bluuebunny/crossref_metadata_2025 huggingface dataset:
Latest reports of primary dysmenorrhea
Authors: Łopuszyńska Anna Małgorzata , Pawlicki Mateusz , Ochyra Łukasz , Piecewicz-Szczęsna Halina
Published: September 2022

Introduction: Primary dysmenorrhea (PD) is a pelvic pain during menstruation in the absence of any pelvic pathologies. This disease mainly affects young women in reproductive age. In addition to pain, patients may experience many other symptoms including: gastrointestinal symptoms, sleep disorders. This contributes to reduction in their mental and physical quality of life.Purpose: the purpose of this review is to draw attention to a problem that affects a large number of society, is often underestimated and largely affects the quality of women's life, as well as to present the latest discoveries and reports on this issue. Material and methods: the scientific literature published in the years 2017-2022 was reviewed in the PubMed scientific database using the following keywords: primary dysmenorrhea, dysmenorrhea.Results: Increased prostaglanding levels, abnormalities in the reward system, oxidative stress, ischemia, and eotaxin may contribute to the development of pain in PD. These findings could open up new diagnostic or therapeutic targets. The first choice in the treatment of PD are NSAIDs, which are taken regularly for many years, so they must be as safe and effective aspossible. Research suggests that thiaprofenic acid and ibuprofen are suitable. For alternative treatments TENS, heat, and acupuncture can be effective. Propolis, ginger, valeric acid, hops and exercise are also promising.Conclusions: PD is a varied disease that affects a large number of women. It leads to a reduction in the quality of life, hence it is necessary to conduct further research on a diverse, large group of respondents, in many centers, with the use of systematized pain scales, and lasting for a certain period of time.
On Integer Programming, Discrepancy, and Convolution
Authors: Jansen Klaus , Rohwedder Lars
Published: September 2022

Integer programs with a fixed number of constraints are solvable in pseudo-polynomial time in the largest coefficient of any constraint. We give a new algorithm which improves the running time of the state of the art. Moreover, we show that improving on our algorithm for any number of constraints is equivalent to improving over the quadratic time algorithm for (min, +)-convolution. This is strong evidence that our algorithm’s running time is the best possible. We also present a specialized algorithm for testing the feasibility of an integer program and give a tight lower bound, which is based on the strong exponential time hypothesis in this case.

Funding: This work was supported by the German Research Foundation [Grants JA 612/16-1, JA 612/20-1].
A prospective clinical pilot study comparing two post-operative dressings in the treatment of surgical incisions in volunteers
Authors: Breisinger Kristy , Harrell Khristina , Serena Laura , Serena Thomas E
Published: September 2022

Objective:

Surgical site infections (SSIs) are one of the leading causes of post-operative morbidity and mortality worldwide. The original post-operative dressing, gauze taped in place, did not protect the incision from contamination. A recent clinical trial demonstrated that transparent films were superior to gauze in reducing SSIs. Transparent films are semi-occlusive (semi-permeable, transparent). They protect the incision from contamination; however, one of the drawbacks of current films is that they may become dislodged during daily activities, such as showering. Patients may not realise that the integrity of the dressing has been compromised, leading to soiling of the incision and possible infection. DrySee (DrySee Inc., US) is a novel film dressing with a colorimetric indicator that alerts the patient when the dressing has been compromised.

Method:

This trial compared the film dressing with the indicator (DSD) to a commonly used post-operative dressing comparator (Tegaderm + Pad; 3M, US). A 1.5cm incision was made in the volar forearm of volunteers. The incisions were randomly treated with the DSD or comparator dressing.

Results:

A cohort of 20 volunteer patients was recruited. The DSD had a greater wear time and patients reported that the DSD dressing stayed in place better during activities compared to the comparator.

Conclusion:

Overall, 75% of patients preferred DSD and 25% preferred the comparator.
Metagenomics of diabetic foot ulcer undergoing treatment with total contact casting: a case study
Authors: Isaac Adam L , Tritto Michael , Colwell Rita R , Armstrong David G
Published: September 2022

Objective:

Diabetic foot ulcers (DFUs) are characterised by the presence of many microbes, some of which may not be identified by traditional culture techniques. Total contact casting (TCC) remains the gold-standard for offloading, yet little is known about the microbiome of wounds that progress from hard-to-heal to closed within a TCC.

Method:

A patient with a DFU underwent weekly treatment with TCC to closure. Samples for next-generation sequencing (NGS) and bioinformatics analysis of tissue samples were collected during each visit. Detection, identification, characterisation of the microbial community and abundance of microbes in each sample were compared.

Results:

Abundance of microbes, identified by species and strain, changed with each treatment visit. By the final week of treatment, species diversity of the wound microbiome had decreased significantly, highlighted by an observed decrease in the number of total microorganisms present. Resistance genes for tetracyclines were detected in the first sample, but not in subsequent samples.

