo , Markos Christos 
Published: September 2021

In this Letter, we present a high-pulse energy (

>

10

µ

J

) Raman laser at 1946 nm wavelength directly pumped with a 1533 nm custom-made fiber laser. The Raman laser is based on stimulated Raman scattering (SRS) in an 8 m carbon dioxide (

C
O

2

)-filled nested anti-resonant hollow-core fiber. The low-energy phonon emission combined with the inherent SRS process along the low-loss fiber allows the generation of high-pulse energy up to 15.4 µJ at atmospheric

C
O

2

pressure. The Raman laser exhibits good long-term stability and low relative intensity noise of less than 4%. We also investigate the pressure-dependent overlap of the Raman laser line with the absorption band of

C
O

2

at the 2 µm spectral range. Our results constitute a novel, to the best of our knowledge, and promising technology towards high-energy 2 µm lasers.
All-cause and cause-specific mortality during and following incarceration in Brazil: A retrospective cohort study
Authors: Liu Yiran E. , Lemos Everton Ferreira , Gonçalves Crhistinne Cavalheiro Maymone , de Oliveira Roberto Dias , Santos Andrea da Silva , do Prado Morais Agne Oliveira , Croda Mariana Garcia , de Lourdes Delgado Alves Maria , Croda Julio , Walter Katharine S. , Andrews Jason R. 
Published: September 2021

Background
Mortality during and after incarceration is poorly understood in low- and middle-income countries (LMICs). The need to address this knowledge gap is especially urgent in South America, which has the fastest growing prison population in the world. In Brazil, insufficient data have precluded our understanding of all-cause and cause-specific mortality during and after incarceration.

Methods and findings
We linked incarceration and mortality databases for the Brazilian state of Mato Grosso do Sul to obtain a retrospective cohort of 114,751 individuals with recent incarceration. Between January 1, 2009 and December 31, 2018, we identified 3,127 deaths of individuals with recent incarceration (705 in detention and 2,422 following release). We analyzed age-standardized, all-cause, and cause-specific mortality rates among individuals detained in different facility types and following release, compared to non-incarcerated residents. We additionally modeled mortality rates over time during and after incarceration for all causes of death, violence, or suicide. Deaths in custody were 2.2 times the number reported by the national prison administration (n = 317). Incarcerated men and boys experienced elevated mortality, compared with the non-incarcerated population, due to increased risk of death from violence, suicide, and communicable diseases, with the highest standardized incidence rate ratio (IRR) in semi-open prisons (2.4; 95% confidence interval [CI]: 2.0 to 2.8), police stations (3.1; 95% CI: 2.5 to 3.9), and youth detention (8.1; 95% CI: 5.9 to 10.8). Incarcerated women experienced increased mortality from suicide (IRR = 6.0, 95% CI: 1.2 to 17.7) and communicable diseases (IRR = 2.5, 95% CI: 1.1 to 5.0). Following release from prison, mortality was markedly elevated for men (IRR = 3.0; 95% CI: 2.8 to 3.1) and women (IRR = 2.4; 95% CI: 2.1 to 2.9). The risk of violent death and suicide was highest immediately post-release and declined over time; however, all-cause mortality remained elevated 8 years post-release. The limitations of this study include inability to establish causality, uncertain reliability of data during incarceration, and underestimation of mortality rates due to imperfect database linkage.

Conclusions
Incarcerated individuals in Brazil experienced increased mortality from violence, suicide, and communicable diseases. Mortality was heightened following release for all leading causes of death, with particularly high risk of early violent death and elevated all-cause mortality up to 8 years post-release. These disparities may have been underrecognized in Brazil due to underreporting and insufficient data.
Blood cancer care in a resource limited setting during the Covid-19 outbreak; a single center experience from Sri Lanka
Authors: Hewamana Saman , Skandarajah Thurairajah , Jayasinghe Chathuri , Deshapriya Samadhi , Senarathna Dhananjani , Arseculeratne Gehan , Harischandra Mahesh , Somasundaram Gnani , Srinivasan Vadivelu , Somiah Surjit , Munasinghe Nihal , Hewawasam Sangeetha , Ekanayake Lalith , Wadanamby Rohini , Galagoda Geethani , Lin Thet Thet , Balawardena Jayantha 
Published: September 2021

Background
The Covid-19 pandemic has caused significant morbidity and mortality among patients with cancer. Most countries employed measures to prevent spread of Covid-19 infection which include shielding, quarantine, lockdown, travel restrictions, physical distancing and the use of personal protective equipment. This study was carried out to assess the change in patient attendance and the efficacy of newly implemented strategies to mitigate the impact of Covid-19 on services at the Lanka Hospital Blood Cancer Centre (LHBCC) in Colombo, Sri Lanka.

