bluuebunny/crossref_metadata_2025 huggingface dataset:
72-Hour transport recovery of antimicrobial resistant Neisseria gonorrhoeae isolates using the InTray® GC method
Authors: Paris Keely S. , Font Brandon , Mehta Sanjay R. , Huerta Irvin , Bristow Claire C.
Published: January 2022

Recovery of Neisseria gonorrhoeae isolates exposed to a range of transport times and temperatures was quantitatively assessed for two transport devices, BioMed Diagnostics’ InTray GC® and Copan Diagnostics’ Liquid Amies Elution Swab (ESwab®) Collection and Transport System. Respective devices were inoculated with N. gonorrhoeae, exposed to simulated transport conditions and spread-plated from serial dilutions in duplicates onto chocolate agar in order to count CFU (colony-forming units) in the range of 25–250. Baseline CFU/mL averages of time-zero transport for each device was compared to either 24 hour (Eswab) or 72 hour (InTray GC) CFU/mL average to assess recovery of six clinical isolates of N. gonorrhoeae, and differences showing no greater than a 3 log10 (± 10%) decline between comparative time points qualified as acceptable. Our findings suggest that the InTray GC system has the potential to transport clinical isolates for ≤72 hours with acceptable N. gonorrhoeae recovery.
Current forecast of COVID-19 in Mexico: A Bayesian and machine learning approaches
Authors: Prieto Kernel
Published: January 2022

The COVID-19 pandemic has been widely spread and affected millions of people and caused hundreds of deaths worldwide, especially in patients with comorbilities and COVID-19. This manuscript aims to present models to predict, firstly, the number of coronavirus cases and secondly, the hospital care demand and mortality based on COVID-19 patients who have been diagnosed with other diseases. For the first part, I present a projection of the spread of coronavirus in Mexico, which is based on a contact tracing model using Bayesian inference. I investigate the health profile of individuals diagnosed with coronavirus to predict their type of patient care (inpatient or outpatient) and survival. Specifically, I analyze the comorbidity associated with coronavirus using Machine Learning. I have implemented two classifiers: I use the first classifier to predict the type of care procedure that a person diagnosed with coronavirus presenting chronic diseases will obtain (i.e. outpatient or hospitalised), in this way I estimate the hospital care demand; I use the second classifier to predict the survival or mortality of the patient (i.e. survived or deceased). I present two techniques to deal with these kinds of unbalanced datasets related to outpatient/hospitalised and survived/deceased cases (which occur in general for these types of coronavirus datasets) to obtain a better performance for the classification.
Rational construction of controllable autoimmune diabetes model depicting clinical features
Authors: Yu Fan , Zhou Xian , Jin Xiang , Zhao Shushu , Zhao Gan , Jiang Sheng , Geng Shuang , Wang Bin
Published: January 2022

Through animal models, particularly non-obesity diabetes model (NOD), pathological understandings of human autoimmune diabetes have been gained. However, features of those mouse models and the human disease are not sufficiently analogous; it is therefore not unexpected that interventions based on the mouse data fail at an alarming rate in clinical settings. An improvised model that maximally resembles the real pathological course is highly desirable. Here we devised a ‘double-hit’ strategy, pancreas was first hit by chemical damage (streptozotocin, STZ) to unleash auto-antigens, then hit second time by transient immune-inflammation (regulatory T cell depletion). Comparing to NOD model, this strategy not only induced classical diabetic symptoms, but also depicted the crucial pathogenic features absent in conventional models, such as CD8+T cell dominant infiltrates, strong ketoacidosis and epitope-specific T cell responses. In addition, this model allowed synchronized control of disease onset, permitting more refined temporal analysis of disease progression. We believe that this model would yield research outcomes with clinically relevant prediction power unattainable previously.
Denoising of pediatric low dose abdominal CT using deep learning based algorithm
Authors: Park Hyoung Suk , Jeon Kiwan , Lee JeongEun , You Sun Kyoung
Published: January 2022

Objectives

To evaluate standard dose-like computed tomography (CT) images generated by a deep learning method, trained using unpaired low-dose CT (LDCT) and standard-dose CT (SDCT) images.

Materials and methods

LDCT (80 kVp, 100 mAs, n = 83) and SDCT (120 kVp, 200 mAs, n = 42) images were divided into training (42 LDCT and 42 SDCT) and validation (41 LDCT) sets. A generative adversarial network framework was used to train unpaired datasets. The trained deep learning method generated virtual SDCT images (VIs) from the original LDCT images (OIs). To test the proposed method, LDCT images (80 kVp, 262 mAs, n = 33) were collected from another CT scanner using iterative reconstruction (IR). Image analyses were performed to evaluate the qualities of VIs in the validation set and to compare the performance of deep learning and IR in the test set.

Results

The noise of the VIs was the lowest in both validation and test sets (all p<0.001). The mean CT number of the VIs for the portal vein and liver was lower than that of OIs in both validation and test sets (all p<0.001) and was similar to those of SDCT. The contrast-to-noise ratio of portal vein and the signal-to-noise ratio (SNR) of portal vein and liver of VIs were higher than those of SDCT (all p<0.05). The SNR of VIs in test sets was the highest among three images.