Conclusion:

The results of this study suggest dynamic microbiological changes associated with DFUs as they progress to healing within a TCC. As NGS becomes more readily available, further studies will be helpful to gain an improved understanding of the significance of the wound microbiome in patients with DFUs.
Unicyclic 3-colored digraphs with bicyclic inverses
Authors: Kalita Debajit , Sarma Kuldeep
Published: September 2022

The class of unicyclic $3$-colored digraphs with the cycle weight $\pm\mathrm{i}$ and with a unique perfect matching, denoted by $\mathcal{U}_g$, is considered in this article. Kalita \& Sarma [On the inverse of unicyclic 3-coloured digraphs, Linear and Multilinear Algebra, DOI: 10.1080/03081087.2021.1948956] introduced the notion of inverse of $3$-colored digraphs. They characterized the unicyclic $3$-colored digraphs in $\mathcal{U}_g$ possessing unicyclic inverses. This article provides a complete characterization of the unicyclic $3$-colored digraphs in $\mathcal{U}_g$ possessing bicyclic inverses.
The Place of Children: Poverty and Promise
Authors: van Vliet— Willem
Published: September 2022

Abstract: This paper is based on a project that raised awareness of the challenges faced by children among the urban poor worldwide and recognized their contributions to their families and communities. In 2008–09, ethnographic fieldwork documented the daily lives of four teenagers in New York City, Rio de Janeiro, Nairobi, and Ankara. In 2021, we followed up with them for updates on their situation. This paper describes the project and its context, concluding with a brief assessment.
Compact asymmetric directional-coupler-based two-mode optical switch utilizing low loss Sb2Se3 phase-change material
Authors: Atri Ali , Zarifkar Abbas
Published: September 2022

Mode division multiplexing (MDM) has provided a new trend in high capacity optical transmission systems. Some of the most important devices in MDM systems are multimode switches that can route signals simultaneously into different paths. In this work, a two-mode

1

×

2

optical switch based on an asymmetric directional coupler and using Sb2Se3 phase-change material is proposed with a compact size of

45

µ

m

×

6

µ

m

. This switch can route the fundamental and first transverse magnetic modes in a wide bandwidth in the third telecommunication window from 1535 to 1565 nm. According to the 3D finite-difference time-domain simulation results, this switch has a low insertion loss of 0.83 dB and cross talk of

−

7.93

d
B

across the bandwidth in the “on” state. In addition, when the switch is off, it has suitable specifications in terms of insertion loss and cross talk with values lower than 0.29 dB and

−

11.98

d
B

across the bandwidth, respectively.
Fabrication of a large scale metasurface with high resolution and enhanced absorption
Authors: Al Hasan Muath , Ullah Zaka , Nawi Illani , Ben Mabrouk Ismail
Published: September 2022

Plasmonic metasurface nanostructures have the potential to enable nonlinear optical functionality in metasurfaces by reducing power operating thresholds and enabling ultra-thin subwavelength devices. However, low absorption caused by resistive losses of unwanted metallic appearance and irregular corners in the fabrication process significantly reduces this promise, leading the metasurface community toward the new approaches to fabricate large area metasurfaces with Electron Beam lithography (EBL). In this article, with controlled proximity effect and high dose exposure rate in EBL setup, large area (2 cm2) metasurfaces are fabricated with high resolution of structure. The effect of absorption resonance in Infrared (LWIR) is experimentally studied through Fourier Transform Infrared Spectroscopy (FTIR). The results signify that the metasurface with high resolution and fine metallic corners outperforms the fabricated prototype with metal residue and non-uniform corners. When compared to conventional EBL, our nanofabrication approach speeds the patterning time by three times. The experimental measurements reveal enhanced absorption performance at 8 µm wavelength. Whereas, the developed metasurface is numerically studied to explain the absorption performance with plasmonic field distributions. This approach could be used in optoelectronic devices involving plasmonic applications, such as biosensing and infrared imaging.
Robust inference of population size histories from genomic sequencing data
Authors: Upadhya Gautam , Steinrücken Matthias
Published: September 2022

Unraveling the complex demographic histories of natural populations is a central problem in population genetics. Understanding past demographic events is of general anthropological interest, but is also an important step in establishing accurate null models when identifying adaptive or disease-associated genetic variation. An important class of tools for inferring past population size changes from genomic sequence data are Coalescent Hidden Markov Models (CHMMs). These models make efficient use of the linkage information in population genomic datasets by using the local genealogies relating sampled individuals as latent states that evolve along the chromosome in an HMM framework. Extending these models to large sample sizes is challenging, since the number of possible latent states increases rapidly.

Here, we present our method CHIMP (CHMM History-Inference Maximum-Likelihood Procedure), a novel CHMM method for inferring the size history of a population. It can be applied to large samples (hundreds of haplotypes) and only requires unphased genomes as input. The two implementations of CHIMP that we present here use either the height of the genealogical tree (TMRCA) or the total branch length, respectively, as the latent variable at each position in the genome. The requisite transition and emission probabilities are obtained by numerically solving certain systems of differential equations derived from the ancestral process with recombination. The parameters of the population size history are subsequently inferred using an Expectation-Maximization algorithm. In addition, we implement a composite likelihood scheme to allow the method to scale to large sample sizes.

