bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of montelukast in children with sickle cell disease (SMILES): a study protocol for a randomised controlled trial
Authors: Hood Anna M. , Stotesbury Hanne , Kölbel Melanie , DeHaan Michelle , Downes Michelle , Kawadler Jamie M. , Sahota Satwinder , Dimitriou Dagmara , Inusa Baba , Wilkey Olu , Pelidis Maria , Trompeter Sara , Leigh Andrea , Younis Janine , Drasar Emma , Chakravorty Subarna , Rees David C. , Height Sue , Lawson Sarah , Gavlak Johanna , Gupta Atul , Ridout Deborah , Clark Christopher A. , Kirkham Fenella J. 
Published: October 2021

AbstractBackgroundYoung children with sickle cell anaemia (SCA) often have slowed processing speed associated with reduced brain white matter integrity, low oxygen saturation, and sleep-disordered breathing (SDB), related in part to enlarged adenoids and tonsils. Common treatments for SDB include adenotonsillectomy and nocturnal continuous positive airway pressure (CPAP), but adenotonsillectomy is an invasive surgical procedure, and CPAP is rarely well-tolerated. Further, there is no current consensus on the ability of these treatments to improve cognitive function. Several double-blind, randomised controlled trials (RCTs) have demonstrated the efficacy of montelukast, a safe, well-tolerated anti-inflammatory agent, as a treatment for airway obstruction and reducing adenoid size for children who do not have SCA. However, we do not yet know whether montelukast reduces adenoid size and improves cognition function in young children with SCA.MethodsThe Study of Montelukast In Children with Sickle Cell Disease (SMILES) is a 12-week multicentre, double-blind, RCT. SMILES aims to recruit 200 paediatric patients with SCA and SDB aged 3–7.99 years to assess the extent to which montelukast can improve cognitive function (i.e. processing speed) and sleep and reduce adenoidal size and white matter damage compared to placebo. Patients will be randomised to either montelukast or placebo for 12 weeks. The primary objective of the SMILES trial is to assess the effect of montelukast on processing speed in young children with SCA. At baseline and post-treatment, we will administer a cognitive evaluation; caregivers will complete questionnaires (e.g. sleep, pain) and measures of demographics. Laboratory values will be obtained from medical records collected as part of standard care. If a family agrees, patients will undergo brain MRIs for adenoid size and other structural and haemodynamic quantitative measures at baseline and post-treatment, and we will obtain overnight oximetry.DiscussionFindings from this study will increase our understanding of whether montelukast is an effective treatment for young children with SCA. Using cognitive testing and MRI, the SMILES trial hopes to gain critical knowledge to help develop targeted interventions to improve the outcomes of young children with SCA.Trial registrationClinicalTrials.govNCT04351698. Registered on April 17, 2020. European Clinical Trials Database (EudraCT No. 2017-004539-36). Registered on May 19, 2020
Estimands in published protocols of randomised trials: urgent improvement needed
Authors: Kahan Brennan C. , Morris Tim P. , White Ian R. , Carpenter James , Cro Suzie 
Published: October 2021

Abstract
Background
An estimand is a precise description of the treatment effect to be estimated from a trial (the question) and is distinct from the methods of statistical analysis (how the question is to be answered). The potential use of estimands to improve trial research and reporting has been underpinned by the recent publication of the ICH E9(R1) Addendum on the use of estimands in clinical trials in 2019. We set out to assess how well estimands are described in published trial protocols.

Methods
We reviewed 50 trial protocols published in October 2020 in Trials and BMJ Open. For each protocol, we determined whether the estimand for the primary outcome was explicitly stated, not stated but inferable (i.e. could be constructed from the information given), or not inferable.

Results
None of the 50 trials explicitly described the estimand for the primary outcome, and in 74% of trials, it was impossible to infer the estimand from the information included in the protocol. The population attribute of the estimand could not be inferred in 36% of trials, the treatment condition attribute in 20%, the population-level summary measure in 34%, and the handling of intercurrent events in 60% (the strategy for handling non-adherence was not inferable in 32% of protocols, and the strategy for handling mortality was not inferable in 80% of the protocols for which it was applicable). Conversely, the outcome attribute was stated for all trials. In 28% of trials, three or more of the five estimand attributes could not be inferred.

