bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of bone-plate materials on the healing process of fractured tibia bone under time-varying conditions: a finite element analysis
Authors: Tan JoonHoe , Natarajan Elango , Lim WeiHong , Ramesh S , Ang ChunKit , Parasuraman S , Singh D Kingsly Jeba
Published: September 2021

Stress shielding is known to cause bone refracture or cause low healing rate in fractured bones. The numerical study of bone healing process of a transverse fractured tibia was conducted in this research to reduce the stress shielding. The stress and strain on the callus were evaluated when bone plates of different metallic and non-metallic biomaterials were used. Time varying material properties of the callus were applied, and loading conditions were coupled with material properties of the callus. The strain distribution on the callus, and the maximum stress on the callus and bone plate were analysed. The analysis results shows that Polyether ether ketone/Nano-Hydroxyapatite/Short Carbon Fibre (PEEK/nano-HA/SCF) is most suitable for bone plating application for tibia. PEEK/nano-HA/SCF is chosen as it provides the optimum strain in the callus to promote bone healing. It has the closest stiffness to the cortical bone and hence stress shielding is minimized extensively. It has a uniform strain distribution at the fractured site for early bone healing process.
Malnormal matrices
Authors: Mulcahy Garrett , Sinclair Thomas
Published: September 2021

We exhibit an operator norm bounded, infinite sequence

{

A
n

}

\{A_n\}

of

3
n
×
3
n

3n \times 3n

complex matrices for which the commutator map

X
↦
X

A
n

−

A
n

X

X\mapsto XA_n - A_nX

is uniformly bounded below as an operator over the space of trace-zero self-adjoint matrices equipped with Hilbert–Schmidt norm. The construction is based on families of quantum expanders. We give several potential applications of these matrices to the study of quantum expanders. We formulate several natural conjectures and provide numerical evidence.
Convergence problem of Schrödinger equation in Fourier-Lebesgue spaces with rough data and random data
Authors: Yan Xiangqian , Zhao Yajuan , Yan Wei
Published: September 2021

In this paper, we consider the convergence problem of Schrödinger equation. Firstly, we show the almost everywhere pointwise convergence of Schrödinger equation in Fourier-Lebesgue spaces
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H
^

1
p

,

p
2

(

R

)
(
4
≤
p
>
∞
)
,

\hat {H}^{\frac {1}{p},\frac {p}{2}}(\mathbf {R})(4\leq p>\infty ),

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H
^

3

s

1

p

,

2
p

3

(

R

2

)
(

s

1

>

1
3

,
3
≤
p
>
∞
)
,

\hat {H}^{\frac {3 s_{1}}{p},\frac {2p}{3}}(\mathbf {R}^{2})(s_{1}>\frac {1}{3},3\leq p>\infty ),

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H
^

2

s

2

p

,
p

(

R

n

)
(

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>

n

2
(
n
+
1
)

,
2
≤
p
>
∞
,
n
≥
3
)

\hat {H}^{\frac {2 s_{2}}{p},p}(\mathbf {R}^{n})(s_{2}>\frac {n}{2(n+1)},2\leq p>\infty ,n\geq 3)

with rough data. Secondly, we show that the maximal function estimate related to one dimensional Schrödinger equation can fail with data in

H
^

s
,

p
2

(

R

)
(
s
>

1
p

)

\hat {H}^{s,\frac {p}{2}}(\mathbf {R})(s>\frac {1}{p})

. Finally, we show the stochastic continuity of Schrödinger equation with random data in

L
^

r

(

R

n

)
(
2
≤
r
>
∞
)

\hat {L}^{r}(\mathbf {R}^{n})(2\leq r>\infty )

almost surely. The main ingredients are maximal function estimates and density theorem in Fourier-Lebesgue spaces as well as some large deviation estimates.
Bronchoalveolar Lavage in a Pediatric Population
Authors: Gami Abhishek , Rinaldi Kristina , Degefe Yordanos T , Vosoughi Arghavan Seyed , Lee Dongwoo , Maleki Zahra
Published: September 2021

Objectives

The cytomorphologic findings of bronchoalveolar lavage (BAL) in pediatrics were correlated with clinical symptoms.

Methods

Patient demographics, clinical symptoms/history, cytomorphologic findings, and oil red O (ORO) staining of 100 pediatric patients who underwent BAL between 2014 and 2016 were reviewed at a large academic institution.

Results

Of the 100 patients (males/females, 62:38), the most common conditions for BAL included cough (46/100), reflux (39/100), pneumonia (30/100), dysphagia (22/100), asthma (19/100), and cystic fibrosis (15/100). Sixteen of 100 patients were admitted with pulmonary symptoms from the emergency department. Cytomorphologic findings showed acute inflammation in 37 BALs and chronic inflammation in 9. Abundant thick mucin was present in 3 cytology cases from patients with cystic fibrosis. Fungal elements were detected in 3 cases (Candida, Aspergillus, and Pneumocystis jirovecii) and viral effects (rhinovirus) in one. Thirty-seven of 100 had rare ORO-positive lipid-laden macrophages (LLMs), 7 of 100 had moderate LLMs, 11 of 100 had numerous LLMs, 18 of 100 had positive staining without the degree of staining, 25 of 100 had negative ORO staining, and 2 of 100 had noncontributory ORO staining. An iron stain was done on 15 BALs (2 positive, 9 negative, and 4 noncontributory).