Conclusion

The deep learning method trained by unpaired datasets could reduce noise of LDCT images and showed similar performance to SAFIRE. It can be applied to LDCT images of older CT scanners without IR.
A comparative study on fatty acid profile in selected vessels of coronary artery bypass graft (CABG)
Authors: Bandara E. M. S. , Edirisinghe D. I. U. , Wanniarachchi D. D. C. de S. , Peiris H. , Perera P. P. R. , Jayakrishan A. G. , Waikar H. D. , Sharma S. K. , Abeysuriya V. , Chandrasena L. G.
Published: January 2022

Atherosclerosis is one of the leading non-communicable diseases in Sri Lanka. Analysis of fatty acid composition in blood vessels is important in understanding the development of atherosclerosis. Here, analyses of fatty acid profiles in major arteries which are commonly used in Coronary Artery Bypass Graft surgery (CABG) were subjected to investigation. Patients (n = 27) undergoing elective CABG were enrolled in the study. A small biopsy segment of the saphenous vein (SV), radial artery (RA), and left internal mammary artery (LIMA) of patients was obtained during the surgery. The fatty acid (FA) profile of tissue samples was analyzed using Gas Chromatography-Mass Spectroscopy (GCMS). Among the different arteries tested, palmitic acid and stearic acid were the predominant fatty acids. As far as monounsaturated FA (MUFA) are concerned, oleic acid was found to be the most abundant MUFA in vessels. The FA profile of LIMA samples had a higher SFA percentage and lower unsaturated FA percentage compared to other vessels. Furthermore, the vessel samples of RA indicated the highest percentage of pro-inflammatory ω -6 polyunsaturated fatty acids (PUFA) as well as a higher percentage ratio between ω -6: ω -3 PUFA. The fatty acid composition and ω -6: ω -3 PUFA ratio suggests that LIMA graft is preferred for CABG over RA and SV.
Transcriptomic profiling suggests candidate molecular responses to waterlogging in cassava
Authors: Cao Min , Zheng Linling , Li Junyi , Mao Yiming , Zhang Rui , Niu Xiaolei , Geng Mengting , Zhang Xiaofei , Huang Wei , Luo Kai , Chen Yinhua
Published: January 2022

Owing to climate change impacts, waterlogging is a serious abiotic stress that affects crops, resulting in stunted growth and loss of productivity. Cassava (Manihot esculentaGrantz) is usually grown in areas that experience high amounts of rainfall; however, little research has been done on the waterlogging tolerance mechanism of this species. Therefore, we investigated the physiological responses of cassava plants to waterlogging stress and analyzed global gene transcription responses in the leaves and roots of waterlogged cassava plants. The results showed that waterlogging stress significantly decreased the leaf chlorophyll content, caused premature senescence, and increased the activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in the leaves and roots. In total, 2538 differentially expressed genes (DEGs) were detected in the leaves and 13364 in the roots, with 1523 genes shared between the two tissues. Comparative analysis revealed that the DEGs were related mainly to photosynthesis, amino metabolism, RNA transport and degradation. We also summarized the functions of the pathways that respond to waterlogging and are involved in photosynthesis, glycolysis and galactose metabolism. Additionally, many transcription factors (TFs), such as MYBs, AP2/ERFs, WRKYs and NACs, were identified, suggesting that they potentially function in the waterlogging response in cassava. The expression of 12 randomly selected genes evaluated via both quantitative real-time PCR (qRT-PCR) and RNA sequencing (RNA-seq) was highly correlated (R2= 0.9077), validating the reliability of the RNA-seq results. The potential waterlogging stress-related transcripts identified in this study are representatives of candidate genes and molecular resources for further understanding the molecular mechanisms underlying the waterlogging response in cassava.
Distinguishability of keystroke dynamic template
Authors: Sae-Bae Napa , Memon Nasir
Published: January 2022

When keystroke dynamics are used for authentication, users tend to get different levels of security due to differences in the quality of their templates. This paper addresses this issue by proposing a metric to quantify the quality of keystroke dynamic templates. That is, in behavioral biometric verification, the user’s templates are generally constructed using multiple enrolled samples to capture intra-user variation. This variation is then used to normalize the distance between a set of enrolled samples and a test sample. Then a normalized distance is compared against a predefined threshold value to derive a verification decision. As a result, the coverage area for accepted samples in the original space of vector representation is discrete. Therefore, users with the higher intra-user variation suffer higher false acceptance rates (FAR). This paper proposes a metric that can be used to reflect the verification performance of individual keystroke dynamic templates in terms of FAR. Specifically, the metric is derived from statistical information of user-specific feature variations, and it has a non-decreasing property when a new feature is added to a template. The experiments are performed based on two public keystroke dynamic datasets comprising of two main types of keystroke dynamics: constrained-text and free-text, namely the CMU keystroke dynamics dataset and the Web-Based Benchmark for keystroke dynamics dataset. Experimental results based on multiple classifiers demonstrate that the proposed metric can be a good indicator of the template’s false acceptance rate. Thus, it can be used to enhance the security of the user authentication system based on keystroke dynamics.
Effectiveness of various cleaning strategies in acute and long-term care facilities during novel corona virus 2019 disease pandemic-related staff shortages
Authors: Lesho Emil , Newhart Donna , Reno Lisa , Sleeper Scott , Nary Julia , Gutowski Jennifer , Yu Stephanie , Walsh Edward , Vargas Roberto , Riedy Dawn , Mayo Robert
Published: January 2022

Background

Cleanliness of hospital surfaces helps prevent healthcare-associated infections, but comparative evaluations of various cleaning strategies during COVID-19 pandemic surges and worker shortages are scarce.

