bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of the secondary distribution of HIV self-testing with and without monetary incentives among Men Who Have Sex with Men living with HIV in China: study protocol for a randomized controlled trial
Authors: Hu Siyue , Lu Ying , He Xi , Zhou Yi , Wu Dan , Tucker Joseph D. , Yang Bin , Tang Weiming 
Published: February 2023

Abstract
Background
The HIV epidemic is still expanding among men who have sex with men (MSM) in China, but HIV testing rates remain suboptimal. Network-based interventions, such as secondary distribution, have shown promise to expand HIV self-testing (HIVST) among partners of MSM living with HIV (MLWH) but have not been widely implemented. Monetary incentives could enhance the secondary distribution of HIVST in some settings. We will conduct a randomized controlled trial to examine the effectiveness of monetary incentives in expanding the secondary distribution of HIVST among MLWH in China.
Methods
We will recruit 200 eligible participants at three antiretroviral therapy (ART) clinics in China. Participants are eligible if they are 18 years of age or over, assigned as male at birth, have had anal sex with men, are living with HIV, are willing to apply for the HIVST kit at ART clinics, and are willing to provide personal contact information for follow-up. Eligible participants will be randomly assigned in a 1:1 ratio to one of two groups: standard secondary distribution group and secondary distribution group with monetary incentives. Participants (defined as "index") will distribute the HIVST kits to members of their social network (defined as "alter") and will be required to complete a baseline survey and a 3-month follow-up survey. All alters will be encouraged to report their testing results by taking photos of used kits and completing an online survey. The primary study outcomes will compare the mean number of alters and newly-tested alters motivated by each index participant in each group. Secondary study outcomes will include the mean number of alters who tested positive, the cost per person tested, and the cost per HIV diagnosed for each group.
Discussion
Few studies have evaluated interventions to enhance the implementation of secondary distribution. Our study will provide information on the effectiveness of monetary incentives in expanding HIVST secondary distribution among MLWH. The findings of this trial will contribute to implementing HIVST secondary distribution services among MLWH in China and facilitating HIV case identifications.
Trial registration
Chinese Clinical Trial Registry ChiCTR2200064517; http://www.chictr.org.cn/showproj.aspx?proj=177896. Registered on 10th October 2022.
Analyzing the Relationship Between Gene Expression and Phenotype in Space-Flown Mice Using a Causal Inference Machine Learning Ensemble
Authors: Casaletto James , Scott Ryan , Myrick Makenna , Mackintosh Graham , Chok Hamed , Saravia-Butler Amanda , Hoarfrost Adrienne , Galazka Jonathan , Sanders Lauren , Costes Sylvain 
Published: February 2023

Abstract
Spaceflight has several detrimental effects on human and rodent health. For example, liver dysfunction is a common phenotype observed in space-flown rodents, and this dysfunction is partially reflected in transcriptomic changes. Studies linking transcriptomics with liver dysfunction rely on tools which exploit correlation, but these tools make no attempt to disambiguate true correlations from spurious ones. In this work, we use a machine learning ensemble of causal inference methods called the Causal Research and Inference Search Platform (CRISP). It was specifically developed to predict causal features of a binary response variable in high-dimensional input. We used CRISP to search gene expression data for genes truly correlated with a lipid density phenotype using transcriptomic and histological data from the NASA Space Biology Open Science Data Repositories (OSDR). Our approach identified genes and molecular targets not predicted by previous traditional system biology approaches. These genes are likely to play a pivotal role in the liver dysfunction observed in space-flown rodents, and this work opens the door to identifying novel countermeasures for space travel.
Deep learning-based image-analysis identifies a DAT-negative subpopulation of dopaminergic neurons in the lateral Substantia nigra.
Authors: Burkert Nicole , Roy Shoumik , Häußler Max , Wuttke Dominik , Müller Sonja , Wiemer Johanna , Hollmann Helene , Ramirez-Franco Jorge , Benkert Julia , Fauler Michael , Duda Johanna , Pötschke Christina , Goillard Jean-Marc , Münchmeyer Moritz , Parlato Rosanna , Liss Birgit 
Published: February 2023