Conclusions

BAL cytology is a useful tool in pediatrics to discriminate underlying causes of aerodigestive system conditions, while ORO staining may occasionally help.
ATPdock: a template-based method for ATP-specific protein–ligand docking
Authors: Rao Liang , Jia Ning-Xin , Hu Jun , Yu Dong-Jun , Zhang Gui-Jun
Published: September 2021

Motivation

Accurately identifying protein–ATP binding poses is significantly valuable for both basic structure biology and drug discovery. Although many docking methods have been designed, most of them require a user-defined binding site and are difficult to achieve a high-quality protein–ATP docking result. It is critical to develop a protein–ATP-specific blind docking method without user-defined binding sites.

Results

Here, we present ATPdock, a template-based method for docking ATP into protein. For each query protein, if no pocket site is given, ATPdock first identifies its most potential pocket using ATPbind, an ATP-binding site predictor; then, the template pocket, which is most similar to the given or identified pocket, is searched from the database of pocket–ligand structures using APoc, a pocket structural alignment tool; thirdly, the rough docking pose of ATP (rdATP) is generated using LS-align, a ligand structural alignment tool, to align the initial ATP pose to the template ligand corresponding to template pocket; finally, the Metropolis Monte Carlo simulation is used to fine-tune the rdATP under the guidance of AutoDock Vina energy function. Benchmark tests show that ATPdock significantly outperforms other state-of-the-art methods in docking accuracy.

Availability and implementation

https://jun-csbio.github.io/atpdock/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Testing microbiome association using integrated quantile regression models
Authors: Wang Tianying , Ling Wodan , Plantinga Anna M , Wu Michael C , Zhan Xiang
Published: September 2021

Motivation

Most existing microbiome association analyses focus on the association between microbiome and conditional mean of health or disease-related outcomes, and within this vein, vast computational tools and methods have been devised for standard binary or continuous outcomes. However, these methods tend to be limited either when the underlying microbiome-outcome association occurs somewhere other than the mean level, or when distribution of the outcome variable is irregular (e.g. zero-inflated or mixtures) such that conditional outcome mean is less meaningful. We address this gap by investigating association analysis between microbiome compositions and conditional outcome quantiles.

Results

We introduce a new association analysis tool named MiRKAT-IQ within the Microbiome Regression-based Kernel Association Test framework using Integrated Quantile regression models to examine the association between microbiome and the distribution of outcome. For an individual quantile, we utilize the existing kernel machine regression framework to examine the association between that conditional outcome quantile and a group of microbial features (e.g. microbiome community compositions). Then, the goal of examining microbiome association with the whole outcome distribution is achieved by integrating all outcome conditional quantiles over a process, and thus our new MiRKAT-IQ test is robust to both the location of association signals (e.g. mean, variance, median) and the heterogeneous distribution of the outcome. Extensive numerical simulation studies have been conducted to show the validity of the new MiRKAT-IQ test. We demonstrate the potential usefulness of MiRKAT-IQ with applications to actual biological data collected from a previous microbiome study.

Availability and implementation

R codes to implement the proposed methodology is provided in the MiRKAT package, which is available on CRAN.

Supplementary information

Supplementary data are available at Bioinformatics online.
Surgical treatment of anorectal melanoma: a systematic review and meta-analysis
Authors: Jutten Esther , Kruijff Schelto , Francken Anne Brecht , Lutke Holzik Martijn F , van Leeuwen Barbara L , van Westreenen Henderik L , Wevers Kevin P
Published: September 2021

Background

Anorectal melanoma is a rare neoplasm with a poor prognosis. The surgical approaches for anorectal melanoma can be categorized into local excision (procedures without lymph node removal and preservation of the rectum) and extensive resection (procedures with rectum and pararectal lymph node removal). The aim of this systematic review and meta-analysis was to compare the survival of patients who underwent extensive resection with that of patients who underwent local excision, stratifying patients according to tumour stage.

Methods

A literature review was performed according to PRISMA guidelines by searching MEDLINE/PubMed for manuscripts published until March 2021. Studies comparing survival outcomes in patients with anorectal melanoma who underwent local excision versus extensive resection were screened for eligibility. Meta-analysis was performed for overall survival after the different surgical approaches, stratified by tumour stage.

Results

There were 347 studiesidentified of which 34 were included for meta-analysis with a total of 1858 patients. There was no significant difference in overall survival between the surgical approaches in patients per stage (stage I odds ratio 1.30 (95 per cent c.i. 0.62 to 2.72, P = 0.49); stage II odds ratio 1.61 (95 per cent c.i. 0.62 to 4.18, P = 0.33); stage I–III odds ratio 1.19 (95 per cent c.i. 0.83 to 1.70, P = 0.35). Subgroup analyses were conducted for the time intervals (<2000, 2001–2010 and 2011–2021) and for continent of study origin. Subgroup analysis for time interval and continent of origin also showed no statistically significant differences in overall survival.

