bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterogeneity in transmission parameters of hookworm infection within the baseline data from the TUMIKIA study in Kenya
Authors: Truscott James E. , Ower Alison K. , Werkman Marleen , Halliday Katherine , Oswald William E. , Gichuki Paul M. , Mcharo Carlos , Brooker Simon , Njenga Sammy M. , Mwandariwo Charles , Walson Judd L. , Pullan Rachel , Anderson Roy 
Published: September 2019

Abstract

Background
As many countries with endemic soil-transmitted helminth (STH) burdens achieve high coverage levels of mass drug administration (MDA) to treat school-aged and pre-school-aged children, understanding the detailed effects of MDA on the epidemiology of STH infections is desirable in formulating future policies for morbidity and/or transmission control. Prevalence and mean intensity of infection are characterized by heterogeneity across a region, leading to uncertainty in the impact of MDA strategies. In this paper, we analyze this heterogeneity in terms of factors that govern the transmission dynamics of the parasite in the host population.

Results
Using data from the TUMIKIA study in Kenya (cluster STH prevalence range at baseline: 0–63%), we estimated these parameters and their variability across 120 population clusters in the study region, using a simple parasite transmission model and Gibbs-sampling Monte Carlo Markov chain techniques. We observed great heterogeneity in R0 values, with estimates ranging from 1.23 to 3.27, while k-values (which vary inversely with the degree of parasite aggregation within the human host population) range from 0.007 to 0.29 in a positive association with increasing prevalence. The main finding of this study is the increasing trend for greater parasite aggregation as prevalence declines to low levels, reflected in the low values of the negative binomial parameter k in clusters with low hookworm prevalence. Localized climatic and socioeconomic factors are investigated as potential drivers of these observed epidemiological patterns.

Conclusions
Our results show that lower prevalence is associated with higher degrees of aggregation and hence prevalence alone is not a good indicator of transmission intensity. As a consequence, approaches to MDA and monitoring and evaluation of community infection status may need to be adapted as transmission elimination is aimed for by targeted treatment approaches.
Estimating helminth burdens using sibship reconstruction
Authors: Neves M. Inês , Webster Joanne P. , Walker Martin 
Published: September 2019

AbstractBackgroundSibship reconstruction is a form of parentage analysis that can be used to identify the number of helminth parental genotypes infecting individual hosts using genetic data on only their offspring. This has the potential to be used for estimating individual worm burdens when adult parasites are otherwise inaccessible, the case for many of the most globally important human helminthiases and neglected tropical diseases. Yet methods of inferring worm burdens from sibship reconstruction data on numbers of unique parental genotypes are lacking, limiting the method’s scope of application.ResultsWe developed a novel statistical method for estimating female worm burdens from data on the number of unique female parental genotypes derived from sibship reconstruction. We illustrate the approach using genotypic data onSchistosoma mansoni(miracidial) offspring collected from schoolchildren in Tanzania. We show how the bias and precision of worm burden estimates critically depends on the number of sampled offspring and we discuss strategies for obtaining sufficient sample sizes and for incorporating judiciously formulated prior information to improve the accuracy of estimates.ConclusionsThis work provides a novel approach for estimating individual-level worm burdens using genetic data on helminth offspring. This represents a step towards a wider scope of application of parentage analysis techniques. We discuss how the method could be used to assist in the interpretation of monitoring and evaluation data collected during mass drug administration programmes targeting human helminthiases and to help resolve outstanding questions on key population biological processes that govern the transmission dynamics of these neglected tropical diseases.
Pooling as a strategy for the timely diagnosis of soil-transmitted helminths in stool: value and reproducibility
Authors: Papaiakovou Marina , Wright James , Pilotte Nils , Chooneea Darren , Schär Fabian , Truscott James E. , Dunn Julia C. , Gardiner Iain , Walson Judd L. , Williams Steven A. , Littlewood D. Timothy J. 
Published: September 2019

Abstract

Background
The strategy of pooling stool specimens has been extensively used in the field of parasitology in order to facilitate the screening of large numbers of samples whilst minimizing the prohibitive cost of single sample analysis. The aim of this study was to develop a standardized reproducible pooling protocol for stool samples, validated between two different laboratories, without jeopardizing the sensitivity of the quantitative polymerase chain reaction (qPCR) assays employed for the detection of soil-transmitted helminths (STHs). Two distinct experimental phases were recruited. First, the sensitivity and specificity of the established protocol was assessed by real-time PCR for each one of the STHs. Secondly, agreement and reproducibility of the protocol between the two different laboratories were tested. The need for multiple stool sampling to avoid false negative results was also assessed. Finally, a cost exercise was conducted which included labour cost in low- and high-wage settings, consumable cost, prevalence of a single STH species, and a simple distribution pattern of the positive samples in pools to estimate time and money savings suggested by the strategy.