Abstract
Here we present a deep learning-based image analysis platform (DLAP), tailored to autonomously quantify numbers of neuronal subtypes in defined areas, and of fluorescence signals, derived from RNAscope probes or immunohistochemistry, in defined cellular compartments. As proof-of-principle, we utilized DLAP to analyse subtypes of dopaminergic midbrain neurons in mouse and human brain-sections. These neurons modulate complex behaviour like voluntary movement, and are differentially affected in Parkinson’s and other diseases. DLAP allows the analysis of large cell numbers from different species, and facilitates the identification of small cellular subpopulations, based on differential mRNA- or protein-expression, and anatomical location. Using DLAP, we identified a small subpopulation of dopaminergic midbrain neurons (~5%), mainly located in the very lateral Substantia nigra (SN), that was immunofluorescence-negative for the plasmalemma dopamine transporter (DAT), with ~30% smaller cell-bodies, and a ~4-fold higher likelihood of calbindin-d28k co-expression. These results have important implications, as DAT is crucial for dopamine-signalling, and its expression is commonly used as marker for dopaminergic SN neurons.
Long-term effective remediation of black-odorous water via regulating calcium nitrate sustained-release
Authors: Wan Rui , Zha Yunyi , Wu Mengqi , Li Xiaoxiao , Yang Haifeng , Liu Hongming 
Published: February 2023

Abstract
Nitrate addition was reported as the cost-effective method for remediating black-odorous water, which was induced by the deficiency of electron acceptors. However, the excessive release of nitrate and nitrite and lack of long-term effectiveness caused by directly dosing nitrate method significantly limited its application. Herein, we constructed a nitrate sustained-release ecoN-concrete, in which calcium nitrate (Ca(NO3)2) was dosed in the concrete revetment, to remediate black-odorous water. Identically, chemical oxygen demand (COD), turbidity, ammonia, phosphates, and sulfate were significantly removed after loading black-odorous water into an ecoN-concrete-contained reactor, and its removal efficiency was largely dependent on Ca(NO3)2 dosage. Meanwhile, the released nitrate was only accounted for 25% of the total dosage and nitrite was lower than 1.5 mg/L via 14 days cultivation. After three recycles, the removal efficiencies of COD and turbidity by ecoN-concrete were still higher than 85% indicating this concrete was good at nitrate sustainable release and controlling water re-blackening and re-stinking in suit. Further investigation illustrated that the ecoN-concrete (1) decreased the abundance of Desulfovibrio, Desulfomonile, and Desulforhabdus in the phylum of Desulfobacterota to alleviate the odorous gases production, (2) significantly increased the abundance of Bacillus and Thermomonas, which utilized the released-nitrate to consume organic matters and ammonia. This study provided an artful Ca(NO3)2 dosing strategy and long-term effective method for black-odorous water remediation.
Systematic Analysis of Levels of Evidence Supporting American Academy of Ophthalmology Preferred Practice Pattern Guidelines, 2012-2021
Authors: Song Ailin , Lusk Jay B. , Kuo Anthony N. , Muir Kelly W. , Stinnett Sandra S. , Borkar Durga S. 
Published: February 2023

Abstract
Background
Despite the increased emphasis on evidence-based medicine, the current state of evidence behind ophthalmology clinical practice guidelines is unknown. The purpose of this systematic analysis was to understand the levels of evidence (LOE) supporting American Academy of Ophthalmology (AAO) Preferred Practice Pattern (PPP) guidelines, assess changes over time, and compare LOE across ophthalmology subspecialties.
Methods
All current PPP guidelines and their immediate predecessors were comprehensively reviewed to identify all recommendations with LOE provided (I [randomized controlled trials], II [case-control or cohort studies], and III [nonanalytic studies]).
Results
Twenty-three out of 24 current PPPs had a prior edition. Among the PPPs with a prior edition, the number of recommendations with LOE decreased from 1254 in prior PPPs to 94 in current PPPs. The number of recommendations with LOE I decreased from 114 to 83, LOE II decreased from 147 to 2, and LOE III decreased from 993 to 9. However, the proportion of LOE I recommendations increased from 9–88%, driven by a disproportionate decrease in reporting of evidence lower than LOE I. Subgroup analysis by subspecialty showed similar trends (LOE I recommendations in prior PPPs vs current PPPs: retina: 57 [12%] vs 19 [100%]; cornea: 33 [17%] vs 24 [100%]; glaucoma: 9 [23%] vs 17 [100%]; cataract: 13 [17%] vs 18 [100%]).
Conclusions
Trends in LOE reporting in PPP guidelines indicate an increasing emphasis on evidence from randomized controlled trials from 2012 to 2021. The decline in the number of recommendations with LOE reported suggests an area for improvement in future guidelines as the presence of LOE is crucial to facilitate interpretation of clinical practice guidelines.
Causes of sudden death in a young (&lt;40 years-old) South European population: a postmortem study
Authors: Carrington Mafalda , de Gouveia Rosa Henriques Henriques , Teixeira Rogério , Corte-Real Francisco , Gonçalves Lino , Providencia Rui 
Published: February 2023