Purpose and methods

To evaluate the effectiveness of daily, enhanced terminal, and contingency-based cleaning strategies in an acute care hospital (ACH) and a long-term care facility (LTCF), using SARS-CoV-2 RT-PCR and adenosine triphosphate (ATP) assays. Daily cleaning involved light dusting and removal of visible debris while a patient is in the room. Enhanced terminal cleaning involved wet moping and surface wiping with disinfectants after a patient is permanently moved out of a room followed by ultraviolet light (UV-C), electrostatic spraying, or room fogging. Contingency-based strategies, performed only at the LTCF, involved cleaning by a commercial environmental remediation company with proprietary chemicals and room fogging. Ambient surface contamination was also assessed randomly, without regard to cleaning times. Near-patient or high-touch stationary and non-stationary environmental surfaces were sampled with pre-moistened swabs in viral transport media.

Results

At the ACH, SARS-CoV-2 RNA was detected on 66% of surfaces before cleaning and on 23% of those surfaces immediately after terminal cleaning, for a 65% post-cleaning reduction (p = 0.001). UV-C enhancement resulted in an 83% reduction (p = 0.023), while enhancement with electrostatic bleach application resulted in a 50% reduction (p = 0.010). ATP levels on RNA positive surfaces were not significantly different from those of RNA negative surfaces. LTCF contamination rates differed between the dementia, rehabilitation, and residential units (p = 0.005). 67% of surfaces had RNA after room fogging without terminal-style wiping. Fogging with wiping led to a -11% change in the proportion of positive surfaces. At the LTCF, mean ATP levels were lower after terminal cleaning (p = 0.016).

Conclusion

Ambient surface contamination varied by type of unit and outbreak conditions, but not facility type. Removal of SARS-CoV-2 RNA varied according to cleaning strategy.

Implications

Previous reports have shown time spent cleaning by hospital employed environmental services staff did not correlate with cleaning thoroughness. However, time spent cleaning by a commercial remediation company in this study was associated with cleaning effectiveness. These findings may be useful for optimizing allocation of cleaning resources during staffing shortages.
Helicobacter pylori infection is not associated with portal hypertension-related gastrointestinal complications: A meta-analysis
Authors: Jun Yu Kyung , Kim Ji Won , Kim Byeong Gwan , Lee Kook Lae , Jung Yong Jin , Kim Won , Park Hyun Sun , Lee Dong Hyeon , Koh Seong-Joon
Published: January 2022

Despite the importance ofHelicobacter pyloriinfection and portal hypertension (PH)-associated gastrointestinal (GI) diseases, such as esophageal varices and portal hypertensive gastropathy (PHG), the impact ofH.pyloriinfection on PH-related GI complications has not yet been elucidated. This meta-analysis investigated the association betweenH.pyloriinfection and the risk of PH-related GI complications. An electronic search for original articles published before May 2020 was performed using PubMed, EMBASE, and the Cochrane Library. Independent reviewers conducted the article screening and data extraction. We used the generic inverse variance method for the meta-analysis, and Begg’s rank correlation test and Egger’s regression test to assess publication bias. A total of 1,148 cases ofH.pyloriinfection and 1,231 uninfected controls were included from 13 studies.H.pyloriinfection had no significant association with esophageal varices [relative risk (RR) = 0.96, 95% confidence interval (CI) = 0.87–1.06 for all selected studies; RR = 0.95, 95% CI = 0.84–1.07 for cohort studies; odds ratio (OR) = 0.96, 95% CI = 0.60–1.54 for case-control studies]. AlthoughH.pyloriinfection was significantly associated with PHG in case-control studies [OR = 1.86, 95% CI = 1.17–2.96], no significant differences were found in the cohort studies [RR = 0.98, 95% CI = 0.91–1.05] or all studies combined [RR = 1.18, 95% CI = 0.93–1.52]. In conclusion,H.pyloriinfection was not associated with the risk of PH-related GI complications. Clinicians should carefully treat cirrhotic patients with PH-related GI complications, regardless ofH.pyloriinfection.
DeLUCS: Deep learning for unsupervised clustering of DNA sequences
Authors: Millán Arias Pablo , Alipour Fatemeh , Hill Kathleen A. , Kari Lila
Published: January 2022

