bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources
Authors: Hanussek Maximilian , Bartusch Felix , Krüger Jens
Published: July 2021

The large amount of biological data available in the current times, makes it necessary to use tools and applications based on sophisticated and efficient algorithms, developed in the area of bioinformatics. Further, access to high performance computing resources is necessary, to achieve results in reasonable time. To speed up applications and utilize available compute resources as efficient as possible, software developers make use of parallelization mechanisms, like multithreading. Many of the available tools in bioinformatics offer multithreading capabilities, but more compute power is not always helpful. In this study we investigated the behavior of well-known applications in bioinformatics, regarding their performance in the terms of scaling, different virtual environments and different datasets with our benchmarking tool suite BOOTABLE. The tool suite includes the tools BBMap, Bowtie2, BWA, Velvet, IDBA, SPAdes, Clustal Omega, MAFFT, SINA and GROMACS. In addition we added an application using the machine learning framework TensorFlow. Machine learning is not directly part of bioinformatics but applied to many biological problems, especially in the context of medical images (X-ray photographs). The mentioned tools have been analyzed in two different virtual environments, a virtual machine environment based on the OpenStack cloud software and in a Docker environment. The gained performance values were compared to a bare-metal setup and among each other. The study reveals, that the used virtual environments produce an overhead in the range of seven to twenty-five percent compared to the bare-metal environment. The scaling measurements showed, that some of the analyzed tools do not benefit from using larger amounts of computing resources, whereas others showed an almost linear scaling behavior. The findings of this study have been generalized as far as possible and should help users to find the best amount of resources for their analysis. Further, the results provide valuable information for resource providers to handle their resources as efficiently as possible and raise the user community’s awareness of the efficient usage of computing resources.
Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species
Authors: Díaz Brenda Gabriela , Zucchi Maria Imaculada , Alves‐Pereira Alessandro , de Almeida Caléo Panhoca , Moraes Aline Costa Lima , Vianna Suelen Alves , Azevedo-Filho Joaquim , Colombo Carlos Augusto
Published: July 2021

Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.
Opportunistic gill infection is associated with TiO2 nanoparticle-induced mortality in zebrafish
Authors: Huang Chiao-Yi , Yu Wei-Sheng , Liu Geng-Chia , Hung Shih-Che , Chang Jen-Hsiang , Chang Jen-Che , Cheng Chia-Liang , Sun Der-Shan , Lin Ming-Der , Lin Wen-Ying , Tzeng Yin-Jeh , Chang Hsin-Hou
Published: July 2021

The large amounts of engineered titanium dioxide nanoparticles (TiO2NPs) that have been manufactured have inevitably been released into the ecosystem. Reports have suggested that TiO2is a relatively inert material that has low toxicity to animals. However, as various types of NPs increasingly accumulate in the ocean, their effects on aquatic life-forms remain unclear. In this study, a zebrafish model was used to investigate TiO2NP-induced injury and mortality. We found that the treatment dosages of TiO2NP are positively associated with increased motility of zebrafish and the bacterial counts in the water. Notably, gill but not dorsal fin and caudal fin of the zebrafish displayed considerably increased bacterial load. Metagenomic analysis further revealed that gut microflora, such as phylaProteobacteria,Bacteroidetes, andActinobacteria, involving more than 95% of total bacteria counts in the NP-injured zebrafish gill samples. These results collectively suggest that opportunistic bacterial infections are associated with TiO2NP-induced mortality in zebrafish. Infections secondary to TiO2NP-induced injury could be a neglected factor determining the detrimental effects of TiO2NPs on wild fish.
Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation
Authors: Velasco Cassandra , Dunn Christopher , Sturdy Cassandra , Izda Vladislav , Martin Jake , Rivas Alexander , McNaughton Jeffrey , Jeffries Matlock A.
Published: July 2021

Objective

Adult elastic cartilage has limited repair capacity. MRL/MpJ (MRL) mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and non-healer mice and to evaluate whether this healing phenotype can be transferred via gut microbiome transplantation.

Methods

We orally transplanted C57BL/6J (B6) mice with MRL/MpJ cecal contents at weaning and as adults (n = 57) and measured ear hole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n = 25) and B6-transplanted MRL (n = 20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n = 58), cecal microbiomes were profiled by 16S sequencing and compared to ear hole closure. Microbial metagenomes were imputed using PICRUSt.