We demonstrate the efficiency and accuracy of our method in a variety of benchmark tests using simulated data and present comparisons to other state-of-the-art methods. Specifically, our implementation using TMRCA as the latent variable shows comparable performance and provides accurate estimates of effective population sizes in intermediate and ancient times. Our method is agnostic to the phasing of the data, which makes it a promising alternative in scenarios where high quality data is not available, and has potential applications for pseudo-haploid data.
Fast and accurate Ab Initio Protein structure prediction using deep learning potentials
Authors: Pearce Robin , Li Yang , Omenn Gilbert S. , Zhang Yang
Published: September 2022

Despite the immense progress recently witnessed in protein structure prediction, the modeling accuracy for proteins that lack sequence and/or structure homologs remains to be improved. We developed an open-source program, DeepFold, which integrates spatial restraints predicted by multi-task deep residual neural-networks along with a knowledge-based energy function to guide its gradient-descent folding simulations. The results on large-scale benchmark tests showed that DeepFold creates full-length models with accuracy significantly beyond classical folding approaches and other leading deep learning methods. Of particular interest is the modeling performance on the most difficult targets with very few homologous sequences, where DeepFold achieved an average TM-score that was 40.3% higher than trRosetta and 44.9% higher than DMPfold. Furthermore, the folding simulations for DeepFold were 262 times faster than traditional fragment assembly simulations. These results demonstrate the power of accurately predicted deep learning potentials to improve both the accuracy and speed of ab initio protein structure prediction.
Engaging community members in setting priorities for nutrition interventions in rural northern Ghana
Authors: Dalaba Maxwell Ayindenaba , Nonterah Engelbert A. , Chatio Samuel T. , Adoctor James K. , Dambayi Edith , Nonterah Esmond W. , Azalia Stephen , Ayi-Bisah Doreen , Erzse Agnes , Watson Daniella , Hardy-Johnson Polly , Kehoe Sarah H. , Tugendhaft Aviva , Ward Kate , Debpuur Cornelius , Oduro Abraham , Ofosu Winfred , Danis Marion , Barker Mary ,   on behalf of the INPreP study group
Published: September 2022

This study used “Choosing All Together” (CHAT), a deliberative engagement tool to prioritise nutrition interventions and to understand reasons for intervention choices of a rural community in northern Ghana. The study took an exploratory cross-sectional design and used a mixed method approach to collect data between December 2020 and February 2021. Eleven nutrition interventions were identified through policy reviews, interaction with different stakeholders and focus group discussions with community members. These interventions were costed for a modified CHAT tool—a board-like game with interventions represented by colour coded pies and the cost of the interventions represented by sticker holes. Supported by trained facilitators, six community groups used the tool to prioritise interventions. Discussions were audio-recoded, transcribed and thematically analysed. The participants prioritised both nutrition-sensitive and nutrition-specific interventions, reflecting the extent of poverty in the study districts and the direct and immediate benefits derived from nutrition-specific interventions. The prioritised interventions involved livelihood empowerment, because they would create an enabling environment for all-year-round agricultural output, leading to improved food security and income for farmers. Another nutrition-sensitive, education-related priority intervention was male involvement in food and nutrition practices; as heads of household and main decision makers, men were believed to be in a position to optimise maternal and child nutrition. The prioritised nutrition-specific intervention was micronutrient supplementation. Despite low literacy, participants were able to use CHAT materials and work collectively to prioritize interventions. In conclusion, it is feasible to modify and use the CHAT tool in public deliberations to prioritize nutrition interventions in rural settings with low levels of literacy. These communities prioritised both nutrition-sensitive and nutrition-specific interventions. Attending to community derived nutrition priorities may improve the relevance and effectiveness of nutrition health policy, since these priorities reflect the context in which such policy is implemented.
Intuitive assessment of spatial navigation beyond episodic memory: Feasibility and proof of concept in middle-aged and elderly individuals
Authors: Rekers Sophia , Niedeggen Michael
Published: September 2022

Deficits in spatial navigation in three-dimensional space are prevalent in various neurological disorders and are a sensitive cognitive marker for prodromal Alzheimer’s disease, but are also associated with non-pathological aging. However, standard neuropsychological tests used in clinical settings lack ecological validity to adequately assess spatial navigation. Experimental paradigms, on the other hand, are often too difficult for seniors or patients with cognitive or motor impairments since most require operating a human interface device (HID) or use complex episodic memory tasks. Here, we introduce an intuitive navigation assessment, which is conceptualized using cognitive models of spatial navigation and designed to account for the limited technical experience and diverging impairments of elderly participants and neurological patients. The brief computer paradigm uses videos of hallways filmed with eye tracking glasses, without employing an episodic memory task or requiring participants to operate a HID. Proof of concept data from 34 healthy, middle-aged and elderly participants (56–78 years) provide evidence for the assessment’s feasibility and construct validity as a navigation paradigm. Test performance showed normal distribution and was sensitive to age and education, which needs to be considered when investigating the assessment’s psychometric properties in larger samples and clinical populations. Correlations of the navigation assessment with other neuropsychological tests confirmed its dependence on visuospatial skills rather than visual episodic memory, with age driving the association with working memory. The novel paradigm is suitable for a differentiated investigation of spatial navigation in elderly individuals and promising for experimental research in clinical settings.
Single- and duplex TaqMan-quantitative PCR for determining the copy numbers of integrated selection markers during site-specific mutagenesis in Toxoplasma gondii by CRISPR-Cas9
Authors: Hänggeli Kai Pascal Alexander , Hemphill Andrew , Müller Norbert , Schimanski Bernd , Olias Philipp , Müller Joachim , Boubaker Ghalia
Published: September 2022