We present a novelDeepLearning method for theUnsupervisedClustering of DNASequences (DeLUCS) that does not require sequence alignment, sequence homology, or (taxonomic) identifiers. DeLUCS uses Frequency Chaos Game Representations (FCGR) of primary DNA sequences, and generates “mimic” sequence FCGRs to self-learn data patterns (genomic signatures) through the optimization of multiple neural networks. A majority voting scheme is then used to determine the final cluster assignment for each sequence. The clusters learned by DeLUCS match true taxonomic groups for large and diverse datasets, with accuracies ranging from 77% to 100%: 2,500 complete vertebrate mitochondrial genomes, at taxonomic levels from sub-phylum to genera; 3,200 randomly selected 400 kbp-long bacterial genome segments, into clusters corresponding to bacterial families; three viral genome and gene datasets, averaging 1,300 sequences each, into clusters corresponding to virus subtypes. DeLUCS significantly outperforms two classic clustering methods (K-means++ and Gaussian Mixture Models) for unlabelled data, by as much as 47%. DeLUCS is highly effective, it is able to cluster datasets of unlabelled primary DNA sequences totalling over 1 billion bp of data, and it bypasses common limitations to classification resulting from the lack of sequence homology, variation in sequence length, and the absence or instability of sequence annotations and taxonomic identifiers. Thus, DeLUCS offers fast and accurate DNA sequence clustering for previously intractable datasets.
Clinical-like cryotherapy in acute knee arthritis of the knee improves inflammation signs, pain, joint swelling, and motor performance in mice
Authors: Castro Paula A. T. S. , Barbosa Germanna M. , Machanocker Dafiner H. , Peres Raphael S. , Cunha Thiago M. , Cunha Jonathan E. , Oliveira Francisco F. B. , Ramalho Fernando Silva , Russo Thiago L. , Cunha Fernando Q. , Salvini Tania F.
Published: January 2022

To assess the effects of clinical-like cryotherapy on inflammatory signs (in vivo neutrophil migration, cytokines, and joint inflammation), pain, joint swelling, balance, and motor coordination in mice with knee arthritis. Young C57BL/6 mice were randomly divided into three groups (8 to 10 mice per group): Control group: mice with no intervention; antigen-induced arthritis (AIA) group: mice sensitized and immunized with intra-articular (i.a.) injection of methylated bovine serum albumin (mBSA); and AIA + cryotherapy group: mice sensitized, immunized with i.a. injection of mBSA, and submitted to a clinical-like cryotherapy protocol. After 21 days of sensitization, AIA and AIA + cryotherapy groups received i.a. injection of mBSA (100 μg/joint) to induce joint inflammation, and a clinical-like cryotherapy protocol was applied to AIA + cryotherapy group (crushed ice bag, two cryotherapy sessions of 20 min every two hours). Experimental analysis was conducted in the initial (immediately after i.a. injection of mBSA) and final periods (two hours after the second cryotherapy session). The number of synovial fluid neutrophils, cytokine levels, joint histology, pain, joint swelling, and motor performance were also analyzed. Our results showed that clinical-like cryotherapy in mice with acute knee arthritis reduced inflammatory signs, pain, and joint swelling, and improved balance and motor coordination.
A PDK-1 allosteric agonist neutralizes insulin signaling derangements and beta-amyloid toxicity in neuronal cells and in vitro
Authors: Querfurth Henry , Marshall John , Parang Keykavous , Rioult-Pedotti Mengia S. , Tiwari Rakesh , Kwon Bumsup , Reisinger Steve , Lee Han-Kyu
Published: January 2022

The Alzheimer’s brain is affected by multiple pathophysiological processes, which include a unique, organ-specific form of insulin resistance that begins early in its course. An additional complexity arises from the four-fold risk of Alzheimer’s Disease (AD) in type 2 diabetics, however there is no definitive proof of causation. Several strategies to improve brain insulin signaling have been proposed and some have been clinically tested. We report findings on a small allosteric molecule that reverses several indices of insulin insensitivity in both cell culture andin vitromodels of AD that emphasize the intracellular accumulation of β-amyloid (Aβi). PS48, a chlorophenyl pentenoic acid, is an allosteric activator of PDK-1, which is an Akt-kinase in the insulin/PI3K pathway. PS48 was active at 10 nM to 1 μM in restoring normal insulin-dependent Akt activation and in mitigating Aβi peptide toxicity. Synaptic plasticity (LTP) in prefrontal cortical slices from normal rat exposed to Aβ oligomers also benefited from PS48. During these experiments, neither overstimulation of PI3K/Akt signaling nor toxic effects on cells was observed. Another neurotoxicity model producing insulin insensitivity, utilizing palmitic acid, also responded to PS48 treatment, thus validating the target and indicating that its therapeutic potential may extend outside of β-amyloid reliance. The describedin vitroandcell based-in vitrocoupled enzymatic assay systems proved suitable platforms to screen a preliminary library of new analogs.
Simulations of goaf surface subsidence via filling control
Authors: Yang Yong , Zhang Minsi , Hu Gaojian , Guan Kai
Published: January 2022

Xincheng Gold Mine is taken as an example to investigate the ground subsidence that results from filling. Both numerical simulations and simulation experiments are conducted to simulate the deformation process at the stope roof and bottom from excavation and filling. The assumption of macroscopic continuity from traditional continuum mechanics models is overcome. The simulation results demonstrate that the ground subsidence is slowed due to filling. The total trends of the top and bottom displacements are sinkable and upturned, respectively. Moreover, with an increased buried depth and lateral pressure coefficient, the displacements of the top and bottom of the stope increase as well. The characteristics and evolution of the displacement vector field of the rock mass are macroscopically and microscopically studied over the excavation progress. This provides technical support for stope safety production.
Self-reported health status and mortality from all-causes of death, cardiovascular disease and cancer in an older adult population in Spain
Authors: Torres-Collado Laura , García de la Hera Manuela , Compañ-Gabucio Laura María , Oncina-Cánovas Alejandro , González-Palacios Sandra , Notario-Barandiaran Leyre , Vioque Jesús
Published: January 2022

Aim

To assess the association between self-reported health (SRH) and mortality from all-causes, cardiovascular disease (CVD) and cancer, in adults 65 years and older in Spain.