Results

Transplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved ear hole closure. B6-vehicle mice healed ear hole punches poorly (0.25±0.03mm, mm ear hole healing 4 weeks after a 2mm ear hole punch [2.0mm—final ear hole size], mean±SEM), whereas MRL-vehicle mice healed well (1.4±0.1mm). MRL-transplanted B6 mice healed roughly three times as well as B6-vehicle mice, and half as well as MRL-vehicle mice (0.74±0.05mm,P= 6.9E-10 vs. B6-vehicle,P= 5.2E-12 vs. MRL-vehicle). Transplantation of MRL mice with B6 cecal material did not reduce MRL healing (B6-transplanted MRL 1.3±0.1 vs. MRL-vehicle 1.4±0.1, p = 0.36). Transplantation prior to ear punch was associated with the greatest ear hole closure. Offspring of transplanted mice healed significantly better than non-transplanted control mice (offspring:0.63±0.03mm, mean±SEM vs. B6-vehicle control:0.25±0.03mm, n = 39 offspring, P = 4.6E-11). Several microbiome clades were correlated with healing, includingFirmicutes(R = 0.84,P= 8.0E-7),Lactobacillales(R = 0.65,P= 1.1E-3), andVerrucomicrobia(R = -0.80,P= 9.2E-6). Females of all groups tended to heal better than males (B6-vehicleP= 0.059, MRL-transplanted B6P= 0.096, offspring of MRL-transplanted B6P= 0.0038, B6-transplanted MRLP= 1.6E-6, MRL-vehicleP= 0.0031). Many clades characteristic of female mouse cecal microbiota vs. males were the same as clades characteristic of MRL and MRL-transplanted B6 mice vs. B6 controls, including including increases inClostridiaand reductions inVerrucomicrobiain female mice.

Conclusion

In this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to non-healer mice via microbiome transplantation. We identified several microbiome clades associated with healing.
Randomised trial on effect of involving media reporters in salt reduction programme to increase media reports and the public’s knowledge, belief and behaviors on salt and health: Changzhi reporters trial
Authors: Li Zhifang , Feng Xiangxian , Wu Tao , Yan Lijing , Elliott Paul , Wu Yangfeng
Published: July 2021

Objective

To assess the effects of a novel mass media intervention in increasing media reports on salt and health by involving media reporters in a scientifically well designed salt reduction trial.

Methods

We recruited and trained 66 media reporters in Changzhi, Shanxi province, China to conduct a randomized controlled trial on blood pressure lowering effect of salt substitute in Dec, 2012 and Jan 2013 among their own relatives or friends (253 from 129 families in the salt substitute arm and 263 from 133 families in the control arm for two months). We shared trial results and other information on salt and health with the reporters within a month after the trial. We monitored all local newspapers for the number of relevant articles in 3 months before, 3 months during and 3 months after the intervention and at the 6th, 12th, 18th, 24th and 48th months after the intervention. Additionally, we conducted two independent surveys on knowledge, belief and behaviours of salt and health among local citizens before and after the intervention.

Results

As expected, systolic blood pressure was reduced significantly more in the salt substitute than the control group (-4.7±11.0 mmHg vs -2.6±10.3 mmHg, p<0.001) in the randomized trial. The monthly mean number of relevant articles increased from 0.7 before to 1.7 during (p = 0.263), and further to 6.0 after the intervention (p<0.001), and varied from 2 (p = 0.170) to 4 (p = 0.008) from the 6th to 48th month; the awareness of knowledge on salt and health among local citizens improved significantly after the intervention.

Conclusions

Media reporters’ participation in a well-designed salt reduction trial significantly increased the number of relevant media reports, and the effect was sustained for a prolonged period. Future mass media public health education programs should consider this innovative strategy for better and sustained impacts.
Impact of IgG response to malaria-specific antigens and immunity against malaria in pre-school children in Ghana. A cluster randomized, placebo-controlled trial
Authors: Tchum Samuel Kofi , Sakyi Samuel Asamoah , Adu Bright , Arthur Fareed , Oppong Felix Boakye , Dzabeng Francis , Amoani Benjamin , Gyan Thomas , Poku-Asante Kwaku
Published: July 2021

Background

Iron fortification and micronutrient initiatives, specifically, vitamin A, and zinc supplementation are the most cost-effective developmental strategies against malnutrition and health emergencies in pre-school children. Iron-deficiency among pre-school children have been documented, however, studies evaluating the impact of immunoglobulin G (IgG) isotype responses among iron-fortified pre-school children in malaria endemic communities has not been assessed. We evaluated the impact of iron fortification on the IgG responses to GLURP R0, GLURP R2 and MSP3 FVO malaria-specific antigens among pre-school children in malaria endemic areas.

Methods

This community-based, placebo-controlled, double-blinded, cluster-randomized trial study was conducted in Wenchi Municipal and Tain District of Bono Region. The trial was registered at ClinicalTrials.gov-registered trial (Identifier: NCT01001871). Ethical approval was obtained and informed consent were sought from each participant parents/guardian. For the current objective, 871 children aged 6–35 months were screened, from which 435 children received semi-liquid home-made meals mixed with 12.5 mg of iron daily (intervention group), and 436 received micronutrient powder without iron (placebo group) for 5 months. Standardized clinical and epidemiological questionnaires were administered and blood samples taken to measure IgG responses to GLURP R0, GLURP R2 and MSP3 FVO recombinant antigens using the Afro Immunoassay (AIA) protocol.