Herein, we developed a single and a duplex TaqMan quantitative PCR (qPCR) for absolute quantification of copy numbers of integrated dihydrofolate reductase-thymidylate synthase (mdhfr-ts) drug selectable marker for pyrimethamine resistance inToxoplasma gondiiknockouts (KOs). The single TaqMan qPCR amplifies a 174 bp DNA fragment of the insertedmdhfr-tsand of the wild-type (WT)dhfr-ts(wtdhfr-ts) which is present as single copy gene inToxoplasmaand encodes a sensitive enzyme to pyrimethamine. Thus, the copy number of thedhfr-tsfragment in a given DNA quantity from KO parasites with a single site-specific integration should be twice the number ofdhfr-tscopies recorded in the same DNA quantity from WT parasites. The duplex TaqMan qPCR allows simultaneous amplification of the 174 bpdhfr-tsfragment and theT.gondii 529-bprepeat element. Accordingly, for a WT DNA sample, the determined number of tachyzoites given bydhfr-tsamplification is equal to the number of tachyzoites determined by amplification of theToxoplasma 529-bp, resulting thus in a ratio of 1. However, for a KO clone having a single site-specific integration ofmdhfr-ts, the calculated ratio is 2. We then applied both approaches to testT.gondiiRH mutants in which themajor surface antigen(SAG1) was disrupted through insertion ofmdhfr-tsusing CRISPR-Cas9. Results from both assays were in correlation showing a high accuracy in detecting KOs with multiple integratedmdhfr-ts. Southern blot analyses using BsaBI and DraIII confirmed qPCRs results. Both TaqMan qPCRs are needed for reliable diagnostic ofT.gondiiKOs following CRISPR-Cas9-mediated mutagenesis, particularly with respect to off-target effects resulting from multiple insertions ofmdhfr-ts. The principle of the duplex TaqMan qPCR is applicable for other selectable markers inToxoplasma. TaqMan qPCR tools may contribute to more frequent use of WTToxoplasmastrains during functional genomics.
Sex differences in susceptibility to influenza A virus infection depend on host genotype
Authors: Sabikunnahar Bristy , Lahue Karolyn G. , Asarian Loredana , Fang Qian , McGill Mahalia M. , Haynes Laura , Teuscher Cory , Krementsov Dimitry N.
Published: September 2022

Infection with the respiratory pathogen influenza A virus (IAV) causes significant morbidity and mortality each year. While host genotype is thought to contribute to severity of disease, naturally occurring genetic determinants remain mostly unknown. Moreover, more severe disease is seen in women compared with men, but genetic mechanisms underlying this sex difference remain obscure. Here, using IAV infection in a mouse model of naturally selected genetic diversity, namely C57BL6/J (B6) mice carrying chromosomes (Chr) derived from the wild-derived and genetically divergent PWD/PhJ (PWD) mouse strain (B6.ChrPWD consomic mice), we examined the effects of genotype and sex on severity of IAV-induced disease. Compared with B6, parental PWD mice were completely protected from IAV-induced disease, a phenotype that was fully recapitulated in the B6.Chr16PWD strain carrying the PWD-derived allele of Mx1. In contrast, several other consomic strains, including B6.Chr3PWD and B6.Chr5PWD, demonstrated greatly increased susceptibility. Notably, B6.Chr5PWD and B6.ChrX.3PWD strains, the latter carrying the distal one-third of ChrX from PWD, exhibited increased morbidity and mortality specifically in male but not female mice. Follow up analyses focused on B6 and B6.ChrX.3PWD strains demonstrated moderately elevated viral load in B6.ChrX3PWD male, but not female mice. Transcriptional profiling demonstrated genotype- and sex-specific gene expression profiles in the infected lung, with male B6.ChrX.3 mice exhibiting the most significant changes, including upregulation of a proinflammatory gene expression program associated with myeloid cells, and altered sex-biased expression of several X-linked genes that represent positional candidates, including Tlr13 and Slc25a53. Taken together, our results identify novel loci on autosomes and the X chromosome regulating IAV susceptibility and demonstrate that sex differences in IAV susceptibility are genotype-dependent, suggesting that future genetic association studies need to consider sex as a covariate.
An active learning-based approach for screening scholarly articles about the origins of SARS-CoV-2
Authors: An Xin , Zhang Mengmeng , Xu Shuo
Published: September 2022