Conclusion

No significant survival benefit exists for patients with anorectal melanoma treated with local excision or extensive resection, independent of tumour stage.
Longitudinal Effects of Physical Activity Change on Hippocampal Volumes over up to 12 Years in Middle and Older Age Community-Dwelling Individuals
Authors: Fraser Mark A , Walsh Erin I , Shaw Marnie E , Anstey Kaarin J , Cherbuin Nicolas
Published: September 2021

The objectives of this study were to investigate the long-term associations between changes in physical activity levels and hippocampal volumes over time, while considering the influence of age, sex, and APOE-ε4 genotype. We investigated the effects of change in physical activity on hippocampal volumes in 411 middle age (mean age = 47.2 years) and 375 older age (mean age = 63.1 years) adults followed up to 12 years. An annual volume decrease was observed in the left (middle age: 0.46%; older age: 0.51%) but not in the right hippocampus. Each additional 10 metabolic equivalents (METs, ~2 h of moderate exercise) increase in weekly physical activity was associated with 0.33% larger hippocampal volume in middle age (equivalent to ~1 year of typical aging). In older age, each additional MET was associated with 0.05% larger hippocampal volume; however, the effects declined with time by 0.005% per year. For older age APOE-ε4 carriers, each additional MET was associated with a 0.10% increase in hippocampal volume. No sex effects of physical activity change were found. Increasing physical activity has long-term positive effects on hippocampal volumes and appears especially beneficial for older APOE-ε4 carriers. To optimize healthy brain aging, physical activity programs should focus on creating long-term exercise habits.
Opinion evolution in society with stubborn agents using Temporal Model for Opinion and Triad Network Formation (TMOTNF)
Authors: Jain Eeti , Singh Anurag
Published: September 2021

Information diffusion is an important part of the social network. Information flows between the individuals in the social networks to shape and update their opinions about various topics. The updated opinion values of them further spread the information in the network. The social network is always evolving by nature, leading to the dynamics of the network. Connections keep on changing among the individuals based on the various characteristics of the networks and individuals. Opinions of individuals may again be affected by the changes in the network which leads to dynamics on the network. Therefore, the co-evolving nature of dynamics on/of the network is proposed. Co-evolving Temporal Model for Opinion and Triad Network Formation is modelled to evaluate the opinion convergence. Some fully stubborn agents are chosen in the network to affect opinion evolution, framing society’s opinion. It is also analysed how these agents can divert the whole network towards their opinion values. When temporal modelling is done using all the three conditions, Triadic Closure, Opinion Threshold value and the Page Rank value over the network, the network does not reach consensus at the convergence point. Various individuals with different opinion values still exist.
Natural variation in reproductive timing and X-chromosome nondisjunction inCaenorhabditis elegans
Authors: Lim Jiseon , Kim Jun , Lee Junho
Published: September 2021

Caenorhabditis elegans hermaphrodites first produce a limited number of sperm cells, before their germline switches to oogenesis. Production of progeny then ensues until sperm is depleted. Male production in the self-progeny of hermaphrodites occurs following X-chromosome nondisjunction during gametogenesis, and in the reference strain increases with age of the hermaphrodite parent. To enhance our understanding of the reproductive timecourse in C. elegans, we measured and compared progeny production and male proportion during the early and late reproductive periods of hermaphrodites for 96 wild C. elegans strains. We found that the two traits exhibited natural phenotypic variation with few outliers and a similar reproductive timing pattern as previous reports. Progeny number and male proportion were not correlated in the wild strains, implying that wild strains with a large brood size did not produce males at a higher rate. We also identified loci and candidate genetic variants significantly associated with male-production rate in the late and total reproductive periods. Our results provide an insight into life-history traits in wild C. elegans strains.
A synthetic lethal screen identifies HDAC4 as a potential target in MELK overexpressing cancers
Authors: Zhou Lin , Zheng Siqi , Rosas Bringas Fernando R , Bakker Bjorn , Simon Judith E , Bakker Petra L , Kazemier Hinke G , Schubert Michael , Roorda Maurits , van Vugt Marcel A T M , Chang Michael , Foijer Floris
Published: September 2021

Maternal embryonic leucine zipper kinase (MELK) is frequently overexpressed in cancer, but the role of MELK in cancer is still poorly understood. MELK was shown to have roles in many cancer-associated processes including tumor growth, chemotherapy resistance, and tumor recurrence. To determine whether the frequent overexpression of MELK can be exploited in therapy, we performed a high-throughput screen using a library of Saccharomyces cerevisiae mutants to identify genes whose functions become essential when MELK is overexpressed. We identified two such genes: LAG2 and HDA3. LAG2 encodes an inhibitor of the Skp, Cullin, F-box containing (SCF) ubiquitin-ligase complex, while HDA3 encodes a subunit of the HDA1 histone deacetylase complex. We find that one of these synthetic lethal interactions is conserved in mammalian cells, as inhibition of a human homolog of HDA3 (Histone Deacetylase 4, HDAC4) is synthetically toxic in MELK overexpression cells. Altogether, our work identified a novel potential drug target for tumors that overexpress MELK.
The Experience of Alzheimer’s Disease Family Caregivers in a Latino Community: Expectations and Incongruences in Support Services
Authors: Martinez Iveris L , Acosta Gonzalez Elaine , Quintero Caroline , Vania Marsha Jenakovich
Published: September 2021

Objectives

Current theoretical constructs on the utilization of formal support for Latino caregivers focus on familism and exclude the cultural values represented in the service system. The purpose of this paper is to highlight the experience of care for Latino family caregivers to persons with Alzheimer’s disease and related dementias (ADRD). We also examine the cultural congruence between provider perspectives with the expectations of Latino ADRD caregivers.

Method

We conducted extended interviews with 24 Latino ADRD caregivers and 10 service providers. Interview transcripts were coded and analyzed using a grounded theory approach.