Results

Baseline anthropometry, malaria diagnosis, anaemia and iron status, demographic features and dietary intake were identical among the groups (p > 0.05). After the intervention, there was no significant difference in the IgG response against GLUP R0, GLUP R2 and MSP3 FVO between the iron-containing micronutrient and placebo groups (p > 0.05). The iron-containing micronutrient powder group who were iron-sufficient or iron replete had significantly higher IgG response to GLURP R0 and GLURP R2 compared to iron-deficient and iron-deficiency anaemia in the same group (p < 0.05). The IgG responses to all the three malaria specific antigens were low among children without malaria episode but high among those with two and four episodes due to exposure differences.

Conclusion

Iron fortification did not influence antibody response against endogenous malaria specific antigens among pre-school children in malaria endemic areas, however, IgG response to malaria specific antigens were high among children with sufficient iron status.
Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics
Authors: Sajjadi Sina , Ejtehadi Mohammad Reza , Ghanbarnejad Fakhteh
Published: July 2021

We first propose a quantitative approach to detect high risk outbreaks of independent and coinfective SIR dynamics on three empirical networks: a school, a conference and a hospital contact network. This measurement is based on the k-means clustering method and identifiesproper samplesfor calculating themean outbreak sizeandthe outbreak probability. Then we systematically study the impact of different temporal correlations on high risk outbreaks over the original and differently shuffled counterparts of each network. We observe that, on the one hand, in the coinfection process, randomization of the sequence of the events increases the mean outbreak size of high-risk cases. On the other hand, these correlations do not have a consistent effect on the independent infection dynamics, and can either decrease or increase this mean. Randomization of the daily pattern correlations has no strong impact on the size of the outbreak in either the coinfection or the independent spreading cases. We also observe that an increase in the mean outbreak size does not always coincide with an increase in the outbreak probability; therefore, we argue that merely considering the mean outbreak size ofall realizationsmay lead us into falsely estimating the outbreak risks. Our results suggest that some sort of contact randomization in the organizational level in schools, events or hospitals might help to suppress the spreading dynamics while the risk of an outbreak is high.
A community-powered search of machine learning strategy space to find NMR property prediction models
Authors: Bratholm Lars A. , Gerrard Will , Anderson Brandon , Bai Shaojie , Choi Sunghwan , Dang Lam , Hanchar Pavel , Howard Addison , Kim Sanghoon , Kolter Zico , Kondor Risi , Kornbluth Mordechai , Lee Youhan , Lee Youngsoo , Mailoa Jonathan P. , Nguyen Thanh Tu , Popovic Milos , Rakocevic Goran , Reade Walter , Song Wonho , Stojanovic Luka , Thiede Erik H. , Tijanic Nebojsa , Torrubia Andres , Willmott Devin , Butts Craig P. , Glowacki David R.
Published: July 2021

The rise of machine learning (ML) has created an explosion in the potential strategies for using data to make scientific predictions. For physical scientists wishing to apply ML strategies to a particular domain, it can be difficult to assess in advance what strategy to adopt within a vast space of possibilities. Here we outline the results of an online community-powered effort to swarm search the space of ML strategies and develop algorithms for predicting atomic-pairwise nuclear magnetic resonance (NMR) properties in molecules. Using an open-source dataset, we worked with Kaggle to design and host a 3-month competition which received 47,800 ML model predictions from 2,700 teams in 84 countries. Within 3 weeks, the Kaggle community produced models with comparable accuracy to our best previously published ‘in-house’ efforts. A meta-ensemble model constructed as a linear combination of the top predictions has a prediction accuracy which exceeds that of any individual model, 7-19x better than our previous state-of-the-art. The results highlight the potential of transformer architectures for predicting quantum mechanical (QM) molecular properties.
An experimental investigation into the borehole drilling and strata characteristics
Authors: Liu Cancan , Zheng Xigui , Shahani Niaz Muhammad , Li Peng , Wang Cong , Guo Xiaowei
Published: July 2021

Measurement while drilling is an important part of the intelligent development of coal mines. The main purpose of this paper is to comprehensively analyze the response characteristics of borehole drilling parameters and find a better method to predict rock mechanical properties based on drilling parameters. Firstly, six concrete blocks and multiple specimens were prepared with different material ratios. Next, the concrete specimens were tested for mechanical properties in the laboratory. Meanwhile, the displacement, rotation speed, torque, and sound pressure level (SPL) were observed during the drilling of the concrete blocks. Finally, the response characteristics of drilling parameters such as rotation speed, rate of penetration (ROP), torque, and SPL were analyzed. Besides, multiple prediction models of rock mechanical parameters were obtained by data analysis. The research results indicate that the drilling process can be classified into the initial stage of drilling (fast speed) and the steady stage of drilling (slow speed). The torque work ratio accounts for more than 99%, which increases with the increase in rock strength. The penetration depth per revolution and torque work ratio are significantly related to rock uniaxial compressive strength, Brazilian tensile strength, cohesion, and elastic modulus. The ROP is the best choice for estimating rock mechanical parameters. This research provides an important reference for laboratory rock mechanics parameter testing and geological features detection based on drilling parameters.
Spatiotemporal dynamics of maximal and minimal EEG spectral power
Authors: Menceloglu Melisa , Grabowecky Marcia , Suzuki Satoru
Published: July 2021