Results
The sensitivity of the pooling method was variable among the STH species but consistent between the two laboratories. Estimates of specificity indicate a ‘pooling approach’ can yield a low frequency of ‘missed’ infections. There were no significant differences regarding the execution of the protocol and the subsequent STH detection between the two laboratories, which suggests in most cases the protocol is reproducible by adequately trained staff. Finally, given the high degree of agreement, there appears to be little or no need for multiple sampling of either individuals or pools.

Conclusions
Our results suggest that the pooling protocol developed herein is a robust and efficient strategy for the detection of STHs in ‘pools-of-five’. There is notable complexity of the pool preparation to ensure even distribution of helminth DNA throughout. Therefore, at a given setting, cost of labour among other logistical and epidemiological factors, is the more concerning and determining factor when choosing pooling strategies, rather than losing sensitivity and/or specificity of the molecular assay or the method.
Impact of urate-lowering drugs on the progression and recovery from chronic kidney disease among gout patients
Authors: Chung Ting-Ting , Yu Kuang-Hui , Kuo Chang-Fu , Luo Shue-Fen , Chiou Meng-Jiun , Lan Wen-Ching , Chen Jung-Sheng , Tseng Wen-Yi , Hsieh Ao-Ho , Wang Lian-Chin 
Published: September 2019

Abstract

Background
This study investigates the association between exposure to urate-lowering drugs (ULDs) and progression and recovery from chronic kidney disease (CKD).

Methods
We identified 5860 incident gout patients at Chang Gung Memorial Hospital from 2012 to 2015. Propensity score (PS)-weighted Cox proportional hazards model was used to estimate hazard ratios (HRs) for CKD progression and improvement. A separate analysis was conducted to assess the HR for CKD progression and CKD recovery among those with worsening CKD.

Results
The incidence of CKD progression among allopurinol, febuxostat and uricosuric agent users were 1.98, 1.88 and 1.64 per 1000 person-days. Compared with allopurinol users, the PS-weighted HR (95% confidence intervals [CIs]) was 1.77 (0.85–1.76) for febuxostat users and 1.37 (0.71–1.37) for uricosuric agent users for CKD progression and 1.43 (1.26–1.62) for febuxostat users and 1.00 (0.88–1.14) for uricosuric agent users for CKD improvement. Compared to allopurinol users, the HRs for CKD progression were 1.14 (0.80–1.66) for febuxostat users and 0.92 (0.67–1.31) for uricosuric agent users. Among 741 patients who had CKD progression, the incidence of CKD recovery was 1.33, 6.21 and 3.53 per 1000 person-days for allopurinol, febuxostat and uricosuric agent users. The HRs (95% CIs) for recovery in febuxostat and uricosuric agent users were 2.17 (1.40–3.47) and 1.80 (1.20–2.83) compared to allopurinol users.

Conclusions
CKD progression and recovery are common in gout patients using ULDs. Febuxostat and benzbromarone were associated with a similar risk of CKD progression with allopurinol, which has a poorer recovery compared with other ULDs.
Routine lung ultrasound to detect postoperative pulmonary complications following major abdominal surgery: a prospective observational feasibility study
Authors: Touw H. R. , Schuitemaker A. E. , Daams F. , van der Peet D. L. , Bronkhorst E. M. , Schober P. , Boer C. , Tuinman P. R. 
Published: September 2019

Abstract

Background
Postoperative pulmonary complications after major abdominal surgery are associated with adverse outcome. The diagnostic accuracy of chest X-rays (CXR) to detect pulmonary disorders is limited. Alternatively, lung ultrasound (LUS) is an established evidence-based point-of-care diagnostic modality which outperforms CXR in critical care. However, its feasibility and diagnostic ability for postoperative pulmonary complications following abdominal surgery are unknown. In this prospective observational feasibility study, we included consecutive patients undergoing major abdominal surgery with an intermediate or high risk developing postoperative pulmonary complications according to the Assess Respiratory risk In Surgical patients in CATalonia (ARISCAT) score. LUS was routinely performed on postoperative days 0–3 by a researcher blinded for CXR or other clinical findings. Then, reports were drawn up for LUS concerning feasibility and detection rates of postoperative pulmonary complications. CXRs were performed on demand according to daily clinical practice. Subsequently, we compared LUS and CXR findings.