Abstract
Aims
To describe the annual incidence and the leading causes of sudden non-cardiac and cardiac death (SCD) in children and young adult Portuguese population.
Methods
We retrospectively reviewed autopsy of sudden unexpected deaths reports from the Portuguese National Institute of Legal Medicine and Forensic Sciences’ database, between 2012 and 2016, for the central region of Portugal, Azores and Madeira (ages 1–40: 26% of the total population).
Results
During a 5-year period, 159 SD were identified, corresponding to an annual incidence of 2,4 (95%confidence interval, 1,5 − 3,6) per 100.000 people-years. Victims had a mean age of 32 ± 7 years-old, and 72,3% were male. There were 70,4% cardiac, 16,4% respiratory and 7,5% neurologic causes of SD. The most frequent cardiac histopathological diagnosis was atherosclerotic coronary artery disease (CAD) (33,0%). There were 15,2% victims with left ventricular hypertrophy, with a diagnosis of hypertrophic cardiomyopathy only possible in 2,7%. The prevalence of cardiac pathological findings of uncertain significance was 30,4%.
Conclusions
The annual incidence of SD was low. Atherosclerotic CAD was diagnosed in 33,0% victims, suggesting the need to intensify primary prevention measures in the young. The high prevalence of pathological findings of uncertain significance emphasizes the importance of molecular autopsy and screening of first-degree relatives.
The prognostic role of coagulation markers in the progression and metastasis of laryngeal squamous cell carcinoma
Authors: Huang Qiongling , Chen Jing , Huang Yanjun , Xiong Yu , Zhou Jiao , Zhang Yizheng , Lu Ming , Hu Weipeng , Zheng Feng , Zheng Chaohui 
Published: February 2023

Abstract
Background
This study explored the prognostic role of coagulation markers in the progression and metastasis of laryngeal squamous cell carcinoma (LSCC).
Methods
Coagulation markers of patients with LSCC receiving surgery in our institute from January 2013 to May 2022 were retrospectively analyzed and compared with those of contemporary patients with benign laryngeal diseases. The prognostic value in the progression and metastasis of LSCC was determined using receiver operating characteristic curve analysis. The relationship between clinicopathological features of LSCC and coagulation parameters was analyzed with the chi-square and rank sum tests.
Results
303 patients with LSCC and 533 patients with benign laryngeal diseases were included in the present analysis. Compared to the control group, prothrombin time (PT) (p < 0.001), activated partial thromboplastin time (APTT) (p = 0.001), and Fib (p < 0.001) in patients with LSCC were significantly higher, while mean platelet volume (MPV) (p < 0.001) was significantly shorter. Significant increases were detected in PT (Z = 14.342, p = 0.002), Fib (Z = 25.985, p < 0.001), platelet count (PC) (Z = 12.768, p = 0.005), PCT (Z = 9.178, p = 0.027), MPV (F = 2.948, p = 0.033) in T4 stage. Fib (Z = 25.832, p < 0.001), PC (Z = 23.842, p < 0.001), and PCT (Z = 20.15, p < 0.001) in N1 and N3 stages were significantly higher than in N0 stage. PT (Z = 12.174, p = 0.007), Fib (Z = 23.873, p < 0.001), PC (Z = 17.785, p < 0.001), and PCT (Z = 14.693, p = 0.002) were significantly higher in stage IV than in stage I and II. APTT (Z=-1.983, p = 0.047), Fib (Z=-2.68, p = 0.007), PC (Z=-2.723, p = 0.006), and PCT (Z=-2.592, p = 0.01) increased significantly when the tumor invaded neurovascular tissue.
Conclusions
Coagulation markers have the potential to act as biomarkers for predicting pathological features of LSCC. The high level of Fib was helpful for the diagnosis of LSCC and the detection of advanced LSCC.
Elevation in white blood cell count and development of hyper LDL cholesterolemia: a retrospective observational study
Authors: Okutsu Shota , Kato Yoshifumi , Takeoka Hiroaki , Funakoshi Shunsuke , Maeda Toshiki , Yoshimura Chikara , Kawazoe Miki , Satoh Atsushi , Tada Kazuhiro , Takahashi Koji , Ito Kenji , Yasuno Tetsuhiko , Fujii Hideyuki , Mukoubara Shigeaki , Saku Keijiro , Kodama Shohta , Kawanami Daiji , Masutani Kosuke , Arima Hisatomi , Nabeshima Shigeki 
Published: February 2023