Oscillatory neural activities are prevalent in the brain with their phase realignment contributing to the coordination of neural communication. Phase realignments may have especially strong (or weak) impact when neural activities are strongly synchronized (or desynchronized) within the interacting populations. We report that the spatiotemporal dynamics of strong regional synchronization measured as maximal EEG spectral power—referred to as activation—and strong regional desynchronization measured as minimal EEG spectral power—referred to as suppression—are characterized by the spatial segregation of small-scale and large-scale networks. Specifically, small-scale spectral-power activations and suppressions involving only 2–7% (1–4 of 60) of EEG scalp sites were prolonged (relative to stochastic dynamics) and consistently co-localized in a frequency specific manner. For example, the small-scale networks for θ, α, β1, and β2 bands (4–30 Hz) consistently included frontal sites when the eyes were closed, whereas the small-scale network for γ band (31–55 Hz) consistently clustered in medial-central-posterior sites whether the eyes were open or closed. Large-scale activations and suppressions involving over 17–30% (10–18 of 60) of EEG sites were also prolonged and generally clustered in regions complementary to where small-scale activations and suppressions clustered. In contrast, intermediate-scale activations and suppressions (involving 7–17% of EEG sites) tended to follow stochastic dynamics and were less consistently localized. These results suggest that strong synchronizations and desynchronizations tend to occur in small-scale and large-scale networks that are spatially segregated and frequency specific. These synchronization networks may broadly segregate the relatively independent and highly cooperative oscillatory processes while phase realignments fine-tune the network configurations based on behavioral demands.
Early detection of COVID-19 outbreaks using human mobility data
Authors: Guan Grace , Dery Yotam , Yechezkel Matan , Ben-Gal Irad , Yamin Dan , Brandeau Margaret L.
Published: July 2021

Background

Contact mixing plays a key role in the spread of COVID-19. Thus, mobility restrictions of varying degrees up to and including nationwide lockdowns have been implemented in over 200 countries. To appropriately target the timing, location, and severity of measures intended to encourage social distancing at a country level, it is essential to predict when and where outbreaks will occur, and how widespread they will be.

Methods

We analyze aggregated, anonymized health data and cell phone mobility data from Israel. We develop predictive models for daily new cases and the test positivity rate over the next 7 days for different geographic regions in Israel. We evaluate model goodness of fit using root mean squared error (RMSE). We use these predictions in a five-tier categorization scheme to predict the severity of COVID-19 in each region over the next week. We measure magnitude accuracy (MA), the extent to which the correct severity tier is predicted.

Results

Models using mobility data outperformed models that did not use mobility data, reducing RMSE by 17.3% when predicting new cases and by 10.2% when predicting the test positivity rate. The best set of predictors for new cases consisted of 1-day lag of past 7-day average new cases, along with a measure of internal movement within a region. The best set of predictors for the test positivity rate consisted of 3-days lag of past 7-day average test positivity rate, along with the same measure of internal movement. Using these predictors, RMSE was 4.812 cases per 100,000 people when predicting new cases and 0.79% when predicting the test positivity rate. MA in predicting new cases was 0.775, and accuracy of prediction to within one tier was 1.0. MA in predicting the test positivity rate was 0.820, and accuracy to within one tier was 0.998.

Conclusions

Using anonymized, macro-level data human mobility data along with health data aids predictions of when and where COVID-19 outbreaks are likely to occur. Our method provides a useful tool for government decision makers, particularly in the post-vaccination era, when focused interventions are needed to contain COVID-19 outbreaks while mitigating the collateral damage from more global restrictions.
Unplanned hospital visits after ambulatory surgical care
Authors: Bongiovanni Tasce , Parzynski Craig , Ranasinghe Isuru , Steinman Michael A. , Ross Joseph S.
Published: July 2021

Objectives

We sought to assess the rate of unplanned hospital visits among patients undergoing ambulatory surgery.

Summary background data

The majority of surgeries performed in the United States now take place in outpatient settings. Post-discharge hospital visit rates have been shown to vary widely, suggesting variation in surgical or discharge care quality. Complicating efforts to address quality, most facilities and surgeons are unaware of their patients’ hospital visits after surgery since patients may present to a different hospital.