Conclusions
The description of estimands in published trial protocols is poor, and in most trials, it is impossible to understand exactly what treatment effect is being estimated. Given the utility of estimands to improve clinical research and reporting, this urgently needs to change.
Biotinylation of the Neospora caninum parasitophorous vacuole reveals novel dense granule proteins
Authors: Yang Congshan , Wang Chenrong , Liu Jing , Liu Qun 
Published: October 2021

Abstract
Background
Neospora caninum is an obligate intracellular parasite that invades host cells and replicates within the parasitophorous vacuole (PV), which resists fusion with host cell lysosomal compartments. To modify the PV, the parasite secretes an array of proteins, including dense granule proteins (GRAs). The vital role of GRAs in the Neospora life cycle cannot be overestimated. Despite this important role, only a subset of these proteins have been identified, and most of their functions have not been elucidated. Our previous study demonstrated that NcGRA17 is specifically targeted to the delimiting membrane of the parasitophorous vacuole membrane (PVM). In this study, we utilize proximity-dependent biotin identification (BioID) to identify novel components of the dense granules.

Methods
NcGRA17 was BirA* epitope-tagged in the Nc1 strain utilizing the CRISPR/Cas9 system to create a fusion of NcGRA17 with the biotin ligase BirA*. The biotinylated proteins were affinity-purified for mass spectrometric analysis, and the candidate GRA proteins from BioID data set were identified by gene tagging. To verify the biological role of novel identified GRA proteins, we constructed the NcGRA23 and NcGRA11 (a–e) knockout strains using the CRISPR/Cas9 system and analyzed the phenotypes of these mutants.

Results
Using NcGRA17-BirA* fusion protein as bait, we have identified some known GRAs and verified localization of 11 novel GRA proteins by gene endogenous tagging or overexpression in the Nc1 strain. We proceeded to functionally characterize NcGRA23 and NcGRA11 (a–e) by gene knockout. The lack of NcGRA23 or NcGRA11 (a–e) did not affect the parasite propagation in vitro and virulence in vivo.

Conclusions
In summary, our findings reveal that BioID is effective in discovering novel constituents of N. caninum dense granules. The exact biological functions of the novel GRA proteins are yet unknown, but this could be explored in future studies.

Graphical abstract
Phylogenetic relationships of the nematode subfamily Phascolostrongylinae from macropodid and vombatid marsupials inferred using mitochondrial protein sequence data
Authors: Sukee Tanapan , Beveridge Ian , Koehler Anson V. , Hall Ross , Gasser Robin B. , Jabbar Abdul 
Published: October 2021

AbstractBackgroundThe subfamily Phascolostrongylinae (Superfamily Strongyloidea) comprises nematodes that are parasitic in the gastrointestinal tracts of macropodid (Family Macropodidae) and vombatid (Family Vombatidae) marsupials. Currently, nine genera and 20 species have been attributed to the subfamily Phascolostrongylinae. Previous studies using sequence data sets for the internal transcribed spacers (ITS) of nuclear ribosomal DNA showed conflicting topologies between the Phascolostrongylinae and related subfamilies. Therefore, the aim of this study was to validate the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae using mitochondrial amino acid sequences.MethodsThe sequences of all 12 mitochondrial protein-coding genes were obtained by next-generation sequencing of individual adult nematodes (n = 8) representing members of the Phascolostrongylinae. These sequences were conceptually translated and the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae were inferred from aligned, concatenated amino acid sequence data sets.ResultsWithin the Phascolostrongylinae, the wombat-specific genera grouped separately from the genera occurring in macropods. Two of the phascolostrongyline tribes were monophyletic, including Phascolostrongylinea and Hypodontinea, whereas the tribe Macropostrongyloidinea was paraphyletic. The tribe Phascolostrongylinea occurring in wombats was closely related toOesophagostomumspp., also from the family Chabertiidae, which formed a sister relationship with the Phascolostrongylinae.ConclusionThe current phylogenetic relationship within the subfamily Phascolostrongylinae supports findings from a previous study based on ITS sequence data. This study contributes also to the understanding of the phylogenetic position of the subfamily Phascolostrongylinae within the Chabertiidae. Future studies investigating the relationships between the Phascolostrongylinae and Cloacininae from macropodid marsupials may advance our knowledge of the phylogeny of strongyloid nematodes in marsupials.Graphical Abstract
Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus
Authors: Soliai Marcus M. , Kato Atsushi , Helling Britney A. , Stanhope Catherine T. , Norton James E. , Naughton Katherine A. , Klinger Aiko I. , Thompson Emma E. , Clay Selene M. , Kim Soyeon , Celedón Juan C. , Gern James E. , Jackson Daniel J. , Altman Matthew C. , Kern Robert C. , Tan Bruce K. , Schleimer Robert P. , Nicolae Dan L. , Pinto Jayant M. , Ober Carole 
Published: October 2021