Results
A total of 98 consecutive patients with an ARISCAT score of 41 (34–49) were included in the study. LUS was feasible in all patients. In 94 (95%) patients, LUS detected one or more postoperative pulmonary complications during the first four postoperative days. On day 0, LUS detected 31 out of 43 patients (72.1%) with one or more postoperative pulmonary complications, compared to 13 out of 36 patients (36.1%) with 1 or more postoperative pulmonary complications detected with CXR RR 2.0 (95 CI [1.24–3.20]) (p = 0.004). The number of discordant observations between both modalities was high for atelectasis 23 (43%) and pleural effusion 29 (54%), but not for pneumothorax, respiratory infection and pulmonary edema 8 (15%), 3 (5%), and 5 (9%), respectively.

Conclusions
This study shows that LUS is highly feasible and frequently detects postoperative pulmonary complications after major abdominal surgery. Discordant observations in atelectasis and pleural effusions for LUS and CXR can be explained by a superior diagnostic ability of LUS in detecting these conditions. The effects of LUS as primary imaging modality on patient outcome should be evaluated in future studies.
A pilot prospective study of sleep patterns and DNA methylation-characterized epigenetic aging in young adults
Authors: Carskadon Mary A. , Chappell Kenneth R. , Barker David H. , Hart Anne C. , Dwyer Kayla , Gredvig-Ardito Caroline , Starr Caitlyn , McGeary John E. 
Published: September 2019

Abstract

Objective
Molecular markers in DNA methylation at a subset of CpG sites are affected by the environment and contribute to biological (epigenetic) age. We hypothesized that shorter sleep duration and possibly irregular sleep would be associated with accelerated epigenetic aging. We examined epigenetic vs. chronological age in 12 young women selected as shorter or longer sleepers studied prospectively across the first 9 weeks of college using a daily online sleep log. Genomic DNA was isolated from two blood samples spanning the interval, and DNA methylation levels were determined and used to measure epigenetic age.

Results
Epigenetic vs. chronological age differences averaged 2.07 at Time 1 and 1.21 at Time 2. Sleep duration was computed as average daily total sleep time and sleep regularity was indexed using the Sleep Regularity Index. Participants with longer and more regular sleep showed reduced age difference: mean = − 2.48 [95% CI − 6.11; 1.15]; those with shorter and more irregular sleep showed an increased age difference: 3.03 [0.02; 6.03]; and those with either shorter or more irregular sleep averaged no significant change: − 0.49 [− 3.55; 2.56]. These pilot data suggest that short and irregular sleep, even in a young healthy sample, may be associated with accelerated epigenetic aging.
Successful balloon valvuloplasty of a subpulmonic membrane associated with cor triatriatum dexter: a case report
Authors: Haboub Meryem , Drighil Abdenasser 
Published: September 2019

Abstract

Background
Subpulmonic membrane as a cause of right ventricular outflow tract obstruction in patients with concordant ventriculoarterial connection and intact ventricular septum is considered to be rare. Association with cor triatriatum dexter and success of subpulmonic balloon valvuloplasty have never been reported, at least to the best of our knowledge.

Case presentation
A 3-year-old Moroccan boy was referred to our tertiary care hospital with complaints of dyspnea on moderate exertion. A physical examination revealed parasternal lift, systolic thrill, and a 4/6 ejection systolic murmur, best heard over the left second intercostal space. His oxygen saturation was 99% on room air. Two-dimensional echocardiography showed a discrete circumferential membrane just below the pulmonic valve and a right atrial membrane. Continuous wave Doppler interrogation showed peak systolic pressure gradient of 85 mmHg across the subpulmonic membrane and no significant gradient across the right atrial membrane. Balloon dilation of the subpulmonic membrane was performed and the pressure gradient came down to 50 mmHg. During follow-up, he reported marked improvement in terms of exercise tolerance. Transthoracic echocardiography showed residual pressure gradient of approximately 40 mmHg across the membrane. Surgery resection of the two membranes was programmed, but he died after an extracardiac disease (appendicular peritonitis).