Methods

We used state-level, administrative data from the Agency for Healthcare Research and Quality’s Healthcare Cost and Utilization Project from California to assess unplanned hospital visits after ambulatory surgery. To compare rates across centers, we determined the age, sex, and procedure-adjusted rates of hospital visits for each facility using 2-level, hierarchical, generalized linear models using methods similar to existing Centers for Medicare and Medicaid Services measures.

Results

Among a total of 1,260,619 ambulatory same-day surgeries from 440 surgical facilities, the risk adjusted 30-day rate of unplanned hospital visits was 4.8%, with emergency department visits of 3.1% and hospital admissions of 1.7%. Several patient characteristics were associated with increased risk of unplanned hospitals visits, including increased age, increased number of comorbidities (using the Elixhauser score), and type of procedure (p<0.001).

Conclusions

The overall rate unplanned hospital visits within 30 days after same-day surgery is low but variable, suggesting a difference in the quality of care provided. Further, these rates are higher among specific patient populations and procedure types, suggesting areas for targeted improvement.
Algorithmic extraction of smartphone accelerometer-derived mechano-biological descriptors of resistance exercise is robust to changes in intensity and velocity
Authors: Viecelli Claudio , Aguayo David , Dällenbach Samuel , Graf David , Achermann Basil , Hafen Ernst , Füchslin Rudolf M.
Published: July 2021

Background

It was shown that single repetition, contraction-phase specific and total time-under-tension (TUT) can be extracted reliably and validly from smartphone accelerometer-derived data of resistance exercise machines using user-determined resistance exercise velocities at 60% one repetition maximum (1-RM). However, it remained unclear how robust the extraction of these mechano-biological descriptors is over a wide range of movement velocities (slow- versus fast-movement velocity) and intensities (30% 1-RM versus 80% 1-RM) that reflect the interindividual variability during resistance exercise.

Objective

In this work, we examined whether the manipulation of velocity or intensity would disrupt an algorithmic extraction of single repetitions, contraction-phase specific and total TUT.

Methods

Twenty-seven participants performed four sets of three repetitions of their 30% and 80% 1-RM with velocities of 1 s, 2 s, 6 s and 8 s per repetition, respectively. An algorithm extracted the number of repetitions, single repetition, contraction-phase specific and total TUT. All exercises were video-recorded. The video recordings served as the gold standard to which algorithmically-derived TUT was compared. The agreement between the methods was examined using Limits of Agreement (LoA). The Pearson correlation coefficients were used to calculate the association, and the intraclass correlation coefficient (ICC 2.1) examined the interrater reliability.

Results

The calculated error rate for the algorithmic detection of the number of single repetitions derived from two smartphones accelerometers was 1.9%. The comparison between algorithmically-derived, contraction-phase specific TUT against video, revealed a high degree of correlation (r > 0.94) for both exercise machines. The agreement between the two methods was high on both exercise machines, intensities and velocities and was as follows:

LoA ranged from -0.21 to 0.22 seconds for single repetition TUT (2.57% of mean TUT), from -0.24 to 0.22 seconds for concentric contraction TUT (6.25% of mean TUT), from -0.22 to 0.24 seconds for eccentric contraction TUT (5.52% of mean TUT) and from -1.97 to 1.00 seconds for total TUT (5.13% of mean TUT). Interrater reliability for single repetition, contraction-phase specific TUT was high (ICC > 0.99).

Conclusion

Neither intensity nor velocity disrupts the proposed algorithmic data extraction approach. Therefore, smartphone accelerometers can be used to extract scientific mechano-biological descriptors of dynamic resistance exercise with intensities ranging from 30% to 80% of the 1-RM with velocities ranging from 1 s to 8 s per repetition, respectively, thus making this simple method a reliable tool for resistance exercise mechano-biological descriptors extraction.
Collective insights of public-private partnership impacts and sustainability: A qualitative analysis
Authors: Strasser Sheryl , Stauber Christine , Shrivastava Ritu , Riley Patricia , O’Quin Karen
Published: July 2021