To build a full picture of previous studies on the origins of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), this paper exploits an active learning-based approach to screen scholarly articles about the origins of SARS-CoV-2 from many scientific publications. In more detail, six seed articles were utilized to manually curate 170 relevant articles and 300 nonrelevant articles. Then, an active learning-based approach with three query strategies and three base classifiers is trained to screen the articles about the origins of SARS-CoV-2. Extensive experimental results show that our active learning-based approach outperforms traditional counterparts, and the uncertain sampling query strategy performs best among the three strategies. By manually checking the top 1,000 articles of each base classifier, we ultimately screened 715 unique scholarly articles to create a publicly available peer-reviewed literature corpus,COVID-Origin. This indicates that our approach for screening articles about the origins of SARS-CoV-2 is feasible.
Cognitive and behavioral effects of whole brain conventional or high dose rate (FLASH) proton irradiation in a neonatal Sprague Dawley rat model
Authors: Williams Michael T. , Sugimoto Chiho , Regan Samantha L. , Pitzer Emily M. , Fritz Adam L. , Sertorio Mathieu , Mascia Anthony E. , Vatner Ralph E. , Perentesis John P. , Vorhees Charles V.
Published: September 2022

Recent studies suggest that ultra-high dose rates of proton radiation (>40 Gy/s; FLASH) confer less toxicity to exposed healthy tissue and reduce cognitive decline compared with conventional radiation dose rates (~1 Gy/s), but further preclinical data are required to demonstrate this sparing effect. In this study, postnatal day 11 (P11) rats were treated with whole brain irradiation with protons at a total dose of 0, 5, or 8 Gy, comparing a conventional dose rate of 1 Gy/s vs. a FLASH dose rate of 100 Gy/s. Beginning on P64, rats were tested for locomotor activity, acoustic and tactile startle responses (ASR, TSR) with or without prepulses, novel object recognition (NOR; 4-object version), striatal dependent egocentric learning ([configuration A] Cincinnati water maze (CWM-A)), prefrontal dependent working memory (radial water maze (RWM)), hippocampal dependent spatial learning (Morris water maze (MWM)), amygdala dependent conditioned freezing, and the mirror image CWM [configuration B (CWM-B)]. All groups had deficits in the CWM-A procedure. Weight reductions, decreased center ambulation in the open-field, increased latency on day-1 of RWM, and deficits in CWM-B were observed in all irradiated groups, except the 5 Gy FLASH group. ASR and TSR were reduced in the 8 Gy FLASH group and day-2 latencies in the RWM were increased in the FLASH groups compared with controls. There were no effects on prepulse trials of ASR or TSR, NOR, MWM, or conditioned freezing. The results suggest striatal and prefrontal cortex are sensitive regions at P11 to proton irradiation, with reduced toxicity from FLASH at 5 Gy.
High throughput embryonic zebrafish test with automated dechorionation to evaluate nanomaterial toxicity
Authors: Carbaugh Chance M. , van der Schalie William H. , Widder Mark W.
Published: September 2022

Engineered nanomaterials pose occupational health and environmental concerns as they possess unique physical and chemical properties that can contribute to toxicity. High throughput toxicity screening methods are needed to address the increasing number of nanomaterials in production. Here we used a zebrafish photomotor response (PMR) test to evaluate a set of fifteen nanomaterials with military relevance. Automated dechorionation of zebrafish embryos was used to enhance nanomaterials bioavailability. Optimal PMR activity in zebrafish embryos was found at 30–31 hours post-fertilization (hpf). Behavioral and toxicological responses were measured at 30 and 120 hpf; behavioral responses were found for thirteen of the fifteen nanomaterials and acute toxicity (LC50) levels for nine of the fifteen nanomaterials below the maximum test concentration of 500 μg/ml. Physico-chemical characterization of the nanomaterials detected endotoxin and bacterial contamination in two of the tested samples, which may have contributed to observed toxicity and reinforces the need for physical and chemical characterization of nanomaterials use in toxicity testing. The zebrafish PMR test, together with automated dechorionation, provides an initial rapid assessment of the behavioral effects and toxicity of engineered nanomaterials that can be followed up by physico-chemical characterization if toxicity is detected, reducing the amount of time and monetary constraints of physico-chemical testing.
Health care providers’ and persons with disabilities’ recommendations for improving access to primary health care services in rural northern Ghana: A qualitative study
Authors: Dassah Ebenezer , Aldersey Heather M. , McColl Mary Ann , Davison Colleen
Published: September 2022