Methods

We analysed data of 894 adults (504 women, 390 men) aged 65 years and above from two population-based studies, the EUREYE-Spain study and the Valencia Nutritional Survey (VNS). SRH was assessed at baseline using a single question which is widely used in epidemiological studies: “Overall, how would you consider your health at present?” and the response options were: 1. Very good, 2. Good, 3. Fair, 4. Poor, 5. Very poor. Deaths were ascertained during a 12-year follow-up period, and we used Cox proportional hazards regression models to obtain adjusted hazard ratios (HR).

Results

During the 12 years of follow-up (8566.2 person-years), we observed 400 deaths, 158 (39.5%) due to CVD and 89 (22.3%) due to cancer. Fair and poor/very poor SRH were significantly associated with higher all-cause mortality after 12-years of follow-up, HR = 1.29 (95% CI, 1.03–1.61) and HR 1.53 (95% CI, 1.09–2.15), respectively. We observed evidence of higher CVD mortality among those who reported fair and poor/very poor SRH, although the association was attenuated and lost statistical significance in the fully adjusted models.

Conclusion

This study suggests that a poor SRH status is associated with a higher all-cause mortality risk among older adults in Spain. Checking SHR status may be useful to plan health care in older adults.
Optimum second call imputation in PPS sampling
Authors: Sohil Fariha , Sohail Muhammad Umair , Shabbir Javid
Published: January 2022

The current study deals with imputation of item non-response in probability proportional to size (PPS) sampling. A new imputation procedure is proposed by using the known co-variance between the study variable and the auxiliary variable in the case of quantitative sensitive study variable by considering the non-response in a randomization mechanism on the second call. An empirical study is conducted at the optimum values ofkogandnogfor the relative comparisons of ratio, difference, and proposed estimators, respectively, with the Hansen-Hurwitz estimator.
Key risk factors for substance use among female sex workers in Soweto and Klerksdorp, South Africa: A cross-sectional study
Authors: Yeo Ellis Jaewon , Hlongwane Khuthadzo , Otwombe Kennedy , Hopkins Kathryn L. , Variava Ebrahim , Martinson Neil , Strathdee Steffanie A. , Coetzee Jenny , Milovanovic Minja
Published: January 2022

Introduction

Sex workers in South Africa experience high levels of trauma and mental health issues, but little is known about their drug and alcohol use. This study assessed the prevalence of substance use and its key risk factors amongst female sex workers (FSWs) at two sites in South Africa.

Methods

Two cross-sectional studies were conducted, in Soweto and Klerksdorp, South Africa. Using respondent-driven sampling (RDS) 508 FSWs in Soweto and 156 in Klerksdorp were enrolled. A study-specific survey was used to collect social and demographic information, substance use, mental ill-health, and HIV status. Raw and RDS-adjusted data were analyzed using Chi-squared tests of association. Weighted and unweighted Poisson regression models were used to assess key risk factors for alcohol and drug use at both univariate and multivariate levels.

Results

Of the 664 FSWs, 56.2% were binge drinkers and 29.4% reported using drugs within the last year. Living in a home with regular food (RR: 1.2597, 95% CI: 1.1009–1.4413) and being HIV positive (RR: 1.1678, 95% CI: 1.0227–1.3334) were associated with a higher risk of binge drinking. Having symptoms suggestive of post-traumatic stress disorder (RR: 1.1803, 95% CI: 1.0025–1.3895) and past year physical/sexual abuse from either intimate (RR: 1.3648, 95% CI: 1.1522–1.6167) or non-intimate partners (RR: 1.3910, 95% CI: 1.1793–1.6407) were associated with a higher risk of drug use.

Discussion

In conclusion, our findings demonstrate a high prevalence of alcohol and drug use among FSWs in Soweto and Klerksdorp with site-specific contextual dynamics driving substance use. Site differences highlight the importance of tailoring site-specific substance use harm mitigation for this key population.
Perception of the local community: What is their relationship with environmental quality indicators of reservoirs?
Authors: Azevêdo Evaldo de Lira , Alves Rômulo Romeu Nóbrega , Dias Thelma Lúcia Pereira , Álvaro Érica Luana Ferreira , Barbosa José Etham de Lucena , Molozzi Joseline
Published: January 2022