The global Coronavirus or COVID-19 pandemic exposed the weakness of healthcare systems including laboratory systems and is a call to action for unprecedented collaboration and partnerships to deal with the global crisis. The United States (U.S.) President’s Emergency Plan for AIDS Relief (PEPFAR) establishes the global HIV/AIDS treatment agenda in alignment with the UNAIDS 90-90-90 treatment targets to achieve epidemic control related to enhanced testing, treatment, and viral suppression. A strategic PEPFAR priority area recognizes that large-scale collective efforts and sharing of resources bear greater potential impact for lasting change than any single organization or entity can achieve alone. An important vehicle utilized within the global public health context is the public-private partnership (PPP) model whereby multiple international organizations forge unified project charters to collectively reach mutually agreed goals. While touted as an ideal mechanism to synthesize resources and maximize gain in numerous applications, little is known from a seasoned stakeholder perspective regarding PPP implementation and sustainability issues. The purpose of this research is to holistically examine perceptions of PPP model sustainability related to inputs and impacts among a collective network of stakeholders experienced with PEPFAR workforce development, laboratory-system strengthening project implementation. Interviews were conducted with frontline stakeholders from public and private sector organizations based in the US and select PEPFAR-supported priority countries. Analysis revealed three dominant themes: PPP impacts, keys of successful collaboration, and logistical challenges and opportunities to enhance sustainability of PPP outcomes in the future.
The potential economic benefits of controlling trypanosomiasis using waterbuck repellent blend in sub-Saharan Africa
Authors: Abro Zewdu , Kassie Menale , Muriithi Beatrice , Okal Michael , Masiga Daniel , Wanda Gift , Gisèle Ouedraogo , Samuel Abah , Nguertoum Etienne , Nina Rock Aimé , Mansinsa Philémon , Adam Yahaya , Camara Mamadou , Olet Pamela , Boucader Diarra , Jamal Susana , Garba Abdoul Razak Issa , Ajakaiye Joseph Joachim , Kinani Jean Felix , Hassan Mohamed Adam , Nonga Hezron , Daffa Joyce , Gidudu Ambrose , Chilongo Kalinga
Published: July 2021

Trypanosomiasis is a significant productivity-limiting livestock disease in sub-Saharan Africa, contributing to poverty and food insecurity. In this paper, we estimate the potential economic gains from adopting Waterbuck Repellent Blend (WRB). The WRB is a new technology that pushes trypanosomiasis-transmitting tsetse fly away from animals, improving animals’ health and increasing meat and milk productivity. We estimate the benefits of WRB on the production of meat and milk using the economic surplus approach. We obtained data from an expert elicitation survey, secondary and experimental sources. Our findings show that the adoption of WRB in 5 to 50% of the animal population would generate an economic surplus of US$ 78–869 million per annum for African 18 countries. The estimated benefit-cost ratio (9:1) further justifies an investment in WRB. The technology’s potential benefits are likely to be underestimated since our estimates did not include the indirect benefits of the technology adoption, such as the increase in the quantity and quality of animals’ draught power services and human and environmental health effects. These benefits suggest that investing in WRB can contribute to nutrition security and sustainable development goals.
How is Etuaptmumk/Two-Eyed Seeing characterized in Indigenous health research? A scoping review
Authors: Roher Sophie I. G. , Yu Ziwa , Martin Debbie H. , Benoit Anita C.
Published: July 2021

Our scoping review sought to consider howEtuaptmumkor Two-Eyed Seeing is described in Indigenous health research and to compare descriptions of Two-Eyed Seeing between original authors (Elders Albert and Murdena Marshall, and Dr. Cheryl Bartlett) and new authors. Using the JBI scoping review methodology and qualitative thematic coding, we identified seven categories describing the meaning of Two-Eyed Seeing from 80 articles: guide for life, responsibility for the greater good and future generations, co-learning journey, multiple or diverse perspectives, spirit, decolonization and self-determination, and humans being part of ecosystems. We discuss inconsistencies between the original and new authors, important observations across the thematic categories, and our reflections from the review process. We intend to contribute to a wider dialogue about how Two-Eyed Seeing is understood in Indigenous health research and to encourage thoughtful and rich descriptions of the guiding principle.
COVID-19 cumulative incidence, asymptomatic infections, and fatality in Long Island, NY, January–August 2020: A cohort of World Trade Center responders
Authors: Morozova Olga , Clouston Sean A. P. , Valentine Jennifer , Newman Alexander , Carr Melissa , Luft Benjamin J.
Published: July 2021

Background

New York City and Long Island, NY were early foci of the COVID-19 epidemic in the US. The effects of COVID-19 on different sub-populations, and its key epidemiologic parameters remain unknown or highly uncertain. We investigated the epidemiology of COVID-19 from January to August of 2020 in an established academic monitoring cohort of N = 9,697 middle-aged World Trade Center responders residing in Long Island, NY.

Methods

A seroprevalence survey and a series of cross-sectional surveys were nested in a prospective cohort study. Measures included IgG antibody testing, SARS-CoV-2 polymerase chain reaction (PCR) testing, review of electronic medical records, and surveys of symptoms. Correlates of infection were analyzed with multivariable logistic regression.

Results

The cohort was predominantly men in their mid-fifties; 6,597 cohort members were successfully contacted (68%); 1,042 (11%) individuals participated in the seroprevalence survey; and 369 individuals (5.6% of 6,597 study participants) underwent PCR testing. The estimated standardized cumulative incidence was 21.9% (95%CI: 20.1–23.9%), the asymptomatic proportion was 16.4% (36/219; 95%CI: 11.8–22.0%), the case hospitalization ratio was 9.4% (36/385; 95%CI: 6.6–12.7%), the case fatality ratio was 1.8% (7/385; 95%CI: 0.7–3.7%), and the hospitalization fatality ratio was 8.3% (3/36; 95%CI: 1.8–22.5%). Confirmed SARS-CoV-2 infection was associated with younger age, race/ethnicity, and being currently employed.