Abstract
Purpose : We investigated the association between white blood cell (WBC) count and future development of hyper- low-density lipoprotein (LDL) cholesterolemia in general Japanese population.
Patients and methods: This is a retrospective study using data of annual health examinations for residents of Iki City, Japan. Participants and Intervention : A total of 3312 participants (aged ≥30 years), who did not have hyper-LDL cholesterolemia at baseline, were registered for the present analysis. Primary outcome was incidence of hyper-LDL cholesterolemia (LDL cholesterol levels of ≥3.62 mmol /L and/or use of lipid lowering drugs).
Results: During an averate follow-up of 4.6 years, development of hyper-LDL cholesterolemia was observed among 698 participants (incidence 46.8 per 1,000 person-years). The incidence of hyper-LDL cholesterolemia increased with elevation of leukocyte count (1st quartile group : 38.5, 2nd quartile group : 47.7, 3rd quartile group : 47.3, and 4th quartile group : 52.4 per 1,000 person-years, P for trend = 0.012). Statistically significant associations were also observed after adjusting for age, gender, smoking, alcohol intake, leisure-time exercise, obesity, hypertension and diabetes: hazard ratio 1.24 (95% confidence interval 0.99 to 1.54) for 2nd quartile group, 1.29 (1.03 to 1.62) for 3rd quartile group and 1.39 (1.10-1.75) for 4th quartile group, compared with 1st quartile group (P for trend = 0.006).
Conclusion : Increased WBC count was related to incidence of hyper-LDL cholesterolemia in general Japanese population.
Clinical characteristics and outcome of COVID-19 patients with non cystic fibrosis bronchiectasis
Authors: Mohamed-Hussein Aliae , Shaddad Ahmad , Hashem Maiada , Okasha Maha 
Published: February 2023

Abstract
Introduction: Non cystic fibrosis bronchiectasis is an uncommon respiratory disease and was described as a rare imaging feature of COVID-19 infection, but no published studies are reporting the clinical course and outcome of coexisting COVID-19 and confirmed cases of bronchiectasis during acute stage. The aim of this study was to assess the course and outcome of COVID-19 infection in bronchiectasis patient.
Patients and methods: A cross-sectional study including 411 COVID-19 confirmed cases that were examined by high resolution computed tomography of the chest during acute phase (4 weeks) of the infection. They were divided into Group A: COVID-19 patients without bronchiectasis (n=400) and Group B included COVID-19 patients with preexisting clinical and radiologic evidence of bronchiectasis (n=11).
Results: Patients with preexisting chronic bronchiectasis (Grup B) had significantly higher cough score, frequency of colored sputum and mMRC score, respiratory distress (p< 0.001) and respiratory failure (p= 0.02) than those without bronchiectasis. They also had the higher frequency of ICU’s admission (p< 0.001), need to non-invasive (p= 0.01), and invasive mechanical ventilation (p= <0.001), duration of mechanical ventilation, ICU’s stay and overall hospital stay (p<0.001). Death rate was also statistically significantly higher in Group B compared to Group A (p= 0.04).
Conclusion: Concomitant bronchiectasis increases disease burden in COVID-19 patients. It increased the severity of presenting symptoms and was associated with worse clinical outcome (ICU admission, need for ventilator support) and mortality.
Transformer-based Deep Learning Empowers the Discovery of Self-Assembling Peptides with over Ten Trillion Sequence Quantities
Authors: Wang Jiaqi , Liu Zihan , Zhao Shuang , Xu Tengyan , Wang Huaimin , Li Stan , Li Wenbin 
Published: February 2023

Abstract
Self-assembling of peptides is essential for a variety of biological and medical applications. However, it is challenging to investigate the self-assembling properties of peptides within the complete sequence space due to the enormous sequence quantities. Here, we demonstrate that a Transformer-based deep learning model is effective in predicting the aggregation propensity (AP) of peptide systems, even for decapeptide and mixed pentapeptide systems with over ten trillion sequence quantities. Based on the predicted AP values, we are not only able to derive the aggregation laws for designing self-assembling peptides, but also reveal the transferability relation among the AP's of pentapeptides, decapeptides, and mixed pentapeptides, leading to discoveries of self-assembling peptides by concatenating or mixing, as consolidated by experiments. Our deep learning approach enables speedy, accurate, and thorough search and design of self-assembling peptides with the complete sequence space of oligopeptides, advancing peptide science by inspiring new biological and medical applications.
Estimating current and future range shifts of exotic species as a tool for protected-area threat assessment in Chile
Authors: Lira Erick , Núñez-Hidalgo Ignacio , Vásquez Alexis E. , Alaniz Alberto J , Carvajal Mario A , Vergara Pablo M 
Published: February 2023