Abstract
Background
Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or environmental factors that affect specific disease risks and outcomes. To address these limitations, we used an upper airway epithelial cell (AEC) culture model to assess transcriptional and epigenetic responses to rhinovirus (RV), an asthma-promoting pathogen, and provide context-specific functional annotations to variants discovered in GWASs of asthma.

Methods
Genome-wide genetic, gene expression, and DNA methylation data in vehicle- and RV-treated upper AECs were collected from 104 individuals who had a diagnosis of airway disease (n=66) or were healthy participants (n=38). We mapped cis expression and methylation quantitative trait loci (cis-eQTLs and cis-meQTLs, respectively) in each treatment condition (RV and vehicle) in AECs from these individuals. A Bayesian test for colocalization between AEC molecular QTLs and adult onset asthma and childhood onset asthma GWAS SNPs, and a multi-ethnic GWAS of asthma, was used to assign the function to variants associated with asthma. We used Mendelian randomization to demonstrate DNA methylation effects on gene expression at asthma colocalized loci.

Results
Asthma and allergic disease-associated GWAS SNPs were specifically enriched among molecular QTLs in AECs, but not in GWASs from non-immune diseases, and in AEC eQTLs, but not among eQTLs from other tissues. Colocalization analyses of AEC QTLs with asthma GWAS variants revealed potential molecular mechanisms of asthma, including QTLs at the TSLP locus that were common to both the RV and vehicle treatments and to both childhood onset and adult onset asthma, as well as QTLs at the 17q12-21 asthma locus that were specific to RV exposure and childhood onset asthma, consistent with clinical and epidemiological studies of these loci.

Conclusions
This study provides evidence of functional effects for asthma risk variants in AECs and insight into RV-mediated transcriptional and epigenetic response mechanisms that modulate genetic effects in the airway and risk for asthma.
Compositional variation of the human fecal microbiome in relation to azo-reducing activity: a pilot study
Authors: Zahran Sara A. , Ali-Tammam Marwa , Ali Amal E. , Aziz Ramy K. 
Published: October 2021

Abstract
Background
Through an arsenal of microbial enzymes, the gut microbiota considerably contributes to human metabolic processes, affecting nutrients, drugs, and environmental poisons. Azoreductases are a predominant group of microbiota-derived enzymes involved in xenobiotic metabolism and drug activation, but little is known about how compositional changes in the gut microbiota correlate with its azo-reducing activity.

Results
To this end, we used high-throughput 16S rRNA amplicon sequencing, with Illumina MiSeq, to determine the microbial community composition of stool samples from 16 adults with different azo-reducing activity. High azo-reducing activity positively
correlated with the relative abundance of phylum Firmicutes (especially genera Streptococcus and Coprococcus) but negatively with phylum Bacteroidetes (especially genus Bacteroides). Typical variations in the Firmicutes-to-Bacteroidetes and Prevotella-to-Bacteroides ratios were observed among samples. Multivariate analysis of the relative abundance of key microbial taxa and other diversity parameters confirmed the Firmicutes proportion as a major variable differentiating high and non-azo-reducers, while Bacteroidetes relative abundance was correlated with azo-reduction, sex, and BMI.