Results

Our study provides a deeper understanding of Latino caregiving experiences and highlights some of the structural and systematic issues in current systems of caregiver support. While Latino families have very specific notions of care, by upholding notions of familism, there is a tendency to not look deeper into how they may be better supported in caregiving and fall into the “culture trap.” The assumption that family should be the natural support network for older adults may lead to health and social systems of care to ignore the specific needs of the Latino population.

Discussion

Services are being provided under a model that was established four decades ago and may not reflect current realities. The concept of “an ethics of care” allows us to move beyond familism and explain that underutilization of services may also be due in part to the cultural incongruence between what service providers offer and the perceived needs of Latino caregivers.
Viral Etiology of Acute Gastroenteritis Among Forcibly Displaced Myanmar Nationals and Adjacent Host Population in Bangladesh
Authors: Hossain Mohammad Enayet , Islam Md Muzahidul , Miah Mojnu , Haque Warda , Vinjé Jan , Rahman Mohammed Ziaur , Faruque Abu Syed Golam , Khan Azharul Islam , Ahmed Tahmeed , Rahman Mustafizur
Published: September 2021

Background

Since August 2017, Myanmar nationals from Rakhine state have crossed the border into Bangladesh and settled in Cox’s Bazar, the World’s largest refugee camp. Due to overcrowding, poor sanitation, and hygienic practices they have been under significant health risks including diarrheal diseases. The objective of this study is to determine the viral etiology of acute gastroenteritis (AGE) among forcibly displaced Myanmar nationals (FDMN) and adjacent Bangladeshi local host population (AHP).

Methods

From April 2018 to April 2019, we collected stool specimens from 764 FDMN and 1159 AHP of all ages. We tested 100 randomly selected specimens from each group for the most common AGE viruses.

Results

Among 200 diarrhea patients, 55% and 64% of FDMN and AHP patients, respectively, had viral infections; the most common viruses were rotavirus (29% vs 44%), adenovirus (24% vs 31%), and norovirus (14% vs 10%). In both populations, viral infections were significantly higher in children less than 5 years of age, compared with bacterial infections that were higher in patients older than 5 years of age (P ≤ .05).

Conclusions

Disparities in viral and bacterial prevalence among various age groups warrant careful antibiotic usage, especially in children less than 5 years of age.
Nonadherence to Ledipasvir/Sofosbuvir Did Not Predict Sustained Virologic Response in a Randomized Controlled Trial of Human Immunodeficiency Virus/Hepatitis C Virus Coinfected Persons Who Use Drugs
Authors: Ward Kathleen M , Falade-Nwulia Oluwaseun , Moon Juhi , Sutcliffe Catherine G , Brinkley Sherilyn , Haselhuhn Taryn , Katz Stephanie , Herne Kayla , Arteaga Lilian , Mehta Shruti H , Latkin Carl , Brooner Robert K , Sulkowski Mark S
Published: September 2021

Background

Eliminating hepatitis C virus (HCV) will require effective treatment delivery to persons with substance use disorders (SUDs). We evaluated the relationship between ledipasvir/sofosbuvir treatment persistence (receiving 84 tablets), adherence, and sustained virologic response (SVR) in persons with human immunodeficiency virus (HIV)/HCV coinfection.

Methods

Of the 144 participants with HIV/HCV and SUDs, 110 initiated a 12-week treatment course under 1 of 3 conditions (usual care, peer mentors, and cash incentives). We used self-report, pharmacy pill counts, and expected date of refill to examine adherence. Persistent participants were categorized as high adherence (taking ≥90% of doses) or low adherence (taking <90% of doses).

Results

Most participants persisted on treatment after initiation (n = 105), with 95% (n = 100) achieving SVR. One third (34%) of participants had moderate/heavy alcohol use by the biomarker phosphatidylethanol ([Peth] ≥50 ng/mL), and 44% had urine toxicology positive for cocaine or heroin at enrollment. The proportion of persons with high adherence was 72% (n = 76), and the proportion of persons with low adherence was 28%. Although low adherence was associated with moderate/heavy alcohol use by PEth (relative risk = 2.77; 95% confidence interval, 1.50–5.12), SVR did not vary according to adherence (P = .702), and most participants (97%) with low adherence achieved SVR.

Conclusions

Treatment persistence led to high SVR rates among persons with HIV/HCV, despite imperfect adherence and SUDs.
Effects of antenatal care visits and health facility delivery on women's choice to circumcise their daughters in sub-Saharan Africa: evidence from demographic and health surveys
Authors: Ahinkorah Bright Opoku , Ameyaw Edward Kwabena , Seidu Abdul-Aziz , Njue Carolyne
Published: September 2021

Background

This study examines the association between maternal healthcare service utilisation and circumcision of daughters in sub-Saharan Africa (SSA).

Methods

This study is based on a cross-sectional study design that draws on analysis of pooled data from current demographic and health surveys conducted between 2010 and 2019 in 12 countries in SSA. Both bivariate and multivariable binary logistic regression models were employed.

Results

Mothers who had four or more antenatal care visits were less likely to circumcise their daughters compared with those who had zero to three visits. Mothers who delivered at a health facility were less likely to circumcise their daughters than those who delivered at home. With the covariates, circumcision of daughters increased with increasing maternal age but decreased with increasing wealth quintile and level of education. Girls born to married women and women who had been circumcised were more likely to be circumcised.