Evaluating the conservation of aquatic ecosystems, especially those which serve to supply, has been carried out using a variety of tools. However, the perception of water quality by the local community which lives in direct contact with water resources has not been considered with enough importance. This study analysed the relationship between the conservation status of reservoirs as perceived by the local community and their conservation status according to physical, chemical, and biological indicators. To do so, we calculated the Trophic State Index (TSI) of the reservoirs, the diversity and richness of benthic macroinvertebrate and we analysed the human influence in the riparian zone. Thus, we created the Community Conservation Perception Index (CCPI) to quantitatively associate the perception of the local community with environmental quality indicators (TSI, diversity, richness and anthropogenic influences in the riparian zone). We found that interviewee perception of reservoir conservation (using the CCPI) was related to trophic state, richness and diversity of benthic macroinvertebrate, and the presence of residences and agriculture in the riparian zone. It is necessary to consider the environmental perception of the local community as a relevant factor in management programmes and the conservation of ecosystems, even if artificial, as is the case with reservoirs. These communities can significantly contribute to maintaining the environmental quality through their performance in participatory management in projects such as: participating in the investigation of pollution in reservoirs, collecting parameters related to water quality, and community action in designing conservation strategies.
Development and Validation of Clinical Diagnostic Model for Girls with Central Precocious Puberty: Machine-learning Approaches
Authors: Huynh Quynh Thi Vu , Le Nguyen Quoc Khanh , Huang Shih-Yi , Ho Ban Tran , Vu Tru Huy , Pham Hong Thi Minh , Pham An Le , Hou Jia-Woei , Nguyen Ngan Thi Kim , Chen Yang Ching
Published: January 2022

Background

A brief gonadotropin-releasing hormone analogues (GnRHa) stimulation test which solely focused on LH 30-minute post-stimulation was considered to identify girls with central precocious puberty (CPP). However, it was tested using traditional statistical methods. With advanced computer science, we aimed to develop a machine learning-based diagnostic model that processed baseline CPP-related variables and a brief GnRHa stimulation test for CPP diagnosis.

Methods

We recruited girls suspected of precocious puberty and underwent a GnRHa stimulation test at Children Hospital 2, Vietnam, and Cathay General Hospital, Taiwan. Clinical data, bone age measurement, and 30-min post-stimulation blood test were used to build up the predictive model. The candidate model was developed by different machine learning algorithms that were mainly evaluated by sensitivity, specificity, the area under the receiver operator characteristic curve (AUC), and F1-score in internal and external validation data to classify girls as CPP and non-CPP at different time-points (0-min, 30-min, 60-min, and 120-min post-stimulation).

Results

Among the 614 girls diagnosed with PP, 524 (85.3%) had CPP. The random forest algorithm yielded the highest value of F1-score (0.976), specificity (0.893), positive predicted value (0.987), and relatively high value of AUC (0.972) that contributed to high probability to identify CPP. The performance metrics of the 30-min post-stimulation diagnostic model including sensitivity and specificity surpassed those of the 0-minute model (0-min) and were equivalent to those of the model obtained 60-min and 120-min post-stimulation. Hence, our machine learning-based model helps shorten the stimulation test to 30 minutes after GnRHa injection, in general, it requires 120 minutes for a completed GnRHa stimulation test.

Conclusions

We developed a diagnostic model based on clinical features and a single sample 30-minute post-stimulation to identify CPP in girls that can reduce distress for children caused by multiple blood samplings.
The acceptability of delayed consent for prehospital emergency care research in the Western Cape province of South Africa
Authors: Stassen Willem , Rambharose Sanjeev , Wallis Lee , Moodley Keymanthri
Published: January 2022

Background

Informed consent is an essential prerequisite for enrolling patients into a study. Obtaining informed consent in an emergency is complex and often impossible. Delayed consent has been suggested for emergency care research. This study aims to determine the acceptability of prehospital emergency care research with delayed consent in the Western Cape community of South Africa.

Methods

This study was an online survey of a stratified, representative sample of community members in the Western Cape province of South Africa. We calculated a powered sample size to be 385, and a stratified sampling method was employed. The survey was based on similar studies and piloted. Data were analysed descriptively.

Results

A total of 807 surveys were returned. Most respondents felt that enrolment into prehospital research would be acceptable if it offered direct benefit to them (n = 455; 68%) or if their condition was life-threatening and the research would identify improved treatment for future patients with a similar condition (n = 474; 70%). Similar results were appreciable when asked about the participation of their family member (n = 445; 66%) or their child (n = 422; 62%) regarding direct prospects of benefit. Overwhelmingly, respondents indicated that they would prefer to be informed of their own (n = 590; 85%), their family member’s (n = 593; 84%) or their child’s (n = 587; 86%) participation in a study immediately or as soon as possible. Only 35% (n = 283) agreed to retention data of deceased patients without the next of kin’s consent.

Conclusion

We report majority agreement of respondents for emergency care research with delayed consent if the interventions offered direct benefit to the research participant, if the participant’s condition was life-threatening and the work held the prospect of benefit for future patients, and if the protocol for delayed consent was approved by a human research ethics committee. These results should be explored using qualitative methods.
Patient perspectives of the Self-management and Educational Technology tool for Atrial Fibrillation (SETAF): A mixed-methods study in Singapore
Authors: Nathania Jennifer , Woo Brigitte Fong Yeong , Cher Boon Piang , Toh Kai Yee , Chia Wei-Yan Aloysius , Lim Yee Wei , Vrijhoef Hubertus J. M. , Lim Toon Wei
Published: January 2022

Background

Atrial fibrillation (AF) is the most common arrythmia and is associated with costly morbidity such as stroke and heart failure. Mobile health (mHealth) has potential to help bridge the gaps of traditional healthcare models that may be poorly suited to the sporadic nature of AF. The Self-management and Educational technology support Tool for AF patients (SETAF) was designed based on the preferences and needs of AF patients but more study is required to assess the acceptance of this novel tool.