Conclusions
Subpulmonic membrane as an isolated cause of right ventricular outflow tract obstruction is rare. Its association with cor triatriatum dexter is even less common. The result of percutaneous balloon valvuloplasty of subpulmonic membrane is an interesting alternative while waiting for surgery. Surgery is currently the preferred modality of treatment with the resection of both right atrial and subpulmonic membranes.
Peripheral and placental immune responses in sheep after experimental infection with Toxoplasma gondii at the three terms of gestation
Authors: Castaño Pablo , Fernández Miguel , Regidor-Cerrillo Javier , Fuertes Miguel , Horcajo Pilar , Ferre Ignacio , Ferreras M. Carmen , Ortega-Mora Luis Miguel , Pérez Valentín , Benavides Julio 
Published: September 2019

Abstract
Although it is known that gestation could influence the clinical course of ovine toxoplasmosis, the precise effect of the term of gestation when sheep are infected are yet mostly unknown. The aim of this study was to evaluate the peripheral and placental immune responses developed in pregnant sheep after experimental infection with Toxoplasma gondii at different times of gestation. Thirty-six pregnant sheep were allocated in different groups, orally inoculated with sporulated oocysts of T. gondii at early, mid and late gestation and culled within 30 days post-infection. The peripheral humoral and cytokine responses were evaluated, as well as the transcription of cytokines at the placenta. Serological analysis revealed that, regardless the term of gestation when infected, specific IgG against T. gondii were detected from day 8 post-infection and there was an early peripheral release of IFN-γ at the first week post-infection followed by a short peak of IL10 and TNF-α at the second week post-infection. There were no significant differences in this response between infected groups. At the placenta, a similar increase in transcription of IFN-γ, and TNF-α was found at the three terms of gestation, while IL-4 increased mainly at the first and second terms and IL-10 transcription was higher at the last term. While these findings show that both Th1 and Th2 cytokines play a key role in the pathogenesis of ovine toxoplasmosis and that placental and peripheral immune responses do not closely correlate, there seems to be no clear modulation of these responses along the gestation.
Optimal Mixture Design of Low-CO2 High-Volume Slag Concrete Considering Climate Change and CO2 Uptake
Authors: Lee Han-Seung , Lim Seung-Min , Wang Xiao-Yong 
Published: September 2019

Abstract
High-volume slag (HVS) can reduce the CO2 emissions of concrete, but increase the carbonation depth of concrete. In particular, because of the effects of climate change, carbonation will accelerate. However, the uptake of CO2 as a result of carbonation can mitigate the harm of CO2 emissions. This study proposes an optimal mixture design method of low-CO2 HVS concrete considering climate change, carbonation, and CO2 uptake. Firstly, net CO2 emissions are calculated by subtracting the CO2 emitted by the material from the uptake of CO2 by carbonation. The strength and depth of carbonation are evaluated by a comprehensive model based on hydration. Secondly, a genetic algorithm (GA) is used to find the optimal mixture. The objective function of the GA is net CO2 emissions. The constraints of the GA include the strength, carbonation, workability, and range of concrete components. Thirdly, the results show that carbonation durability is a control factor of the mixture design of low-strength HVS concrete, while strength is a control factor of the mixture design of high-strength HVS concrete. After considering climate change, the threshold of strength control increases. With the increase of strength, the net CO2 emissions increase, while the CO2 uptake ratio decreases.
Effect of different dietary protein levels and amino acids supplementation patterns on growth performance, carcass characteristics and nitrogen excretion in growing-finishing pigs
Authors: Zhao Yumei , Tian Gang , Chen Daiwen , Zheng Ping , Yu Jie , He Jun , Mao Xiangbing , Huang Zhiqing , Luo Yuheng , Luo Junqiu , Yu Bing 
Published: September 2019

Abstract

Background
This study was conducted to determine the effects of different dietary protein levels and amino acids supplementation patterns in low protein diets on the growth performance, carcass characteristics and nitrogen excretion in growing-finishing pigs.
Forty-two barrows (25.00 ± 0.39 kg) were randomly assigned to 7 diets. Diet 1: the high crude protein diet with balanced for 10 essential amino acids (EAAs). Diet 2: the medium crude protein diet with 2% (approx) decreased protein level of Diet 1 and balanced 10 EAAs. Diet 3: the low crude protein diet with 4% decreased protein level of Diet 1 and balanced 10 EAAs. The protein levels of Diet 4, 5, 6 and 7 were the same as that of Diet 3. Diet 4 was only balanced for lysine (Lys), methionine (Met), threonine (Thr) and tryptophan (Trp); Diet 5 and 6 were further supplemented with extra isoleucine (Ile) or valine (Val), respectively; Diet 7 was further supplemented with extra Ile + Val.