Conclusions

This study established an association between maternal healthcare service utilisation and circumcision of girls from birth to age 14 y in SSA. The findings highlight the need to strengthen policies that promote maternal healthcare service utilisation (antenatal care and health facility delivery) by integrating female genital mutilation (FGM) information and education in countries studied.
Nephrotoxicity of continuous amphotericin B in critically ill patients with abdominal sepsis: a retrospective analysis with propensity score matching
Authors: Geersing T H , Franssen E J F , Spronk P E , van Kan H J M , den Reijer M , van der Voort P H J
Published: September 2021

Background

Continuous infusion of conventional amphotericin B (CCAB) is used in ICUs for pre-emptive treatment of invasive fungal infections. Amphotericin B has previously been associated with nephrotoxicity.

Objectives

To investigate if CCAB with therapeutic drug monitoring (TDM) results in renal impairment over time in critically ill patients with abdominal sepsis.

Patients and methods

The study was conducted at mixed medical-surgical ICUs of two large teaching hospitals in the Netherlands. Consecutive patients who were treated on the ICUs between 2006 and 2019 for abdominal sepsis, with or without CCAB, were included. CCAB dosing was guided by TDM. Serum creatinine concentrations and renal failure scores of patients with CCAB treatment were compared with those without CCAB treatment. Excluded were: (i) patients treated with CCAB for less than 72 h; and (ii) patients with renal replacement therapy.

Results

A total of 319 patients were included (185 treated with CCAB and 134 controls). A multiple linear regression model showed that the serum creatinine concentration was independent of CCAB treatment (β = −0.023; 95% CI = −12.2 to 7.2; P = 0.615). Propensity score matching resulted in 134 pairs of CCAB-treated and non-treated patients. Again, the analysis of these pairs showed that the cumulative CCAB dose was not associated with serum creatinine concentration during intensive care treatment (β = 0.299; 95% CI = −0.38 to 0.98; P = 0.388).

Conclusions

CCAB with TDM did not result in renal impairment over time in critically ill patients with abdominal sepsis.
Intestinal malrotation in one adult patient affected by SARS-CoV-2 infection: occlusion misdiagnosed as COVID gastroenteritis. Case report and literature review
Authors: Cestino Luca , Mantova Serena , Festa Federico , Carbonaro Giulia , Dani Luca , Fiore Alessia , Bonatti Luca , Soncini Stefania , Quaglino Francesco
Published: September 2021

Malrotation of the gut is a rare occurrence, commonly diagnosed during childhood, but occasionally diagnosed in adults.

In children, intestinal obstruction is the most common manifestation, whereas in adult patients, the diagnosis is more challenging since the symptoms are less specific with several episodes of abdominal pain and vomit.

In a particular epidemic period, like the one we are going through, these generic symptoms may mislead to a wrong diagnosis.

We present the case of a young man in which occlusion due to intestinal malrotation has been misinterpreted as gastroenteric symptoms of severe acute respiratory syndrome coronavirus 2 infection, and we also overview the correct Ladd’s technique, commonly performed by pediatrical surgeon, but unusual operation for adult general surgeons.
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types
Authors: Payne Leighton J , Todeschini Thomas C , Wu Yi , Perry Benjamin J , Ronson Clive W , Fineran Peter C , Nobrega Franklin L , Jackson Simon A
Published: September 2021

To provide protection against viral infection and limit the uptake of mobile genetic elements, bacteria and archaea have evolved many diverse defence systems. The discovery and application of CRISPR-Cas adaptive immune systems has spurred recent interest in the identification and classification of new types of defence systems. Many new defence systems have recently been reported but there is a lack of accessible tools available to identify homologs of these systems in different genomes. Here, we report the Prokaryotic Antiviral Defence LOCator (PADLOC), a flexible and scalable open-source tool for defence system identification. With PADLOC, defence system genes are identified using HMM-based homologue searches, followed by validation of system completeness using gene presence/absence and synteny criteria specified by customisable system classifications. We show that PADLOC identifies defence systems with high accuracy and sensitivity. Our modular approach to organising the HMMs and system classifications allows additional defence systems to be easily integrated into the PADLOC database. To demonstrate application of PADLOC to biological questions, we used PADLOC to identify six new subtypes of known defence systems and a putative novel defence system comprised of a helicase, methylase and ATPase. PADLOC is available as a standalone package (https://github.com/padlocbio/padloc) and as a webserver (https://padloc.otago.ac.nz).
Leg movements during sleep in children treated with serotonergic antidepressants
Authors: Ferri Raffaele , Mogavero Maria P , Bruni Oliviero , Picchietti Daniel L , Kapoor Vidhi , DelRosso Lourdes M
Published: September 2021

Study Objectives

To evaluate leg movements during sleep (LMS) in children taking serotonergic antidepressants, compared to those of children with restless legs syndrome (RLS) and controls, and to assess the time structure of intermovement intervals (IMI).

Methods

Twenty-three children (12 girls, mean age 14.1 years) on antidepressants and with a total LMS index ≥ 15/h, 21 drug-naïve RLS children (11 girls, mean age 13.6 years) also with total LMS index ≥ 15/h, and 35 control children (17 girls, mean age 14.3 years) were recruited. LMS were scored and a series of parameters was calculated, along with the analysis of their time structure.