Objective

Explore the usability and acceptance of SETAF among AF patients in Singapore.

Methods

A mixed methods study was conducted with AF patients who were purposively sampled from an outpatient cardiology clinic in Singapore. After 6 weeks of using SETAF, semi-structured interviews were performed, and data were analyzed inductively following a thematic analysis approach. Results from a short 4-item survey and application usage data were also analyzed descriptively. Both qualitative and quantitative results were organized and presented following the Technology Acceptance Model (TAM) framework.

Results

A total of 37 patients participated in the study and 19 were interviewed. Participants perceived SETAF as useful for improving AF knowledge, self-management and access to healthcare providers and was easy to use due to the guided tutorial and user-friendly interface. They also identified the need for better personalization of content, psychosocial support features and reduction of language barriers. Application usage data revealed preference for AF related content and decreased interaction with the motivational message component of SETAF over time. Overall, most of the participants would continue using SETAF and were willing to pay for it.

Conclusions

AF patients in Singapore found SETAF useful and acceptable as a tool for AF management. The insights from this study not only support the potential of mHealth but may also inform the design and implementation of future mHealth tools for AF patients.
A test of the effort equalization hypothesis in children with cerebral palsy who have an asymmetric gait
Authors: Kulmala Juha-Pekka , Haakana Piia , Nurminen Jussi , Ylitalo Elina , Niemelä Tuula , Marttinen Rossi Essi , Mäenpää Helena , Piitulainen Harri
Published: January 2022

Healthy people can walk nearly effortlessly thanks to their instinctively adaptive gait patterns that tend to minimize metabolic energy consumption. However, the economy of gait is severely impaired in many neurological disorders such as stroke or cerebral palsy (CP). Moreover, self-selected asymmetry of impaired gait does not seem to unequivocally coincide with the minimal energy cost, suggesting the presence of other adaptive origins. Here, we used hemiparetic CP gait as a model to test the hypothesis that pathological asymmetric gait patterns are chosen to equalize the relative muscle efforts between the affected and unaffected limbs. We determined the relative muscle efforts for the ankle and knee extensors by relating extensor joint moments during gait to maximum moments obtained from all-out hopping reference test. During asymmetric CP gait, the unaffected limb generated greater ankle (1.36±0.15 vs 1.17±0.16 Nm/kg, p = 0.002) and knee (0.74±0.33 vs 0.44±0.19 Nm/kg, p = 0.007) extensor moments compared with the affected limb. Similarly, the maximum moment generation capacity was greater in the unaffected limb versus the affected limb (ankle extensors: 1.81±0.39 Nm/kg vs 1.51±0.34 Nm/kg, p = 0.033; knee extensors: 1.83±0.37 Nm/kg vs 1.34±0.38 Nm/kg, p = 0.021) in our force reference test. As a consequence, no differences were found in the relative efforts between unaffected and affected limb ankle extensors (77±12% vs 80±16%, p = 0.69) and knee extensors (41±17% vs 38±23%, p = 0.54). In conclusion, asymmetric CP gait resulted in similar relative muscle efforts between affected and unaffected limbs. The tendency for effort equalization may thus be an important driver of self-selected gait asymmetry patterns, and consequently advantageous for preventing fatigue of the weaker affected side musculature.
Engineering solutions for biological studies of flow-exposed endothelial cells on orbital shakers
Authors: Fernandes Andreia , Hosseini Vahid , Vogel Viola , Lovchik Robert D.
Published: January 2022

Shear stress is extremely important for endothelial cell (EC) function. The popularity of 6-well plates on orbital shakers to impose shear stress on ECs has increased among biologists due to their low cost and simplicity. One characteristic of such a platform is the heterogeneous flow profile within a well. While cells in the periphery are exposed to a laminar and high-velocity pulsatile flow that mimics physiological conditions, the flow in the center is disturbed and imposes low shear stress on the cells, which is characteristic of atheroprone regions. For studies where such heterogeneity is not desired, we present a simple cell-patterning technique to selectively prevent cell growth in the center of the well and facilitate the exclusive collection and analysis of cells in the periphery. This guarantees that cell phenotypes will not be influenced by secreted factors from cells exposed to other shear profiles nor that interesting results are obscured by mixing cells from different regions. We also present a multi-staining platform that compartmentalizes each well into 5 smaller independent regions: four at the periphery and one in the center. This is ideal for studies that aim to grow cells on the whole well surface, for comparison with previous work and minimal interference in the cell culture, but require screening of markers by immunostaining afterwards. It allows to compare different regions of the well, reduces antibody-related costs, and allows the exploration of multiple markers essential for high-content screening of cell response. By increasing the versatility of the 6-well plate on an orbital shaker system, we hope that these two solutions motivate biologists to pursue studies on EC mechanobiology and beyond.
A Bayesian approach to combining multiple information sources: Estimating and forecasting childhood obesity in Thailand
Authors: Bryant John , Rittirong Jongjit , Aekplakorn Wichai , Mo-suwan Ladda , Nitnara Pimolpan
Published: January 2022