Conclusions
This pilot study showed that stool samples with higher azo-reducing activity were enriched in Firmicutes but with relatively fewer Bacteroidetes. More samples and studies from different geographical areas are needed to bolster this conclusion. Better characterization of different azoreductase-producing gut microbes will increase our knowledge about the fate and differential human responses to azodye-containing drugs or orally consumed chemicals, thus contributing to efforts towards implementing microbiome testing in precision medicine and toxicology.
Comparison of the efficiency and performance of two systems and three membranes for blood feeding mosquitoes
Authors: Seck Fatoumata , Cailleau Aurélie , Diallo Mawlouth , Dia Ibrahima 
Published: October 2021

Abstract
Objective
Due to different concerns in using appropriate mosquito blood feeding techniques, this work focused on evaluating the effectiveness of two artificial mosquito feeding systems (Rutledge and Hemotek) and three different membranes (Parafilm, mouse and chicken skins). Female mosquitoes from an An. coluzzii strain aged between 2 and 5 days were exposed to blood with the two systems at time intervals (5, 10, 15, 20, 25 and 30 min) with blood used on the day of collection, the next day and 2 days after.

Results
Our results showed that the Hemotek system gave better blood feeding rates than the Rutledge system. Among the three membranes, the blood feeding rates with chicken and mouse skins were higher than those provided by the Parafilm membrane. Likewise, blood stored 1 day after collection gave higher levels than blood used on the day of collection and 2 days after. Regardless of the system, the lowest blood feeding rates were observed at 5 min compared to the other exposure times.
Gallbladder volvulus: a case report
Authors: Croce Phillip , Licata Samuel 
Published: October 2021

Abstract
Background
Gallbladder volvulus is a rare pathology first reported by Wendel in 1898. Although the main pathological process associated with gallbladder volvulus is not known, there is clinical evidence suggesting that lack of gallbladder adhesions to the liver leads to an eventual twisting around the cystic bile duct (a process that seems to favor older female populations).

Case presentation
In this report, an 81-year-old Caucasian elderly female presented to the emergency department with acute/severe right upper quadrant pain, which was also accompanied by an elevated leukocyte count. Relevant imaging showed a distended gallbladder with gallbladder wall thickening and a dilated common bile duct. The patient was subsequently admitted to the hospital for acute cholecystitis and scheduled for surgery the next day. Upon laparoscopic surgery, the gallbladder was black and gangrenous with no visible adhesions to the liver. Further inspection demonstrated that the gallbladder had twisted clockwise around the cystic bile duct.

Conclusions
While many previous cases have been reported since Wendel, further case studies are nevertheless important to help guide proper clinic evaluation and pinpoint the potential for a gallbladder volvulus.
On the existence of mild solutions for nonlocal differential equations of the second order with conformable fractional derivative
Authors: Atraoui Mustapha , Bouaouid Mohamed 
Published: October 2021

AbstractIn the work (Bouaouid et al. in Adv. Differ. Equ. 2019:21, 2019), the authors have used the Krasnoselskii fixed point theorem for showing the existence of mild solutions of an abstract class of conformable fractional differential equations of the form: $\frac{d^{\alpha }}{dt^{\alpha }}[\frac{d^{\alpha }x(t)}{dt^{\alpha }}]=Ax(t)+f(t,x(t))$

d
α

d

t
α

[

d
α

x
(
t
)

d

t
α

]
=
A
x
(
t
)
+
f
(
t
,
x
(
t
)
)
, $t\in [0,\tau ]$
t
∈
[
0
,
τ
]
subject to the nonlocal conditions $x(0)=x_{0}+g(x)$
x
(
0
)
=

x
0

+
g
(
x
)
and $\frac{d^{\alpha }x(0)}{dt^{\alpha }}=x_{1}+h(x)$

d
α

x
(
0
)

d

t
α

=

x
1

+
h
(
x
)
, where $\frac{d^{\alpha }(\cdot)}{dt^{\alpha }}$

d
α

(
⋅
)

d

t
α

is the conformable fractional derivative of order $\alpha \in\, ]0,1]$
α
∈

]
0
,
1
]
and A is the infinitesimal generator of a cosine family $(\{C(t),S(t)\})_{t\in \mathbb{R}}$

