bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monthly biological larviciding associated with a tenfold decrease in larval density in fish farming ponds and reduced community-wide malaria incidence in northwestern Brazil
Authors: Fontoura Pablo S. , Silva Marcos F. , da Costa Anderson S. , Ribeiro Francismar S. , Ferreira Marcílio S. , Ladeia-Andrade Simone , Tonini Juliana , Rodrigues Priscila T. , Castro Marcia C. , Ferreira Marcelo U. 
Published: September 2021

Abstract
Background
Larvicides are typically applied to fixed and findable mosquito breeding sites, such as fish farming ponds used in commercial aquaculture, to kill immature forms and thereby reduce the size of adult malaria vector populations. However, there is little evidence suggesting that larviciding may suppress community-wide malaria transmission outside Africa. Here, we tested whether the biological larvicide VectoMax FG applied at monthly intervals to fish farming ponds can reduce malaria incidence in Amazonian Brazil.

Methods
This study was carried out in Vila Assis Brasil (VAB; population 1700), a peri-urban malaria hotspot in northwestern Brazil with a baseline annual parasite incidence of 553 malaria cases per 1000 inhabitants. The intervention consisted of monthly treatments with 20 kg/ha of VectoMax FG of all water-filled fish ponds in VAB (n ranging between 167 and 170) with a surface area between 20 and 8000 m2, using knapsack power mistblowers. We used single-group interrupted time-series analysis to compare monthly larval density measurements in fish ponds during a 14-month pre-intervention period (September 2017–October 2018), with measurements made during November 2018–October 2019 and shortly after the 12-month intervention (November 2019). We used interrupted time-series analysis with a comparison group to contrast the malaria incidence trends in VAB and nearby nonintervention localities before and during the intervention.

Results
Average larval densities decreased tenfold in treated fish farming ponds, from 0.467 (95% confidence interval [CI], 0.444–0.490) anopheline larvae per dip pre-intervention (September 2017–October 2018) to 0.046 (95% CI, 0.041–0.051) larvae per dip during (November 2018–October 2019) and shortly after the intervention (November 2019). Average malaria incidence rates decreased by 0.08 (95% CI, 0.04–0.11) cases per 100 person-months (P < 0.0001) during the intervention in VAB and remained nearly unchanged in comparison localities. We estimate that the intervention averted 24.5 (95% CI, 6.2–42.8) malaria cases in VAB between January and December 2019.

Conclusions
Regular larviciding is associated with a dramatic decrease in larval density and a modest but significant decrease in community-wide malaria incidence. Larviciding may provide a valuable complementary vector control strategy in commercial aquaculture settings across the Amazon.

Graphical abstract
Longitudinal trends in screening males and females for intimate partner violence as part of a systemic multi-specialty health system intervention
Authors: Clark Cari Jo , Renner Lynette M. , Wang Qi , Flowers Nyla I. , Morrow Grace , Logeais Mary 
Published: September 2021

Abstract
Objective
To assess intimate partner violence screening for males and females in a health system that underwent a systemic intervention to improve survivor identification and response. Electronic health record data from 13 clinics were accessed for February of 2017, 2018, and 2019 to calculate screening rates and positive screening rates for intimate partner violence by clinic and sex-race groups (n  =  11,693 non-Hispanic White females; n  =  4318 Other females; n  =  9184 non-Hispanic White males; n  =  3441 Other males). Linear mixed effects models were used to examine whether screening rates differed significantly over time and by sex-race group.

Results
Screening rates were 31% for the first 2 years and 16% for 2019. Screening rates varied greatly by clinic. Dermatology, psychiatry, and otolaryngology clinics had average or above screening rates all 3 years. Differences in screening rates across sex-race groups were minimal. Average positive screen rates were 1.3%, 0.4%, and 2.6% in 2017, 2018, and 2019, respectively, with psychiatry having the highest positive screen rate. Positive screen rates were highest for non-Hispanic White females (3.5%). Universal screening in this health system was not yielding survivors comparable to existing estimates among clinic-based populations. Other identification approaches require testing to effectively identify survivors within the health sector.
Tubulointerstitial nephritis and uveitis syndrome in an adolescent female: a case report
Authors: Petek Tadej , Frelih Maja , Marčun Varda Nataša 
Published: September 2021

Abstract
Background
Tubulointerstitial nephritis with uveitis syndrome is a rare disease affecting mainly children and young women. Tubulointerstitial nephritis with uveitis is a diagnosis of exclusion, requiring a high degree of clinical suspicion. Studies report recent infections or certain drugs as precipitating factors of a lymphocytic oculorenal immune response. The prognosis is usually favorable with topical and systemic corticosteroid therapy.