We estimate and forecast childhood obesity by age, sex, region, and urban-rural residence in Thailand, using a Bayesian approach to combining multiple source of information. Our main sources of information are survey data and administrative data, but we also make use of informative prior distributions based on international estimates of obesity trends and on expectations about smoothness. Although the final model is complex, the difficulty of building and understanding the model is reduced by the fact that it is composed of many smaller submodels. For instance, the submodel describing trends in prevalences is specified separately from the submodels describing errors in the data sources. None of our Thai data sources has more than 7 time points. However, by combining multiple data sources, we are able to fit relatively complicated time series models. Our results suggest that obesity prevalence has recently starting rising quickly among Thai teenagers throughout the country, but has been stable among children under 5 years old.
TGF-β1 in plasma and cerebrospinal fluid can be used as a biological indicator of chronic pain in patients with osteoarthritis
Authors: Liu Yen-Chin , Hsiao Hung-Tsung , Wang Jeffrey Chi-Fei , Wen Tzu-Cheng , Chen Shiou-Lan
Published: January 2022

Introduction

Previous studies have demonstrated that cytokines, transforming growth factor (TGF-β1), and brain-derived neurotrophic factor (BDNF) can impact the intensity of pain in rodents. However, the roles of cytokines, TGF-β1 and BDNF in humans with chronic pain in osteoarthritis remains unclear, and no comparison between plasma and central cerebral spinal fluid (CSF) has been conducted.

Methods

Patients with osteoarthritis who were scheduled to receive spinal anesthesia were enrolled. The intensity of pain was evaluated with a visual analogue scale (VAS). In addition, patients with genitourinary system (GU) diseases and without obvious pain (VAS 0–1) were included as a comparison (control) group. The levels of TGF-β1, BDNF, tumor necrosis factor-α (TNF-α), and interleukin (IL)-8 within the CSF and plasma were collected and evaluated before surgery.

Results

The plasma and CSF TGF-β1 levels were significantly lower in the osteoarthritis patients with pain (VAS ≥ 3) than in the GU control patients. Downregulation of plasma BDNF was also found in osteoarthritis patients with pain. The Spearman correlation analysis showed that the VAS pain scores were significantly negatively correlated with the levels of TGF-β1 in the CSF of patients with osteoarthritis. However, there was no significant correlations between the pain scores and the levels of BDNF, TNF-α, and IL-8 in either the CSF or plasma.

Conclusions

TGF-β1 but not BDNF, TNF-α, or IL-8 may be an important biological indicator in the CSF of osteoarthritis patients with chronic pain.
How informative were early SARS-CoV-2 treatment and prevention trials? a longitudinal cohort analysis of trials registered on ClinicalTrials.gov
Authors: Hutchinson Nora , Klas Katarzyna , Carlisle Benjamin G. , Kimmelman Jonathan , Waligora Marcin
Published: January 2022

Background

Early in the SARS-CoV-2 pandemic, commentators warned that some COVID trials were inadequately conceived, designed and reported. Here, we retrospectively assess the prevalence of informative COVID trials launched in the first 6 months of the pandemic.

Methods

Based on prespecified eligibility criteria, we created a cohort of Phase 1/2, Phase 2, Phase 2/3 and Phase 3 SARS-CoV-2 treatment and prevention efficacy trials that were initiated from 2020-01-01 to 2020-06-30 using ClinicalTrials.gov registration records. We excluded trials evaluating behavioural interventions and natural products, which are not regulated by the U.S. Food and Drug Administration (FDA). We evaluated trials on 3 criteria of informativeness: potential redundancy (comparing trial phase, type, patient-participant characteristics, treatment regimen, comparator arms and primary outcome), trials design (according to the recommendations set-out in the May 2020 FDA guidance document on SARS-CoV-2 treatment and prevention trials) and feasibility of patient-participant recruitment (based on timeliness and success of recruitment).

Results

We included all 500 eligible trials in our cohort, 58% of which were Phase 2 and 84.8% were directed towards the treatment of SARS-CoV-2. Close to one third of trials met all three criteria and were deemed informative (29.9% (95% Confidence Interval 23.7–36.9)). The proportion of potentially redundant trials in our cohort was 4.1%. Over half of the trials in our cohort (56.2%) did not meet our criteria for high quality trial design. The proportion of trials with infeasible patient-participant recruitment was 22.6%.

Conclusions

Less than one third of COVID-19 trials registered on ClinicalTrials.gov during the first six months met all three criteria for informativeness. Shortcomings in trial design, recruitment feasibility and redundancy reflect longstanding weaknesses in the clinical research enterprise that were likely amplified by the exceptional circumstances of a pandemic.
A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments
Authors: Guo Zhenhua , Lv Lei , Liu Di , He Xinmiao , Wang Wentao , Feng Yanzhong , Islam Md. Saiful , Wang Qiuju , Chen Wengui , Liu Ziguang , Wu Saihui , Abied Adam
Published: January 2022

The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: −1.15 and M-I: −1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.