(
{
C
(
t
)
,
S
(
t
)
}
)

t
∈
R

on a Banach space X. The elements $x_{0}$

x
0

and $x_{1}$

x
1

are two fixed vectors in X, and f, g, h are given functions. The present paper is a continuation of the work (Bouaouid et al. in Adv. Differ. Equ. 2019:21, 2019) in order to use the Darbo–Sadovskii fixed point theorem for proving the same existence result given in (Bouaouid et al. in Adv. Differ. Equ. 2019:21, 2019) [Theorem 3.1] without assuming the compactness of the family $(S(t))_{t>0}$

(
S
(
t
)
)

t
>
0

and any Lipschitz conditions on the functions g and h.
Heritability and genetic variance estimation of Osteosarcoma (OSA) in Irish Wolfhound, using deep pedigree information
Authors: Momen Mehdi , Kohler Nyah L. , Binversie Emily E. , Dentino Mariellen , Sample Susannah J. 
Published: October 2021

Abstract
Background
Osteosarcoma (OSA) is a devastating disease that is common in the Irish Wolfhound breed. The aim of this study was to use a pedigree-based approach to determine the heritability of OSA in the Irish Wolfhound using data from a large publically available database.

Results
The pedigree used for this study included 5110 pure-bred Irish Wolfhounds, including 332 dogs diagnosed with OSA and 360 control dogs; dogs were considered controls if they lived over 10 years of age and were not reported to have developed OSA. The estimated heritability of OSA in the Irish Wolfhound was 0.65.

Conclusion
The results of this study indicate that OSA in the Irish Wolfhound is highly heritable, and support the need for future research investigating associated genetic mutations.
Phytochemicals and in vitro anti-apoptotic properties of ethanol and hot water extracts of Cassava (Manihot esculenta Crantz) peel biogas slurry following anaerobic degradation
Authors: Olaniyan Oluwaseyi Paul , Ajayi Ebenezer Idowu O. 
Published: October 2021

Abstract
Background
Wastes emanating from cassava (Manihot Esculenta Crantz) processing in African countries significantly contribute to environmental pollution, besides, such toxic wastes contribute to greenhouse gas emission. Although cassava peel has been successfully used as a raw material in mushroom cultivation, feedstock for livestock, biogas production but the bio-transformed products recovered from the anaerobic digestion of cassava wastes, especially the peels have often been overlooked. Therefore, this research aimed at quantifying the secondary metabolites in the slurry recovered from ethanol and hot water extraction of cassava peel subjected to biogas production, in vitro, for anti-apoptotic properties.

Methods
Fresh cassava peels were allowed to ferment anaerobically to produce three states of matter; gas, solid, and liquid/slurry. The slurry was extracted using 95 % ethanol and 100 oC hot water to obtain crude extracts, which were then subjected to anti-apoptotic screening using the mitochondrial swelling assay. The qualitative phytochemical analysis of the crude extracts was done using standard methods. Further characterization of the crude extracts was done by FTIR for the chemical elucidation of the functional groups present.

Results
The qualitative phytoconstituents revealed that the slurry extracts are naturally enriched with alkaloids, steroids, flavonoids, and saponins. The infrared spectrum of the crude extracts revealed the presence of hydroxyl, alkane, carboxyl groups in the ethanol extract, and hydroxyl, alkene, amide, carbonyl groups in the hot water extract. In the presence and absence of exogenous Ca2+, both extracts of the slurry induced liver mitochondrial permeability transition pore opening albeit at low amplitude swelling as the mean absorbance was less than one (at 540 nm).

Conclusions
Based on these results obtained, the crude extracts of cassava peel biogas slurry have been proven to possess bioactive compounds that could induce liver mitochondrial permeability transition pore opening, in vitro.