Conclusions

The results of the present study suggest a high cumulative incidence of SARS-CoV-2 among WTC responders in the spring and summer of 2020 and contribute to narrowing the plausible range of the proportion of infections that exhibit no symptoms. An increased risk of infection among younger employed individuals is likely to reflect a higher probability of exposure to the virus, and the racial disparities in the infection risk warrant further investigation.
Effects of passive heat stress and recovery on human cognitive function: An ERP study
Authors: Nakata Hiroki , Kakigi Ryusuke , Shibasaki Manabu
Published: July 2021

Using event-related potentials (ERPs), we investigated the effects of passive heat stress and recovery on the human cognitive function with Flanker tasks, involving congruent and incongruent stimuli. We hypothesized that modulation of the peak amplitude and latency of the P300 component in ERP waveforms would differ with task difficulty during passive heat stress and recovery. Subjects performed the Flanker tasks before (Pre), at the end of whole body heating (Heat: internal temperature increase of ~1.2°C from the pre-heat baseline), and after the internal temperature had returned to the pre-heat baseline (Recovery). The internal temperature was regulated by a tube-lined suit by perfusing 50°C water for heat stress and 25°C water for recovery immediately after the heat stress. Regardless of task difficulty, the reaction time (RT) was shortened during Heat rather than Pre and Recovery, and standard deviations of RT (i.e., response variability) were significantly smaller during Heat than Pre. However, the peak amplitudes of the P300 component in ERPs, which involved selective attention, expectancy, and memory updating, were significantly smaller during Heat than during Pre, suggesting the impairment of neural activity in cognitive function. Notably, the peak amplitudes of the P300 component were higher during Recovery than during Heat, indicating that the impaired neural activity had recovered after sufficient whole-body cooling. An indicator of the stimulus classification/evaluation time (peak latency of P300) and the RT were shortened during Heat stress, but such shortening was not noted after whole-body cooling. These results suggest that hyperthermia affects the human cognitive function, reflected by the peak amplitude and latency of the P300 component in ERPs during the Flanker tasks, but sufficient treatment such as whole-body cooling performed in this study can recover those functions.
Behavioral effect of mismatch negativity neurofeedback on foreign language learning
Authors: Chang Ming , Ando Hideyuki , Maeda Taro , Naruse Yasushi
Published: July 2021

Listening is critical for foreign language learning. Listening difficulties can occur because of an inability to perceive or recognize sounds while listening to speech, whereas successful listening can boost understanding and improve speaking when learning a foreign language. Previous studies in our laboratory revealed that EEG-neurofeedback (NF) using mismatch negativity event-related brain potential successfully induced unconscious learning in terms of auditory discrimination of speech sounds. Here, we conducted a feasibility study with a small participant group (NF group and control group; six participants each) to examine the practical effects of mismatch negativity NF for improving the perception of speech sounds in a foreign language. Native Japanese speakers completed a task in which they learned to perceive and recognize spoken English words containing the consonants “l” or “r”. Participants received neurofeedback training while not explicitly attending to auditory stimuli. The results revealed that NF training significantly improved the proportion of correct in discrimination and recognition trials, even though the training time for each word pair was reduced to 20% of the training time reported in our previous study. The learning effect was not affected by training with three pairs of words with different vowels. The current results indicate that NF resulted in long-term learning that persisted for at least 2 months.
The association of severe anemia, red blood cell transfusion and necrotizing enterocolitis in neonates
Authors: Song Juan , Dong Huimin , Xu Falin , Wang Yong , Li Wendong , Jue Zhenzhen , Wei Lele , Yue Yuyang , Zhu Changlian
Published: July 2021

Background

The relationship between severe anemia, red blood cell transfusion and Neonatal necrotizing enterocolitis (NEC) remains controversial. The purpose of this study was to determine the association of severe anemia and RBC transfusion with NEC in neonates.

Methods

The clinical characteristics of NEC were observed in 467 infants with different birth weights from January 2012 to July 2020. A 1:1 ratio case-control study was performed in very low birth weight (VLBW) infants. Severe anemia, RBC transfusion, and confounding factors, including maternal and perinatal complications, feeding, and antibiotics administration were collected in both groups. Univariate and multivariate analyses were used to investigate effects on the risk of NEC.

Results

The day of NEC onset and mortality were inversely associated with birth weight. In VLBW infants, adjusting for other factors, severe anemia within 72 h [OR = 2.404, P = 0.016], RBC transfusion within 24 h [OR = 4.905, P = 0.016], within 48 h [OR = 5.587, P = 0.008], and within 72 h [OR = 2.858, P = 0.011] increased the risk of NEC.