Abstract
Although protected areas (PAs) are considered fundamental to the conservation of nature, exotic species (ES) impose challenges on their role as biodiversity reservoirs, especially under climate change scenarios. In this regard, PAs of temperate & non-tropical countries of the Southern Hemisphere, like Chile, may be particularly vulnerable to ES due to the high endemism plus the expense due to control programs of exotic species and of the environmental conditions suitable for them. Here, we evaluated how vulnerable PAs are to the exposure of some of the “100 of The World’s Worst Invasive Alien Species”, which include animals and plants introduced in Chile, by combining climate change scenarios and ecological niche modeling. We projected the niche requirement of these exotic species on two alternative emission scenarios with varying levels of mitigation by 2050. We found that the central-southern and southern macro-regions are the most susceptible to be invaded in mainland Chile, with the occurrence of at least 80% of evaluated species. National Reserves (homologated with category IV IUCN) of the central and southern regions were the PAs most exposed sites to the spread of the evaluated species under climate change scenarios. These findings provide helpful evidence of the vulnerability of Chilean PAs and important insights into the need for urgent management intended to avoid future climate change-induced establishment of exotic species.
Adapting Tools of Causality to Analyze the Obesity Paradox
Authors: Mitra Prasenjit , Zhang Xinyuan (Cindy) , Heaton Connor 
Published: February 2023

Abstract
The prevailing sentiment in the general population is that a Body Mass Index (BMI) above desired levels leads to less than optimal health outcomes and increased likelihood of death. Recent medical studies, however, have found evidence that the opposite is true for a certain subset of the population, particularly those with a history of cardiovascular disease (CVD). These studies found that individuals with a BMI slightly above desired experience more optimal health outcomes compared to those with a BMI in the \textit{desired} range - a phenomenon known as the ``obesity paradox.'' However, these studies have primarily been performed using classical tools of probability and statistics. In this study, we apply tools appropriated from causal inference, with some loosened restrictions, to the age >= 65 population of the Kailuan dataset, a longitudinal dataset tracking almost 15,000 patients, 10,005 of which have a history of CVD , 4,641 have a BMI slightly above desired, 5,863 have a BMI in the desired range, and 317 a BMI slightly below desired. We ultimately find some evidence of the obesity paradox in this dataset.
Human health risk assessment of potentially toxic elements in vegetables irrigated with wastewater from an urban market drain in Zaria, Nigeria
Authors: Tanimu Yahuza , Lawal Khadijah , Ahmed Bilkisu 
Published: February 2023

Abstract
The use of wastewater for the irrigation of vegetables is on the increase because of its richness in nutrients and it reduces the pressure on available freshwater resources. Untreated wastewater may, however, be a source of contamination of the vegetables by potentially toxic elements, which may, in turn, constitute a health risk to consumers. Samples of seven vegetables: cabbage, onion bulbs, bitter leaf, jute mallow, spinach, tomato, and lettuce irrigated with wastewater were collected and analysed for potentially toxic elements using Energy Dispersive X-ray Fluorescence. The Target Hazard Quotient (THQ) and Health Index (HI) were determined based on the estimated daily metal intake of Cd, Ni, Pb, Zn, Cu, Fe Mg, and Mn through the consumption of these vegetables. Cancer Risk was assessed for Cd, Ni, and Pb. Except for Mg, for which no guideline value was found for vegetables, the concentration of Cu in cabbage and Mn in tomato were found to be within the permissible limit, whereas Cd, Ni, Pb Zn, and Fe were found to be above the permissible limits of the FAO/WHO in all the vegetables. The Target Hazard Quotient (THQ) shows that adult consumers of all seven vegetables are at risk of non-carcinogenic toxicity of Cd, Ni, and Pb, while in children, the risk extends to Zn, Cu, Fe, and Mn (with tomato as the only exception for Mn). The Health Index being greater than 1in all vegetables means there is a non-carcinogenic risk health risk associated with the consumption of all vegetables by children and adults. The Target cancer Risk shows that adults are exposed to cancer risk from the consumption of all the vegetables due to Ni and Cd contamination (except onion for cadmium), while in children, the risk extends to Pb (except for onion). The consumption of vegetables irrigated with untreated wastewater from the Sabon Gari market drain is an exposure route to potentially toxic elements such as Cd, Ni, Pb, Zn, Cu, Fe, and Mn, with resultant non-carcinogenic and carcinogenic health risks. These health risks were found to be higher in children.