In Ghana, many persons with physical disabilities are members of populations who face health disparities including physical, structural, knowledge, attitudinal and financial barriers to various health care services compared to those without disabilities. However, there is limited evidence on how to improve access to primary health care services for persons with physical disabilities. This study aimed to understand persons with physical disabilities’ experiences and health care providers’ perspectives for improving access to primary health care for persons with disabilities in rural Ghana. We used a qualitative approach and interviewed 33 persons with physical disabilities and health care providers, and thematically analysed data from in-depth interviews. We identified 4 major themes. According to the participants, health care could be more accessible by: i) Making it more affordable; ii) Increasing the availability of providers and services; iii) Providing more education about system navigation; and iv) Improving access to disability friendly health facilities and equipment. Participants’ recommendations were nested in the areas of policy and practice modifications. Policy makers need to consider supporting persons with physical disabilities who cannot afford non-medical services (i.e., cost of transportation). In terms of practice, the provision of education and training related to physical disability issues should be extended to both clinical and nonclinical health workers for better client centered care. There is an urgent need for policy makers and relevant key stakeholders to include persons with physical disabilities in designing and implementing policies and programs to ensure that they are meeting their needs.
Rapid genotyping of targeted viral samples using Illumina short-read sequencing data
Authors: Váradi Alex , Kaszab Eszter , Kardos Gábor , Prépost Eszter , Szarka Krisztina , Laczkó Levente
Published: September 2022

The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project’s GitHub page (https://github.com/laczkol/QVG).
Empiric recommendations for population disaggregation under different data scenarios
Authors: Sapena Marta , Kühnl Marlene , Wurm Michael , Patino Jorge E. , Duque Juan C. , Taubenböck Hannes
Published: September 2022

High-resolution population mapping is of high relevance for developing and implementing tailored actions in several fields: From decision making in crisis management to urban planning. Earth Observation has considerably contributed to the development of methods for disaggregating population figures with higher resolution data into fine-grained population maps. However, which method is most suitable on the basis of the available data, and how the spatial units and accuracy metrics affect the validation process is not fully known. We aim to provide recommendations to researches that attempt to produce high-resolution population maps using remote sensing and geospatial information in heterogeneous urban landscapes. For this purpose, we performed a comprehensive experimental research on population disaggregation methods with thirty-six different scenarios. We combined five different top-down methods (from basic to complex, i.e., binary and categorical dasymetric, statistical, and binary and categorical hybrid approaches) on different subsets of data with diverse resolutions and degrees of availability (poor, average and rich). Then, the resulting population maps were systematically validated with a two-fold approach using six accuracy metrics. We found that when only using remotely sensed data the combination of statistical and dasymetric methods provide better results, while highly-resolved data require simpler methods. Besides, the use of at least three relative accuracy metrics is highly encouraged since the validation depends on level and method. We also analysed the behaviour of relative errors and how they are affected by the heterogeneity of the urban landscape. We hope that our recommendations save additional efforts and time in future population mapping.
Performance of the UNICEF/UN Washington Group tool for identifying functional difficulty in rural Zimbabwean children
Authors: Dunne Thomas Frederick , Chandna Jaya , Majo Florence , Tavengwa Naume , Mutasa Batsirai , Chasekwa Bernard , Ntozini Robert , Prendergast Andrew J. , Humphrey Jean H. , Gladstone Melissa J.
Published: September 2022

Introduction

Over one billion people live with disability worldwide, of whom 80% are in developing countries. Robust childhood disability data are limited, particularly as tools for identifying disability function poorly at young ages.

Methods

A subgroup of children enrolled in the Sanitation Hygiene Infant Nutrition Efficacy (SHINE) trial (a cluster-randomised, community-based, 2x2 factorial trial in two rural districts in Zimbabwe) had neurodevelopmental assessments at 2 years of age. We evaluated functional difficulty prevalence in HIV-exposed and HIV-unexposed children using the Washington Group Child Functioning Module (WGCFM), comparing absolute difference using chi-squared or Fisher’s exact tests. Concurrent validity with the Malawi Developmental Assessment Tool (MDAT) was assessed using logistic regression with cohort MDAT score quartiles, linear regression for unit-increase in raw scores and a Generalised Estimating Equation approach (to adjust for clusters) to compare MDAT scores of those with and without functional difficulty. A 3-step, cluster-adjusted multivariable regression model was then carried out to examine risk factors for functional difficulty.

Findings

Functional Difficulty prevalence was 4.2% (95%CI: 3.2%, 5.2%) in HIV-unexposed children (n = 1606) versus 6.1% (95%CI: 3.5%, 8.9%) in HIV-exposed children (n = 314) (absolute difference 1.9%, 95%CI: -0.93%, 4.69%; p = 0.14). Functional difficulty score correlated negatively with MDAT: for each unit increase in WGCFM score, children completed 2.6 (95%CI: 2.2, 3.1) fewer MDAT items (p = 0.001). Children from families with food insecurity and poorer housing were more at risk of functional difficulty.

Interpretation

Functional difficulty was identified in approximately 1-in-20 children in rural Zimbabwe, which is comparable to prevalence in previous studies. WGCFM showed concurrent validity with the MDAT, supporting its use in early childhood.
Out-of-pocket expenditure on medicines in Bangladesh: An analysis of the national household income and expenditure survey 2016–17
Authors: Serván-Mori Edson , Islam Md Deen , Kaplan Warren A. , Thrasher Rachel , Wirtz Veronika J.
Published: September 2022

Background and objectives

High out-of-pocket expenditures (OOPE) increases the probability that households will become impoverished or will forgo needed care. The aim of this paper is to study household medicines expenditure and its associated determining factors to develop policies to protect households from financial hardship.