Case presentation
We report a literature review and the case of a 14-year-old white girl, who presented to the ophthalmology department with features of one-sided uveitis. Upon transfer of patient to nephrological care, diagnostic work-up revealed renal involvement. Renal biopsy showed a mixed-cell and granulomatous tubulointerstitial nephritis with some noncaseating granulomas, leading to a diagnosis of tubulointerstitial nephritis with uveitis syndrome. With topical ocular and systemic corticosteroid therapy, the patients’ condition improved over several weeks.

Conclusions
Our case highlights the importance of early recognition and treatment of this syndrome, where cross-specialty care typically leads to a favorable outcome.
Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products
Authors: Tam Jason Y. C. , Lorsbach Tim , Schmidt Sebastian , Wicker Jörg S. 
Published: September 2021

AbstractThe prediction of metabolism and biotransformation pathways of xenobiotics is a highly desired tool in environmental sciences, drug discovery, and (eco)toxicology. Several systems predict single transformation steps or complete pathways as series of parallel and subsequent steps. Their performance is commonly evaluated on the level of a single transformation step. Such an approach cannot account for some specific challenges that are caused by specific properties of biotransformation experiments. That is, missing transformation products in the reference data that occur only in low concentrations, e.g. transient intermediates or higher-generation metabolites. Furthermore, some rule-based prediction systems evaluate the performance only based on the defined set of transformation rules. Therefore, the performance of these models cannot be directly compared. In this paper, we introduce a new evaluation framework that extends the evaluation of biotransformation prediction from single transformations to whole pathways, taking into account multiple generations of metabolites. We introduce a procedure to address transient intermediates and propose a weighted scoring system that acknowledges the uncertainty of higher-generation metabolites. We implemented this framework in enviPath and demonstrate its strict performance metrics on predictions of in vitro biotransformation and degradation of xenobiotics in soil. Our approach is model-agnostic and can be transferred to other prediction systems. It is also capable of revealing knowledge gaps in terms of incompletely defined sets of transformation rules.
Simvastatin does not alleviate muscle pathology in a mouse model of Duchenne muscular dystrophy
Authors: Mucha Olga , Podkalicka Paulina , Kaziród Katarzyna , Samborowska Emilia , Dulak Józef , Łoboda Agnieszka 
Published: September 2021

Abstract
Background
Duchenne muscular dystrophy (DMD) is an incurable disease, caused by the mutations in the DMD gene, encoding dystrophin, an actin-binding cytoskeletal protein. Lack of functional dystrophin results in muscle weakness, degeneration, and as an outcome cardiac and respiratory failure. As there is still no cure for affected individuals, the pharmacological compounds with the potential to treat or at least attenuate the symptoms of the disease are under constant evaluation. The pleiotropic agents, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors, known as statins, have been suggested to exert beneficial effects in the mouse model of DMD. On the other hand, they were also reported to induce skeletal-muscle myopathy. Therefore, we decided to verify the hypothesis that simvastatin may be considered a potential therapeutic agent in DMD.

Methods
Several methods including functional assessment of muscle function via grip strength measurement, treadmill test, and single-muscle force estimation, enzymatic assays, histological analysis of muscle damage, gene expression evaluation, and immunofluorescence staining were conducted to study simvastatin-related alterations in the mdx mouse model of DMD.