Methodology
Telephone consultation, infection control, personal protective measures and emergency admission policy were implemented with the aim of having a Covid-19 free ward and to prevent cross-infections. This descriptive cross-sectional study was conducted with 1399 patient episodes (in-patient care or day-case review). We analysed patients treated as in-patient as well as day-case basis between 01st April 2020 and 31st December 2020.

Results
There were 977 day-case based episodes and 422 in-patient based episodes. There was a 14% drop in episode numbers compared to same period in 2019. There was no cross infection and no patients with Covid-19 related symptoms or positive test results entered the LHBCC during the study period.

Conclusion
Services in blood cancer care were maintained to prevent late stage presentation and adverse outcome. Measures implemented to prevent Covid-19 were effective to allow continuation of treatment. This study highlights the importance of implementing strict protocols, clinical screening, use of appropriate personal protective equipment in delivering blood cancer care during the Covid-19 pandemic. This is the only documented study relating to outcome and successful applicability of measures to prevent spread of Covid-19 infection and maintaining services among blood cancer patients in Sri Lanka.
COVID-19 in Brazilian cities: Impact of social determinants, coverage and quality of primary health care
Authors: Guedes Marcello Barbosa Otoni Gonçalves , de Assis Sanderson José Costa , Sanchis Geronimo José Bouzas , Araujo Diego Neves , Oliveira Angelo Giuseppe Roncalli Da Costa , Lopes Johnnatas Mikael 
Published: September 2021

Background
Brazil, as many other countries, have been heavily affected by COVID-19. This study aimed to analyze the impact of Primary health care and the family health strategy (FHS) coverage, the scores of the National Program for Improving Primary Care Access and Quality (PMAQ), and socioeconomic and social indicators in the number of COVID-19 cases in Brazilian largest cities.

Methods
This is an ecological study, carried out through the analysis of secondary data on the population of all Brazilian main cities, based on the analysis of a 26-week epidemiological epidemic week series by COVID-19. Statistical analysis was performed using Generalized Linear Models with an Autoregressive work correlation matrix.

Results
It was shown that greater PHC coverage and greater FHS coverage together with an above average PMAQ score are associated with slower dissemination and lower burden of COVID-19.

Conclusion
It is evident that cities with less social inequality and restrictions of social protection combined with social development have a milder pandemic scenario. It is necessary to act quickly on these conditions for COVID-19 dissemination by timely actions with high capillarity. Expanding access to PHC and social support strategies for the vulnerable are essential.
Spinoza’s Monism I: Ruling Out Eternal-Durational Causation
Authors: Primus Kristin 
Published: September 2021

AbstractIn this essay, I suggest that Spinoza acknowledges a distinction between formal reality that is infinite and timelessly eternal and formal reality that is non-infinite (i. e., finite or indefinite) and non-eternal (i. e., enduring). I also argue that if, in Spinoza’s system, only intelligible causation is genuine causation, then infinite, timelessly eternal formal reality cannot cause non-infinite, non-eternal formal reality. A denial of eternal-durational causation generates a puzzle, however: ifnoenduring thing – not even the sempiternal, indefinite individual composed of all finite, enduring things – is caused by the infinite, eternal substance, then how can Spinoza consistently hold that the one infinite, eternal substance is the cause ofallthings and thatallthings are modes of that substance? At the end of this essay, I sketch how Spinoza could deny eternal-durational causation while still holding that an infinite, eternal God is the cause of all things and that all things are modes. I develop the interpretation more in the companion essay.1 1 In “Spinoza’s Monism II,” in the next issue of this journal.
The development of autoverification system of lymphocyte subset assays on the flow cytometry platform
Authors: Shi Jue , Mu Run-Qing , Wang Pan , Geng Wen-Qing , Jiang Yong-Jun , Zhao Min , Shang Hong , Zhang Zi-Ning 
Published: September 2021

Abstract

Objectives
Peripheral blood lymphocyte subsets are important parameters for monitoring immune status; however, lymphocyte subset detection is time-consuming and error-prone. This study aimed to explore a highly efficient and clinically useful autoverification system for lymphocyte subset assays performed on the flow cytometry platform.