Results

Children taking antidepressants showed higher total and periodic LMS (PLMS) indexes than both controls and RLS children, as well as higher short-interval and isolated LMS indexes than controls. LMS periodicity was highest in children on antidepressants. In children taking antidepressants, a well-defined PLMS IMI peak corresponding to approximately 10–60 s, with a maximum at approximately 20 s was present, which was much less evident in RLS patients and absent in controls. A progressive decrease of PLMS during the night and more frequent arousals were found in children on antidepressants and with RLS.

Conclusions

Children taking serotonergic antidepressants show higher periodicity LMS than children with RLS or controls and have a higher number of PLMS through the night. Antidepressant-associated PLMS in children seem to have features similar to PLMS of adults with RLS. Whether this is a marker of an increased risk to develop RLS later in life needs to be determined.
Multilocus Phylogenetic Analyses of Colletotrichum gloeosporioides Species Complex Causing Crown Rot on Strawberry in Florida
Authors: Oliveira Michelle S. , Wang Nan-Yi , Peres Natalia A.
Published: September 2021

Colletotrichum gloeosporioides is the causal agent of Colletotrichum crown rot of strawberry in the southern United States. Recent multigene studies defined C. gloeosporioides as a complex species comprised of 37 species. In our study, we phylogenetically characterized C. gloeosporioides isolates from strawberry and other noncultivated plants around strawberry fields. One hundred fifteen strawberry isolates and 38 isolates from noncultivated hosts were sequenced for five genomic regions: internal transcribed spacer, actin, calmodulin, chitin synthase, and glyceraldehyde-3-phosphate dehydrogenase. Phylogenetic analysis using the maximum likelihood and Bayesian inference methods, based on partition-specific models, revealed that most of the isolates in Florida (86%) were closely related to C. siamense, whereas 14 isolates were closely related to C. theobromicola (syn. C. fragariae), four isolates were C. fructicola, and three isolates were C. clidemiae. However, only the first three species were pathogenic to strawberry. Morphological characteristics evaluated show that mycelial growth of all species is approximately 5 mm/day, but colony morphology varies by species and incubation conditions. In vitro mating of the isolates demonstrated that C. fructicola is homothallic whereas C. siamense and C. theobromicola isolates are heterothallic. The biological importance of these different Colletotrichum species is currently being investigated to determine whether different management strategies are needed in strawberry production fields.
Postresuscitation care and prognostication
Authors: Nolan Jerry P. , Abella Benjamin S.
Published: September 2021

Purpose of review

Most patients who are successfully resuscitated after cardiac arrest are initially comatose and require mechanical ventilation and other organ support in an ICU. Knowledge about the optimal strategy for treating these patients is evolving rapidly. This review will summarize the evidence on key aspects of postarrest care and prognostication, with a focus on actionable parameters that may impact patient survival and neurologic outcomes.

Recent findings

Optimal targets for arterial blood oxygen and carbon dioxide in comatose postcardiac arrest patients remain uncertain. Observational data are conflicting and the few randomized controlled trials to date have failed to show that different ranges of blood oxygen and carbon dioxide values impact on biomarkers of neurological injury. The Targeted Temperature Management 2 (TTM-2) trial has documented no difference in 6-month mortality among comatose postcardiac arrest patients managed at 33 oC versus controlled normothermia. An extensive systematic review of the evidence on prognostication of outcome among comatose postcardiac arrest patients underpins new prognostication guidelines.

Clinical guidelines for postresuscitation care have recently been updated and incorporate all the available science supporting the treatment of postcardiac arrests. At a minimum, fever should be strictly avoided in comatose postcardiac patients. Prognostication must involve multiple modalities and should not be attempted until assessment confounders have been sufficiently excluded.
Effects of Bathing in a Tub on Physical and Psychological Symptoms of End-of-Life Cancer Patients
Authors: Hayashi Eriko , Aoyama Maho , Fukano Fumiyasu , Takano Junko , Shimizu Yoichi , Miyashita Mitsunori
Published: September 2021

This observational, controlled study explored the effects of bathing on the physical and psychological aspects of terminal cancer patients on a palliative care ward. With nurses' assistance, the patients evaluated and recorded the severity of their symptoms at 10:00 am, 30 minutes after initial bathing, and at 5:00 pm. The bathing care was provided as routine care according to the patients' wishes. Twelve symptoms were measured using 9 items (numbers 1-9) from the Edmonton Symptom Assessment System-Revised Japanese version and 3 items from the Cancer Fatigue Scale. Outcomes were compared between bathing days and nonbathing days (control) and between before and after bathing.

Of the 57 bathers, data were available for both bathing days and nonbathing days for 42 bathers. In the comparison between bathing and nonbathing days, tiredness was significantly improved (effect size [ES], 0.35; P = .02). On the basis of the pre-post bathing comparison, 6 symptoms, namely, tiredness (ES, 0.40; P < .01), lack of appetite (ES, 0.36; P = .01), decreased well-being (ES, 0.33; P = .01), anxiety (ES, 0.36; P = .01), pain (ES, 0.31; P = .02), and depression (ES, 0.30; P = .02), were significantly improved. Bathing in a tub effectively improves tiredness and might be effective for distressing symptoms in end-of-life cancer patients.
Self-perceived Burden
Authors: Bigger Sharon E. , Vo Timothea
Published: September 2021