Methods

The present cross-sectional and population-level study used the Bangladesh 2016–17 National Household Income and Expenditure Survey (HIES). The final sample size was 46,080 households. We analyzed the probability of OOPE for medicines, the share of total OOPE due to medicines out of total OOPE in health (reported as a ratio between zero and one), the OOPE amount for medicines reported (in United States Dollars), and the share of OOPE amount on medicines out of total household expenditure (reported as a ratio between zero and one). Predictors of analyzed outcomes were identified using three regression models.

Results

Out of those households who spent on healthcare, the probability of having any OOPE on medicines was 87.9%. Of those who spent on medicines, the median monthly expenditure was US$3.03. The poorest households spent 9.97% of their total household expenditure as OOPE on medicines, nearly double that of the wealthiest households (5.86%). The characteristic which showed the most significant correlation to a high OOPE on medicines was the presence of chronic diseases, especially cancer. Twenty six percent of all surveyed households spend more than 10% of their OOPE on medicines.

Conclusions

Our study shows that financial protection should be targeted at the poorest quintiles and such protection should include enrollment of rural households. Further, outpatient medicines benefits should include those for non-communicable diseases (NCDs).
Incarceration status and cancer mortality: A population-based study
Authors: Oladeru Oluwadamilola T. , Aminawung Jenerius A. , Lin Hsiu-Ju , Gonsalves Lou , Puglisi Lisa , Mun Sophia , Gallagher Colleen , Soulos Pamela , Gross Cary P. , Wang Emily A.
Published: September 2022

Background

The complex relationship between incarceration and cancer survival has not been thoroughly evaluated. We assessed whether cancer diagnosis during incarceration or the immediate post-release period is associated with higher rates of mortality compared with those never incarcerated.

Methods

We conducted a population-based study using a statewide linkage of tumor registry and correctional system movement data for Connecticut adult residents diagnosed with invasive cancer from 2005 through 2016. The independent variable was place of cancer diagnosis: during incarceration, within 12 months post-release, and never incarcerated. The dependent variables were five-year cancer-related and overall survival rates.

Results

Of the 216,540 adults diagnosed with invasive cancer during the study period, 239 (0.11%) people were diagnosed during incarceration, 479 (0.22%) within 12 months following release, and the remaining were never incarcerated. After accounting for demographics and cancer characteristics, including stage of diagnosis, the risk for cancer-related death at five years was significantly higher among those diagnosed while incarcerated (AHR = 1.39, 95% CI = 1.12–1.73) and those recently released (AHR = 1.82, 95% CI = 1.57–2.10) compared to the never-incarcerated group. The risk for all-cause mortality was also higher for those diagnosed with cancer while incarcerated (AHR = 1.92, 95% CI = 1.63–2.26) and those recently released (AHR = 2.18, 95% CI = 1.94–2.45).

Conclusions and relevance

There is a higher risk of cancer mortality among individuals diagnosed with cancer during incarceration and in the first-year post-release, which is not fully explained by stage of diagnosis. Cancer prevention and treatment efforts should target people who experience incarceration and identify why incarceration is associated with worse outcomes.
Empowering families to take on a palliative caregiver role for patients with cancer in India: Persistent challenges and promising strategies
Authors: Fereydooni Soraya , Lorenz Karl A. , Ganesh Archana , Satija Anchal , Spruijt Odette , Bhatnagar Sushma , Gamboa Raziel C. , Singh Nainwant , Giannitrapani Karleen F.
Published: September 2022

Background

The population of patients with cancer requiring palliative care (PC) is on the rise in India. Family caregivers will be essential members of the care team in the provision of PC.

Objective

We aimed to characterize provider perspectives of the challenges that Indian families face in taking on a palliative caregiving role.

Method

Data for this analysis came from an evaluation of the PC-PAICE project, a series of quality improvement interventions for PC in India. We conducted 44 in-depth semi-structured interviews with organizational leaders and clinical team members at seven geographically and structurally diverse settings. Through thematic content analysis, themes relating to the caregivers’ role were identified using a combination of deductive and inductive approaches.

Result

Contextual challenges to taking up the PC caregiving role included family members’ limited knowledge about PC and cancer, the necessity of training for caregiving responsibilities, and cultural preferences for pursuing curative treatments over palliative ones. Some logistical challenges include financial, time, and mental health limitations that family caregivers may encounter when navigating the expectations of taking on the caregiving role. Strategies to facilitate family buy-in for PC provision include adopting a family care model, connecting them to services provided by Non-Governmental Organizations, leveraging volunteers and social workers to foster PC awareness and training, and responding specifically to family’s requests.