Methods
A total of 94,402 lymphocyte subset test results were collected. To establish the limited-range rules, 80,427 results were first used (69,135 T lymphocyte subset tests and 11,292 NK, B, T lymphocyte tests), of which 15,000 T lymphocyte subset tests from human immunodeficiency virus (HIV) infected patients were used to set customized limited-range rules for HIV infected patients. Subsequently, 13,975 results were used for historical data validation and online test validation.

Results
Three key autoverification rules were established, including limited-range, delta-check, and logical rules. Guidelines for addressing the issues that trigger these rules were summarized. The historical data during the validation phase showed that the total autoverification passing rate of lymphocyte subset assays was 69.65% (6,941/9,966), with a 67.93% (5,268/7,755) passing rate for T lymphocyte subset tests and 75.67% (1,673/2,211) for NK, B, T lymphocyte tests. For online test validation, the total autoverification passing rate was 75.26% (3,017/4,009), with 73.23% (2,191/2,992) for the T lymphocyte subset test and 81.22% (826/1,017) for the NK, B, T lymphocyte test. The turnaround time (TAT) was reduced from 228 to 167 min using the autoverification system.

Conclusions
The autoverification system based on the laboratory information system for lymphocyte subset assays reduced TAT and the number of error reports and helped in the identification of abnormal cell populations that may offer clues for clinical interventions.
Pancreatic lipase: why laboratory community does not take enough care of this clinically important test?
Authors: Pasqualetti Sara , Borrillo Francesca , Rovegno Leila , Panteghini Mauro 
Published: September 2021

Abstract
Although being the recommended laboratory test to diagnose acute pancreatitis, serum pancreatic lipase (LIP) is among the poorly standardized laboratory tests, and laboratory stakeholders often appear to not take enough care of the quality of its measurements. Here we discuss some important issues that, if not correctly managed and solved, make misdiagnosis of acute pancreatitis by using serum LIP a real possibility. First, the current unavailability of a suitable higher-order reference material to be used as common calibrator should be filled up to definitively improve the inter-method bias. Second, knowledge of the analytical characteristics that may explain the defective performance of LIP assays should be deepened. IVD manufacturers should be more explicit in providing this information, including description of their internal protocol for transferring LIP values from internal references to commercial calibrators. Third, recommended models for accurately estimating measurement uncertainty and reliably defining analytical performance specifications for LIP measurements should be applied. Finally, investments considering alternative options for measuring LIP (e.g., targeted to the development of automated LIP immunoassays) should be warranted. All involved stakeholders (standardization bodies, higher-order reference providers, in vitro diagnostics manufacturers, and laboratory professionals) should contribute to fill the existing gap.
Exploiting symmetries of high-level Petri games in distributed synthesis
Authors: Würdemann Nick 
Published: September 2021

AbstractDistributed Synthesis is the problem of automatically generating correct controllers for individual agents in a distributed system. Petri games model this problem by a game between two teams of players on a Petri net structure. Under some restrictions, Petri games can be solved by a reduction to a two player game. The concept of symmetries in Petri nets is closely related to high-level representations of Petri games. Applying symmetries to the states in the two-player game results in a significant state space reduction. We give an overview about (high-level) Petri games and the application of symmetries in this setting. We present ongoing work aiming to concisely describe solutions of Petri games by a high-level representation.
Backchannels in video-mediated ELF conversations: a case study
Authors: Fernández Polo Francisco Javier 
Published: September 2021

Abstract
There are few studies on backchannels in ELF and none concerns computer-mediated conversations. Backchannelling has been associated with good listenership and enhanced cooperativeness, an intrinsic feature of ELF. They would also play a key role in computer-mediated communication, maintaining a sense of affective equilibrium among participants and compensating for medium-related limitations. We analyze backchanneling in an ELF conversation between a Spanish female and a German male student from the Corpus of Video-Mediated English as a Lingua Franca Conversations (ViMELF). Backchanneling seems to be particularly intense in the opening and closing sections of the exchange, where interpersonal work is the most needed. While significant idiolectal differences are observed between the two participants, both show a marked preference for and a tendency to concentrate realizations on a few weak backchanneling forms, conferring the exchange a general impression of monotony and emotional flatness. Some backchanneling features in the exchange may be described as typical of ELF: backchannels tend to occur in moments when speakers sense that understanding may be compromised and are frequently complemented by supportive material reinforcing the speaker’s point. The analysis also reveals some characteristic awkward usage, with tokens which are clearly “overdone,” while others are too weak and disappointing or behave disruptively by occurring in unexpected positions and interrupting the flow of the conversation. Research on ELF video conversations is particularly timely given the recent surge in videoconferencing propitiated by the COVID pandemic, a tendency which is likely to stay in post-pandemic times.