The purpose of this article is to critically analyze the concept of self-perceived burden. The Rodgers Evolutionary Model is augmented with concept critique, a dialogic process grounded in critical hermeneutics. Self-perceived burden is a relatively mature concept with psychological, relational, and dimensional attributes that are shaped by culture and sociopolitical structures. The antecedents are demographics, circumstances, diagnoses, symptoms, prognosis, comorbidities, and knowledge and beliefs. The consequences are psychological, decisional, relational, and existential. Sociocultural factors such as universal health coverage, Confucian ethics, Buddhist/Taoist ethics, karma, and individualist- versus communitarian-based relationships are brought to light. Psychological and relational antecedents and consequences of self-perceived burden were found to be salient.
Chlamydial Infection Among Adolescents and Young Adults Receiving Sexual and Reproductive Health Care During the COVID-19 Pandemic
Authors: Hill Brandon J. , Anderson Brie , Lock Li
Published: September 2021

The impact of the COVID-19 pandemic on adolescent and young adult chlamydial infection is unknown. Patient testing data were extracted from the electronic health records of 10 family planning clinics. Prepandemic and pandemic comparisons revealed an increase in observed chlamydial infection, with greater positivity among Black/African American female adolescent patients.
Pooled 3-Anatomic-Site Testing for Chlamydia trachomatis and Neisseria gonorrhoeae: A Systematic Review and Meta-Analysis
Authors: Almeria Jasmine , Pham Joshua , Paris Keely S. , Heskett Karen M. , Romyco Irvin , Bristow Claire C.
Published: September 2021

Background

Pooled testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) may be a cost-saving solution to increase screening by simplifying testing procedures and reducing resource burdens. We conducted a systematic review and meta-analysis to examine the performance of pooled 3-anatomic-site testing (pharyngeal, rectal, and urogenital sites) for CT and NG in comparison with single-anatomic-site testing.

Methods

We conducted a systematic literature search in PubMed, Embase, and Web of Science to identify original evaluation studies of the performance of pooled testing for CT and NG infections and identified 14 studies for inclusion. Each study was systematically evaluated for bias. We conducted bivariate fixed-effects and random-effects meta-analyses using a full Bayesian method of the positive percent agreement and negative percent agreement.

Results

The combined positive percent agreement for CT was 93.11% (95% confidence interval [CI], 91.51%–94.55%), and the negative percent agreement was 99.44% (95% CI, 99.18%–99.65%). For NG, the combined positive percent agreement was 93.80% (95% CI, 90.26%–96.61%), and the negative percent agreement was 99.73% (95% CI, 99.30%–99.97%).

Conclusions

We found that pooled 3-anatomic-site tests performed similarly to single-anatomic-site tests for the detection of CT and NG. The pooled 3-anatomic-site tests have the added potential benefit of reduced cost and resource requirement, which could lead to improved testing access and screening uptake.
Human Immunodeficiency Virus/Sexually Transmitted Infection Testing Preferences for Young Black Men Who Have Sex With Men in the Southeastern United States: Implications for a Post–COVID-19 Era
Authors: Van Gerwen Olivia T. , Talluri Rajesh , Camino Andres F. , Mena Leandro A. , Chamberlain Nicholas , Ford Eric W. , Eaton Ellen F. , Muzny Christina A.
Published: September 2021

Background

Little is known regarding human immunodeficiency virus (HIV)/sexually transmitted infection (STI) testing preferences for location, staffing, and hours of operation among Young Black men who have sex with men (YBMSM) in the Southeastern United States, a population at high risk for HIV/STIs. We used a discrete choice experiment to explore these preferences.

Methods

Young Black men who have sex with men ages 16 to 35 years in Birmingham, AL and Jackson, MS completed online surveys evaluating their preferences (best/worst) for HIV/STI testing locations, staffing, hours, method of results notification, and cost. They also selected preferred combinations of these variables through choice tasks. Results were analyzed using joint best/worst and discrete choice experiment models.

Results

Between June 2018 and December 2019, participants in Alabama (n = 54) and Mississippi (n = 159) completed online surveys. Both groups preferred stationary testing locations over mobile testing vans, with the most significant difference favoring STI testing-only clinics in Mississippi and local health departments in Alabama (P < 0.001). Technician-performed tests or self-testing were significantly less preferred compared with clinician-performed testing for both groups (P < 0.0001 and P < 0.0001, respectively). Free testing and phone results notification (versus text) were preferred by both groups. The most desirable combination among all participants was weekday clinician-performed testing at the health department for $5.

Conclusions

Young Black men who have sex with men in the Southeastern United States prefer traditional testing locations staffed by experienced personnel. Combination choices are influenced by services that are low or no cost. More research is needed to inform the best way(s) to provide affordable, high-quality HIV/STI testing services for YBMSM, particularly in the post–COVID-19 era when sexual health care delivery models are evolving toward home-based and remote health-focused strategies.
Enhanced sucrose fermentation by introduction of heterologous sucrose transporter and invertase into
Clostridium beijerinckii
for acetone–butanol–ethanol production
Authors: Lin Lihua , Zhang Zhikai , Tang Hongchi , Guo Yuan , Zhou Bingqing , Liu Yi , Huang Ribo , Du Liqin , Pang Hao
Published: September 2021