Results
In our study, simvastatin treatment of mdx mice did not result in improved running performance, grip strength, or specific force of the single muscle. Creatine kinase and lactate dehydrogenase activity, markers of muscle injury, were also unaffected by simvastatin delivery in mdx mice. Furthermore, no significant changes in inflammation, fibrosis, and angiogenesis were noted. Despite the decreased percentage of centrally nucleated myofibers in gastrocnemius muscle after simvastatin delivery, no changes were noticed in other regeneration-related parameters. Of note, even an increased rate of necrosis was found in simvastatin-treated mdx mice.

Conclusion
In conclusion, our study revealed that simvastatin does not ameliorate DMD pathology.
Growth performances, gastrointestinal epithelium and bacteria responses of Yellow-feathered chickens to kudzu-leaf flavonoids supplement
Authors: Xue Fuguang , Wan Gen , Xiao Yunsen , Chen Chuanbin , Qu Mingren , Xu Lanjiao 
Published: September 2021

AbstractThe objective of this study was to investigate the effects of replacing antibiotics with Kudzu-leaf flavonoids (KLF) on the growth performances, gut epithelial development, and gastrointestinal bacteria diversities of Yellow-feathered broilers. For this purpose, total of 216 1-day-old male Yellow-feathered chickens with the similar birth weight (31.0  ±  1.0 g) were randomly divided into 3 treatments: the control treatment (CON), the kudzu-leaf flavonoids supplement treatment (KLF), and the antibiotics supplement treatment (AGP). All birds were provided with a 56 d-feeding procedure, followed by the measurement of production performances, immune organs, blood anti-oxidant parameters, intestine epithelium development, and cecal microbiota. Results showed the feed conversion ratio significantly decreased after KLF supplement compared with CON (P  <  0.05). KLF supplement partly promoted the anti-oxidant capacity on account of the increased activity of Superoxide dismutase (SOD) and the decrease content of malondialdehyde (MDA). Further, as referred to the gastrointestinal development and bacteria, ratio of villus/crypt significantly increased of ileum in KLF treatment (P  <  0.05) while a significant promition of bacterial diversity and partial representative probiotic bacteria (P  <  0.05) after KLF supplementation. Moreover, correlation analysis indicated that probitics including Bifidobacterium, Butyricimonas, Lactobacillus and Streptococcus positively correlated with production performances. In conclusion, KLF supplement may promote feed efficiency and benefit the gastrointestinal health through improving gut bacterial diversity and probiotic bacteria. The KLF might be applied as a proper antibiotic alternative.
The weak solutions of a nonlinear parabolic equation from two-phase problem
Authors: Huang Zhisheng 
Published: September 2021

AbstractA nonlinear parabolic equation from a two-phase problem is considered in this paper. The existence of weak solutions is proved by the standard parabolically regularized method. Different from the related papers, one of diffusion coefficients in the equation, $b(x)$
b
(
x
)
, is degenerate on the boundary. Then the Dirichlet boundary value condition may be overdetermined. In order to study the stability of weak solution, how to find a suitable partial boundary value condition is the foremost work. Once such a partial boundary value condition is found, the stability of weak solutions will naturally follow.
A Jackson-type inequality associated with wavelet bases decomposition
Authors: Wang Kai-Cheng 
Published: September 2021

AbstractAlthough wavelet decompositions of functions in Besov spaces have been extensively investigated, those involved with mild decay bases are relatively unexplored. In this paper, we study wavelet bases of Besov spaces and the relation between norms and wavelet coefficients. We establish the $l^{p}$

l
p

-stability as a measure of how effectively the Besov norm of a function is evaluated by its wavelet coefficients and the $L^{p}$

L
p

-completeness of wavelet bases. We also discuss wavelets with decay conditions and establish the Jackson inequality.
Analysing the relationship between CO2 emissions and GDP in China: a fractional integration and cointegration approach
Authors: Caporale Guglielmo Maria , Claudio-Quiroga Gloria , Gil-Alana Luis A. 
Published: September 2021