Conclusion

Both severe anemia and RBC transfusion appears to increase the risk of NEC in VLBW infants. The early prevention and treatment of anemia, strict evaluation of the indications for transfusion and enhanced monitoring after transfusion is encouraged in the NICU.
Analysis on outsourcing service behavior of rice pest and disease control based on Heckman selection model—A case study of ten counties in Fujian Province
Authors: Cai Liangmei , Wang Linping
Published: July 2021

Under the background of relatively slow agricultural labor transfer and land circulation, agricultural production outsourcing has become the main means of agricultural modernization. In order to provide a beneficial perspective for appropriately expanding the scale of rice control outsourcing services, we investigated the situation of rice control outsourcing in ten counties of Fujian Province, and analyzed the factors influencing rice farmers’ decision-making and control degree by using Heckman model. First of all, the main factors affecting farmers’ participation in outsourcing are agricultural labor force, whether family members are cooperative members, planting area, proportion of grain income, degree of organization of outsourcing team, region and so on. Secondly, agricultural labor force, cooperative members, planting area, part-time behavior, mechanical efficiency of prevention and control organization, and region are the main factors affecting the scale of control outsourcing. Thirdly, from a regional perspective, the rice farmers in northern and Western Fujian are more dependent on outsourcing services consumption compared with the rice farmers in Southern Fujian. These results have a clear impact on policymakers, indicating that policy and measures should encourage the prevention and control of the nature of cooperation, and improve the advanced nature of outsourcing facilities of plant protection equipment, thereby effectively improving the professional level of rice pest and disease control.
Spatiotemporal pattern and coordination relationship between urban residential land price and land use intensity in 31 provinces and cities in China
Authors: Cai Xingran , Liang Yanqing , Huang Zhiying , Ge Jingfeng
Published: July 2021

The trend towards efficient and intensive use of land resources is an inevitable outcome of current social development. The rational matching of urban land prices and land use intensity has become an important factor under accelerating urbanization, and promotes the healthy development of the social economy. Using data on residential land price and on land use intensity for 31 provinces and cities in China, we employ the E-G cointegration test and quadrant map classification to determine the coordination relationship between land price and land use intensity. We then employ HR coordination to calculate the coordination degree of land price and land use intensity, and classify the coordination type accordingly. Our results are as follows. (1) The spatio-temporal distribution of urban land price shows high variability with multiple maxima, and follows a decreasing trend from the southeast coastal area to the northwest inland area and the northeast. (2) The overall land use intensity is at or above the middle level, and shows large spatial differences between provinces, but the agglomeration between provinces is increasing. (3) From the perspective of the relationship between urban land price and land use intensity at the inter-provincial scale, we find that the land price and land use intensity are well coordinated, and the number of provinces has been dynamically changing during different development periods. There is an east-west difference in the spatial distribution of land price and land use intensity coordination level. Different provinces and cities with the same coordination stage show differences in their land price and land use intensity level.
CBS-derived H2S facilitates host colonization of Vibrio cholerae by promoting the iron-dependent catalase activity of KatB
Authors: Ma Yao , Yang Xiaoman , Wang Hongou , Qin Zixin , Yi Chunrong , Shi Changping , Luo Mei , Chen Guozhong , Yan Jin , Liu Xiaoyun , Liu Zhi
Published: July 2021

Sensing and resisting oxidative stress is critical forVibrio choleraeto survive in either the aquatic environment or the gastrointestinal tract. Previous studies mainly focused on the mechanisms of oxidative stress response regulation that rely on enzymatic antioxidant systems, while functions of non-enzymatic antioxidants are rarely discussed inV.cholerae. For the first time, we investigated the role of hydrogen sulfide (H2S), the simplest thiol compound, in protectingV.choleraeagainst oxidative stress. We found that degradation of L-cysteine by putative cystathionine β-synthase (CBS) is the major source of endogenous H2S inV.cholerae. Our results indicate that intracellular H2S level has a positive correlation withcbsexpression, while the enhanced H2S production can renderV.choleraecells less susceptible to H2O2in vitro. Using proteome analysis and real-time qPCR assay, we found thatcbsexpression could stimulate the expression of several enzymatic antioxidants, including reactive oxygen species (ROS) detoxifying enzymes SodB, KatG and AhpC, the DNA protective protein DPS and the protein redox regulator Trx1. Assays of ROS detoxification capacities revealed that CBS-derived H2S could promote catalase activity at the post-translational level, especially for KatB, which serves as an important way that endogenous H2S participates in H2O2detoxification. The enhancement of catalase activity by H2S is achieved through facilitating the uptake of iron. Adult mice experiments showed thatcbsmutant has colonization defect, while either complementation ofcbsor exogenous supplement of N-Acetyl-L-Cysteine restores its fitness in the host environment. Herein, we proposed thatV.choleraeregulates CBS-dependent H2S production for better survival and proliferation under ROS stress.