A heterologous pathway for sucrose transport and metabolism was introduced into
Clostridium beijerinckii
to improve sucrose use for
n
-butanol production. The combined expression of
StSUT1
, encoding a sucrose transporter from potato (
Solanum tuberosum
), and
SUC2
, encoding a sucrose invertase from
Saccharomyces cerevisiae
, remarkably enhanced
n
-butanol production. With sucrose, sugarcane molasses and sugarcane juice as substrates, the
C. beijerinckii
strain harbouring
StSUT1
and
SUC2
increased acetone–butanol–ethanol production by 38.7%, 22.3% and 52.8%, respectively, compared with the wild-type strain. This is the first report to demonstrate enhanced sucrose fermentation due to the heterologous expression of a sucrose transporter and invertase in
Clostridium
. The metabolic engineering strategy used in this study can be widely applied in other microorganisms to enhance the production of high-value compounds from sucrose-based biomass.
Highly porous Co-doped NiO nanorods: facile hydrothermal synthesis and electrocatalytic oxygen evolution properties
Authors: Cuong Nguyen Duc , Tran Tien D. , Nguyen Quyen T. , Van Minh Hai Ho , Hoa Tran Thai , Quang Duong Tuan , Klysubun Wantana , Tran Phong D.
Published: September 2021

Highly porous 3d transition metal oxide nanostructures are opening up the exciting area of oxygen evolution reaction (OER) catalysts in alkaline medium thanks to their good thermal and chemical stability, excellent physiochemical properties, high specific surface area and abundant nanopores. In this paper, highly porous Co-doped NiO nanorods were successfully synthesized by a simple hydrothermal method. The porous rod-like nanostructures were preserved with the added cobalt dopant ranging from 1 to 5 at% but were broken into aggregated nanoparticles at higher concentrations of additional cobalt. The catalytic activity of Co-doped NiO nanostructures for OER in an alkaline medium was assayed. The 5%Co-NiO sample showed a drastically enhanced activity. This result could originate from the combination of advantageous characteristics of highly porous NiO nanorods such as large surface area and high porosity as well as the important role of Co dopant that could provide more catalytic active sites, leading to an enhanced catalytic activity of the nanocatalyst.
Ramlibacter algicola sp. nov., isolated from a freshwater alga Cryptomonas obovoidea
Authors: Kim Hyung Min , Han Dong Min , Chun Byung Hee , Jung Hye Su , Kim Kyung Hyun , Jeon Che Ok
Published: September 2021

A Gram-stain-negative, strictly aerobic, catalase-negative, oxidase-positive and non-motile rod-shaped bacterium, designated strain CrO1T, was isolated from a freshwater alga Cryptomonas obovoidea in the Nakdong river of South Korea. Colonies of CrO1T were white, convex and circular and growth was observed at 25–40 °C (optimum, 37 °C) and pH 6.0–9.0 (optimum, pH 7) and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). CrO1T contained C16 : 0, summed feature 5 (comprising C18 : 0ante and/or C18 : 2ω6,9c), C18 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) as the major cellular fatty acids (>5 %) and ubiquinone-8 as the sole respiratory quinone. Phosphatidylethanolamine was detected as the major polar lipid. The DNA G+C content of CrO1T, calculated from the whole genome sequence was 69.6 mol%. CrO1T was most closely related to

Ramlibacter humi

18x22-1T with a 97.6 % 16S rRNA sequence similarity and shared less than 97.4 % 16S rRNA sequence similarities with other type strains. Phylogenetic analyses based on the 16S rRNA gene and whole genome sequences revealed that CrO1T formed a distinct phyletic lineage within the genus

Ramlibacter

. On the basis of the results of phenotypic, chemotaxonomic and molecular analysis, CrO1T clearly represents a novel species of the genus

Ramlibacter

, for which the name Ramlibacter algicola sp. nov. is proposed. The type strain is CrO1T (=KACC 19926T=JCM 33302T).
Potential antibiotic production of Streptomyces justiciae sp. nov., isolated from the root of Justicia subcoriacea
Authors: Phongsopitanun Wongsakorn , Kanchanasin Pawina , Sripreechasak Paranee , Rueangsawang Kanokorn , Athipornchai Anan , Supong Khomsan , Pittayakhajonwut Pattama , Tanasupawat Somboon
Published: September 2021

Endophytic actinobacterial strain 3R004T was isolated from a root of Justicia subcoriacea collected in Thailand. In this report, the taxonomic position of this strain is described using a polyphasic approach. Based on the morphological characteristics and chemical composition of its cells, strain 3R004T was identified as a member of the genus

Streptomyces

. It produced a long chain of cylindrical spores on aerial mycelia. ll-Diaminopimelic acid was detected in the cell wall peptidoglycan. The menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8). C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0 were detected as the major cellular fatty acids. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and one unidentified lipid. Strain 3R004T showed the highest 16S rRNA gene similarity of 99.45 % to

Streptomyces cyaneochromogenes

MK-45T. The phylogenomic results indicated that strain 3R004T was close to

Streptomyces aquilus

GGCR-6T and

Streptomyces antibioticus

DSM 40234T. The DNA–DNA hybridization and average nucleotide identity values among strain 3R004T and closely related

Streptomyces

species were 35.5–63.1 % and 82.7–94.3 %, respectively. The type strain produced actinomycin D antibiotic as the major secondary metabolite. The maximum productivity of the actinomycin D (378 mg l−1) was observed when the strain was grown in 301 broth at 30 °C, 180 r.p.m. for 12 days. On the basis of phenotypic and genotypic evidence, strain 3R004T represents a novel species of the genus

Streptomyces

, for which the name Streptomyces justiciae is proposed. The type strain is 3R004T (=LMG 32138T=TBRC 13128T=NBRC 115065T).