AbstractThis paper examines the relationship between the logarithms of carbon dioxide (CO2) emissions and real Gross Domestic Product (GDP) in China by applying fractional integration and cointegration methods. These are more general than the standard methods based on the dichotomy between stationary and non-stationary series, allow for a much wider variety of dynamic processes, and provide information about the persistence and long-memory properties of the series and thus on whether or not the effects of shocks are long-lived. The univariate results indicate that the two series are highly persistent, their orders of integration being around 2, whilst the cointegration tests (using both standard and fractional techniques) imply that there exists a long-run equilibrium relationship between the two variables in first differences, i.e. their growth rates are linked together in the long run. This suggests the need for environmental policies aimed at reducing emissions during periods of economic growth.
What evidence exists on the relationship between agricultural production and biodiversity in tropical rainforest areas? A systematic map protocol
Authors: Apriyani Via , Holle Mukhlish J. M. , Silangen Christian , Oktalira Fitria T. , Mumbunan Sonny 
Published: September 2021

AbstractBackgroundAgriculture produces food for billions of humans and creates livelihoods for farmers. However, the current food production systems, driven by the increasing food demand and the ever-growing human population, are undermining ecological resources, primarily those related to biodiversity. Accordingly, agricultural production in tropical rainforest countries has been a trade-off, as regions harbor high biodiversity while also being pressured by agricultural land expansion. Consequently, threats to biodiversity are inevitable and will likely affect the ecosystem service provisions necessary for the agricultural process. Presently, no study reviews and maps the evidence of relationships between biodiversity and agriculture in the tropical rainforest landscape. Therefore, such a study is necessary to identify the knowledge gaps and provide scientific evidence to the relevant policymakers for safeguarding biodiversity within agricultural policies. This study aims to collect available published literature that evaluates the relations of agricultural production and biodiversity. We will focus on the agriculture and priority crops in the countries producing the commodities situated in the tropical rainforest landscape.MethodsGeneric search terms derived from research question elements will be used to search relevant articles. These terms are in English, and the searches will encompass global tropical rainforest countries. Peer-reviewed and gray literature articles retrieved from search engines and databases will be screened first using the title and abstract and second at the full-text level. The latter screening process will involve data coding to retrieve relevant characteristics from each eligible study and finally collate these characteristics into an evidence map, which will provide a current state of knowledge and further support evidence-informed policy formulation. The map presentation in the final report will also be complemented by a narrative synthesis explaining the trends, pinpointing the knowledge gluts and gaps, serving relevant information, and searchable databases for associated stakeholders.
Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage–bacteria interplay in deep-sea snail holobionts
Authors: Zhou Kun , Xu Ying , Zhang Rui , Qian Pei-Yuan 
Published: September 2021

Abstract
Background
Deep-sea animals in hydrothermal vents often form endosymbioses with chemosynthetic bacteria. Endosymbionts serve essential biochemical and ecological functions, but the prokaryotic viruses (phages) that determine their fate are unknown.

Results
We conducted metagenomic analysis of a deep-sea vent snail. We assembled four genome bins for Caudovirales phages that had developed dual endosymbiosis with sulphur-oxidising bacteria (SOB) and methane-oxidising bacteria (MOB). Clustered regularly interspaced short palindromic repeat (CRISPR) spacer mapping, genome comparison, and transcriptomic profiling revealed that phages Bin1, Bin2, and Bin4 infected SOB and MOB. The observation of prophages in the snail endosymbionts and expression of the phage integrase gene suggested the presence of lysogenic infection, and the expression of phage structural protein and lysozyme genes indicated active lytic infection. Furthermore, SOB and MOB appear to employ adaptive CRISPR–Cas systems to target phage DNA. Additional expressed defence systems, such as innate restriction–modification systems and dormancy-inducing toxin–antitoxin systems, may co-function and form multiple lines for anti-viral defence. To counter host defence, phages Bin1, Bin2, and Bin3 appear to have evolved anti-restriction mechanisms and expressed methyltransferase genes that potentially counterbalance host restriction activity. In addition, the high-level expression of the auxiliary metabolic genes narGH, which encode nitrate reductase subunits, may promote ATP production, thereby benefiting phage DNA packaging for replication.