Conclusion

Understanding and addressing the various challenges that families face in adopting the caregiver role are essential steps in the provision and expansion of PC in India. Locally initiated quality improvement projects can be a way to address these challenges based on the context.
Challenges and Opportunities in Teaching Writing Online Amidst the Pandemic: Voices from English Language Teachers in Philippine Universities
Authors:   University of Santo Tomas, Manila, the Philippines, Tarrayo Veronico , Anudin Ali ,   Philippine Normal University, Manila, the Philippines, Mendoza Henelsie ,   Philippine Normal University, Manila, the Philippines, Parungao-Callueng Erly ,   Philippine Normal University, Manila, the Philippines
Published: September 2022

With the sudden transition to online instruction in most educational institutions caused by the COVID-19 pandemic, it can be assumed that there is paucity in research as regards the teaching of writing online during this crisis moment. To address this niche, 13 Filipino university English language teachers were asked to participate in both online semi-structured and follow-up email interviews to describe their experiences in teaching writing online during the pandemic, particularly the challenges they faced, their coping strategies to address these challenges, and the opportunities in online teaching they valued. The interview responses revealed three major challenges in teaching writing online: technological concerns and equity issues, vague response of schools to emergency remote teaching, and problems in assessment. Three key strategies to cope with these challenges were found: flexibility in communicating with students and in accommodating their concerns, initiatives for professional development, and gaining support from colleagues and students. Despite the challenges of online instruction, two opportunities for development in online writing instruction were identified: optimizing the use of online-teaching platforms and resources, and enhancing one’s reflective practice. Implications for teaching writing online in particular and for online learning and teacher education in general are discussed in the paper.
High free sugars content in regular and low-calorie sweetened beverages from the argentine market
Authors: Chulibert María Eugenia , Lupo Maela , Fina Brenda L. , Olguin María C. , Garcia Fabiana , Posadas Marta , Rigalli Alfredo , Lombarte Mercedes
Published: September 2022

Introduction: Sugar-sweetened beverages (SSBs) contain significant amounts of free sugars. SSBs consumption is strongly associated with overweight/obesity, dental caries, type 2 diabetes mellitus, cardiovascular disease, and other illnesses. The aim of this work was to evaluate the content of free sugars in Argentinian SSBs.
Methods: fructose, glucose and sucrose concentrations were measured in 53 samples from carbonated and non-carbonated SSBs through colorimetric techniques; regular (n=26) and low-calorie (n=27) beverages, classified according to nutritional label, were included. The total amount of sugars was calculated and compared with the declared value.
Results: regular and low-calorie SSBs differ in their glucose, fructose and sucrose concentrations, but do not differ in their free fructose concentrations. Furthermore, SSBs display higher concentrations of fructose compared to glucose, with a fructose/glucose ratio of 1.45.
Conclusions: Regular and low-calorie SSBs differ respect of the free fructose content. This study, also, provides evidence of the variability in sugar composition in similar beverages of different brands, which can be a confounding factor for consumers. Besides the importance of the sugar content of food, it is necessary to evaluate the other components present to assess comprehensively their nutritional quality.
Bowel Preparation Efficacy and Safety of 1 L vs 2 L Polyethylene Glycol With Ascorbic Acid for Colonoscopy: A Randomized Controlled Trial
Authors: Jeon Han Jo , Keum Bora , Bang Eun Ju , Lee Kang Won , Kim Sang Hyun , Lee Jae Min , Choi Hyuk Soon , Kim Eun Sun , Jeen Yoon Tae , Lee Hong Sik , Chun Hoon Jai
Published: September 2022

INTRODUCTION:

Polyethylene glycol with ascorbic acid (PEG/Asc) is a well-established bowel preparation solution with guaranteed effectiveness and safety. A new low-volume agent, 1 L-PEG/Asc, has recently been released. This study aimed to compare the bowel cleansing efficacy and safety of 1 L-PEG/Asc and 2 L-PEG/Asc administered to adult outpatients in a split-dose manner.

METHODS:

Outpatients undergoing colonoscopy enrolled in a single-blinded, single-center, noninferiority study conducted between July and October 2021 were randomized in a 1:1 manner to a 1 L-PEG/Asc or 2 L-PEG/Asc group. Bowel cleansing was assessed using the Boston Bowel Preparation Scale (BBPS) and the Harefield Cleansing Scale in intention-to-treat and per-protocol populations.

RESULTS:

Two hundred forty participants were randomized and allocated, with 120 patients in the 1 L and 2 L-PEG/Asc groups, respectively. Noninferiority was demonstrated for overall successful bowel cleansing (BBPS: 92.5% vs 90.8%; 95% confidence interval [CI], −0.054 to 0.087) and the high-quality cleansing rate of the right-sided colon (BBPS = 3, 40.0% vs 35.8%; 95% CI, −0.082 to 0.165; Harefield Cleansing Scale ≥3, 50.0% vs 43.3%; 95% CI, −0.060 to 0.194) in the intention-to-treat population. The overall incidence of adverse events was similar in both groups ([82/120] 68.3% vs [72/120] 60.0%; P = 0.178). The tolerability, acceptability, and compliance rates of both regimens were similar, with no significant differences.

DISCUSSION:

Compared with 2 L-PEG/Asc, 1 L-PEG/Asc achieved successful overall bowel cleansing efficacy with high-quality cleansing in the proximal colon and proved its noninferiority. Therefore, 1 L-PEG/Asc is an acceptable alternative bowel cleansing solution.