Results
Over the 112 days trial, the reduction of dietary protein by 2% or 4% with balanced10 EAAs significantly decreased nitrogen excretion (P <  0.05), but had no effects on growth performance and carcass characteristics (P > 0.05). In low protein diet, Val supplementation significantly increased body weight gain at 25–50 kg phase (P <  0.05), while Ile supplementation at 75–100 kg phase and 100–125 kg phase significantly reduced the ratio of feed to gain (P <  0.05). No effect of different dietary protein levels and amino acids supplementation patterns in low protein diets on carcass characteristics was observed (P > 0.05). The total N excretion of pigs supplemented with only Lys, Met, Thr and Trp was numerically higher than that of pigs fed with extra Ile, or Val, or Ile + Val diets.

Conclusion
In low protein diet, Val is more required than Ile in the early growing phage (25–50 kg), while Ile becomes more required in the late growing and finishing phage (75–125 kg).
Silver staining (Campbell-Switzer) of neuronal α-synuclein assemblies induced by multiple system atrophy and Parkinson’s disease brain extracts in transgenic mice
Authors: Lavenir Isabelle , Passarella Daniela , Masuda-Suzukake Masami , Curry Annabelle , Holton Janice L. , Ghetti Bernardino , Goedert Michel 
Published: September 2019

AbstractSynucleinopathies [Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA)] share filamentous α-synuclein assemblies in nerve cells and glial cells. We compared the abilities of brain extracts from MSA and PD patients to induce neuronal α-synuclein assembly and neurodegeneration following intracerebral injection in heterozygous mice transgenic for human mutant A53T α-synuclein. MSA extracts were more potent than PD extracts in inducing α-synuclein assembly and in causing neurodegeneration. MSA assemblies were Campbell-Switzer- and Gallyas-silver-positive, whereas PD assemblies were only Campbell-Switzer-positive, in confirmation of previous findings. However, induced α-synuclein inclusions were invariably Campbell-Switzer-positive and Gallyas-negative, irrespective of whether MSA or PD brain extracts were injected. The α-synuclein inclusions of non-injected homozygous mice transgenic for A53T α-synuclein were also Campbell-Switzer-positive and Gallyas-negative. These findings demonstrate that transgene expression and its intracellular environment dominated over the silver staining properties of the conformers of assembled α-synuclein.
Fading into the background: the dark space surrounding Vermeer’s Girl with a Pearl Earring
Authors: Vandivere Abbie , van Loon Annelies , Callewaert Tom , Haswell Ralph , Proaño Gaibor Art Ness , van Keulen Henk , Leonhardt Emilien , Dik Joris 
Published: September 2019

Abstract
The background of Vermeer’s Girl with a Pearl Earring (c. 1665, Mauritshuis) has, until recently, been interpreted as a flat dark space. The painting was examined in 2018 as part of the research project The Girl in the Spotlight using a combination of micro- and macro-scale analytical techniques. The stratigraphy of the background was determined from samples mounted as cross-sections, and its material composition was analysed using electron microscopy and chromatographic techniques. The underlayer contains mainly charcoal black, and the glaze contains two organic colourants—indigo and weld—and a copper drier. Deterioration of the glaze has made features in the background difficult to discern with the naked eye. Complementary imaging techniques were able to visualise Vermeer’s signature, and the suggestion of folded fabric (possibly a curtain) on the right side of the painting. The distribution of the layer(s) in the background were imaged using: infrared reflectography (900–1100 nm), multi-scale optical coherence tomography scanning, macroscopic X-ray fluorescence and 3D digital microscopy. Vermeer applied the black underlayer vigorously with overlapping brushstrokes that varied in thickness. When he applied the glaze on top, it levelled out to make a smooth flat surface. The visual effect of the background contrasts the figure of the Girl and projects her forward in space, closer to the viewer.