Conclusions
This study provides new insights into phage–bacteria interplay in intracellular environments of a deep-sea vent snail.
Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Authors: Ling Wodan , Zhao Ni , Plantinga Anna M. , Launer Lenore J. , Fodor Anthony A. , Meyer Katie A. , Wu Michael C. 
Published: September 2021

AbstractBackgroundIdentification of bacterial taxa associated with diseases, exposures, and other variables of interest offers a more comprehensive understanding of the role of microbes in many conditions. However, despite considerable research in statistical methods for association testing with microbiome data, approaches that are generally applicable remain elusive. Classical tests often do not accommodate the realities of microbiome data, leading to power loss. Approaches tailored for microbiome data depend highly upon the normalization strategies used to handle differential read depth and other data characteristics, and they often have unacceptably high false positive rates, generally due to unsatisfied distributional assumptions. On the other hand, many non-parametric tests suffer from loss of power and may also present difficulties in adjusting for potential covariates. Most extant approaches also fail in the presence of heterogeneous effects. The field needs new non-parametric approaches that are tailored to microbiome data, robust to distributional assumptions, and powerful under heterogeneous effects, while permitting adjustment for covariates.MethodsAs an alternative to existing approaches, we propose a zero-inflated quantile approach (ZINQ), which uses a two-part quantile regression model to accommodate the zero inflation in microbiome data. For a given taxon, ZINQ consists of a valid test in logistic regression to model the zero counts, followed by a series of quantile rank-score based tests on multiple quantiles of the non-zero part with adjustment for the zero inflation. As a regression and quantile-based approach, the method is non-parametric and robust to irregular distributions, while providing an allowance for covariate adjustment. Since no distributional assumptions are made, ZINQ can be applied to data that has been processed under any normalization strategy.ResultsThorough simulations based on real data across a range of scenarios and application to real data sets show that ZINQ often has equivalent or higher power compared to existing tests even as it offers better control of false positives.ConclusionsWe present ZINQ, a quantile-based association test between microbiota and dichotomous or quantitative clinical variables, providing a powerful and robust alternative for the current microbiome differential abundance analysis.
Migration and survival of Okanagan River Sockeye Salmon Oncorhynchus nerka, 2012–2019
Authors: Murauskas Josh , Hyatt Kim , Fryer Jeff , Koontz Elliot , Folks Skyeler , Bussanich Richard , Shelby Katy 
Published: September 2021

Abstract
Background
Okanagan River Sockeye Salmon Oncorhynchus nerka (Okanagan Sockeye) are one of two remaining self-sustaining Sockeye Salmon populations in the Columbia River Basin. We used detection histories of smolts implanted with passive integrated transponder (PIT) tags between 2012 and 2019 to estimate survival and behavioral metrics during reintroduction efforts and changing environmental conditions over the monitoring period.

Results
Smolts migrating to McNary Dam, whose route includes 130 km of the Okanagan River and 388 km of the Columbia River, generally had high survival (mean of 87.0% per 100 km) and fast migration speeds (up to 50 km/day) relative to other salmonids in the region. Smolt-to-adult returns (SARs) ranged from 0.4 to 6.1% and were greater for fish originating from Skaha Lake compared to cohorts tagged in Osoyoos Lake. Most adults returned after 2 years in the ocean (69%), followed by jacks (27%), and adults that spent 3 years at sea (4%), though Skaha Lake adults had a significantly younger age structure than cohorts from Osoyoos Lake. Survival of adults from Bonneville Dam (rkm 235) upstream to Wells Dam (rkm 830) was generally high (80–92%), and migration speed decreased in upstream reaches. Survival from Wells Dam to the Okanagan River was only estimable in 2018, where 64% of adults survived to the spawning grounds. The upstream migration of adult Okanagan Sockeye was significantly compromised during the drought of 2015 when less than 5% of Okanagan Sockeye that returned to the Columbia River reached spawning grounds.

Conclusions
Our results indicate that Okanagan Sockeye have exceptional survival and migratory ability relative to other salmonids, though poor ocean conditions combined with warming water temperatures in freshwater habitats in recent years have the potential to devastate the population. The success of reintroduction efforts to increase spatial structure and diversity of Okanagan Sockeye is, therefore, critical to maintaining the population in years to come.