bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective whole-genome sequencing of
Plasmodium
parasites directly from blood samples by nanopore adaptive sampling
Authors: De Meulenaere Katlijn , Cuypers Wim L. , Gauglitz Julia M. , Guetens Pieter , Rosanas-Urgell Anna , Laukens Kris , Cuypers Bart
Published: December 2023

Whole-genome sequencing of
Plasmodium
is becoming an increasingly important tool for genomic surveillance of malaria. Due to the predominance of human DNA in a patient blood sample, time-consuming laboratory procedures are required to deplete human DNA or enrich
Plasmodium
DNA. Here, we investigated the potential of nanopore adaptive sampling to enrich
Plasmodium falciparum
reads while sequencing unenriched patient blood samples. To compare adaptive sampling versus regular sequencing on a MinION device, a dilution series consisting of 0%–84%
P
.
falciparum
DNA in human DNA was sequenced. Half of the flow cell channels were run in adaptive sampling mode, enriching for the
P. falciparum
reference genome, resulting in a three- to five-fold enrichment of
P. falciparum
bases in samples containing 0.1%–8.4%
P. falciparum
DNA. This finding was confirmed by sequencing three
P. falciparum
patient blood samples with common levels of parasitemia, that is, 0.1%, 0.2%, and 0.6% in adaptive mode. Their estimated enrichment was 5.8, 3.9, and 2.7, respectively, which was sufficient to cover at least 97% of the
P. falciparum
reference genome at a median depth of 5 (lowest parasitemia) or 355 (highest parasitemia). In all, 38 drug resistance loci were compared to Sanger sequencing results, showing high concordance, which suggests that the obtained sequencing data are of sufficient quality to address common clinical research questions for patients with parasitemias of 0.1% and higher. Overall, our results indicate that adaptive nanopore sequencing has the potential to replace more time-consuming
Plasmodium
enrichment protocols in the future.

IMPORTANCE

Malaria is caused by parasites of the genus
Plasmodium
, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich
Plasmodium
DNA. We used the Oxford Nanopore Technologies’ adaptive sampling feature to circumvent this problem and enrich
Plasmodium
reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches
Plasmodium
reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.
Crosstalk between glucagon-like peptide 1 and gut microbiota in metabolic diseases
Authors: Zeng Yuan , Wu Yifan , Zhang Qian , Xiao Xinhua
Published: December 2023

Gut microbiota exert influence on gastrointestinal mucosal permeability, bile acid metabolism, short-chain fatty acid synthesis, dietary fiber fermentation, and farnesoid X receptor/Takeda G protein-coupled receptor 5 (TGR5) signal transduction. The incretin glucagon-like peptide 1 (GLP-1) is mainly produced by L cells in the gut and regulates postprandial blood glucose. Changes in gut microbiota composition and function have been observed in obesity and type 2 diabetes (T2D). Meanwhile, the function and rhythm of GLP-1 have also been affected in subjects with obesity or T2D. Therefore, it is necessary to discuss the link between the gut microbiome and GLP-1. In this review, we describe the interaction between GLP-1 and the gut microbiota in metabolic diseases. On the one hand, gut microbiota metabolites stimulate GLP-1 secretion, and gut microbiota affect GLP-1 function and rhythm. On the other hand, the mechanism of action of GLP-1 on gut microbiota involves the inflammatory response. Additionally, we discuss the effects and mechanism of various interventions, such as prebiotics, probiotics, antidiabetic drugs, and bariatric surgery, on the crosstalk between gut microbiota and GLP-1. Finally, we stress that gut microbiota can be used as a target for metabolic diseases, and the clinical application of GLP-1 receptor agonists should be individualized.
Phosphatase to kinase switch of a critical enzyme contributes to timing of cell differentiation
Authors: Chong Trisha N. , Panjalingam Mayura , Saurabh Saumya , Shapiro Lucy
Published: December 2023

Cell differentiation is an essential biological process that is subject to strict temporal regulation.
Caulobacter crescentus
undergoes obligate differentiation from a swarmer cell to a stationary, replication-competent stalked cell with each cell cycle. We report that the switch from phosphatase to kinase activity of the histidine kinase PleC contributes to timing this differentiation event. PleC
P
er-
A
rnt-
S
im (PAS) domain interaction with the polar scaffold protein PodJ localizes PleC to the cell pole and inhibits
in vivo
kinase activity. Upon PodJ degradation, released PleC switches to its kinase form and phosphorylates the PleD diguanylate cyclase, initiating the signaling pathway responsible for differentiation. While PodJ inhibits PleC kinase activity, it does not impact PleC phosphatase activity on DivK, which is required for pili biogenesis and flagellar rotation. Thus, PleC PAS domains affect enzymatic function on diverse substrates by relying on context-dependent binding partners, thereby controlling the timing of
Caulobacter
cell differentiation.

IMPORTANCE

The process of cell differentiation is highly regulated in both prokaryotic and eukaryotic organisms. The aquatic bacterium,
Caulobacter crescentus
, undergoes programmed cell differentiation from a motile swarmer cell to a stationary stalked cell with each cell cycle. This critical event is regulated at multiple levels. Kinase activity of the bifunctional enzyme, PleC, is limited to a brief period when it initiates the molecular signaling cascade that results in cell differentiation. Conversely, PleC phosphatase activity is required for pili formation and flagellar rotation. We show that PleC is localized to the flagellar pole by the scaffold protein, PodJ, which is known to suppress PleC kinase activity
in vitro
. PleC mutants that are unable to bind PodJ have increased kinase activity
in vivo
, resulting in premature differentiation. We propose a model in which PodJ regulation of PleC’s enzymatic activity contributes to the robust timing of cell differentiation during the
Caulobacter
cell cycle.
Increased environmental microbial diversity reduces the disease risk of a mosquitocidal pathogen
Authors: Kang Zhiwei , Martinson Vincent G. , Wang Yin , Coon Kerri L. , Valzania Luca , Strand Michael R.
Published: December 2023

Increased diversity in host-associated microbial communities often benefits animal health by provisioning nutrients and protecting against pathogens. In contrast, whether the diversity of environmental microbial communities can also benefit animal health is much less studied. In aquatic environments, water enables environmental microbes to more directly interact with pathogens and animals than in terrestrial environments, which also suggests the potential for community diversity to benefit animal health. In this study, we addressed this question by identifying a strain of
Chromobacterium haemolyticum
named Rain 0013 (
Ch_
R13) that is a virulent pathogen of mosquito larvae, which live in aquatic habitats. Comparative genomic and functional data suggested many
Chromobacterium
are both mosquitocidal and opportunistic pathogens of other animals due to conservation of virulence factors that include a broad-spectrum toxin (cyanide). However, we also identified a strongly negative correlation between diversity of the environmental microbiota and disease severity due to
Ch_
R13 needing to achieve a threshold density to kill mosquito larvae. Experiments using defined (gnotobiotic) microbial communities further suggested certain environmental community members reduced
Ch_
R13 densities more than others. Altogether, our results indicate
Ch_
R13 and other
Chromobacterium
have the potential to broadly cause disease but the environmental communities of microbes in aquatic habitats attenuate disease risk.

IMPORTANCE

The host-specific microbiotas of animals can both reduce and increase disease risks from pathogens. In contrast, how environmental microbial communities affect pathogens is largely unexplored. Aquatic habitats are of interest because water enables environmental microbes to readily interact with animal pathogens. Here, we focused on mosquitoes, which are important disease vectors as terrestrial adults but are strictly aquatic as larvae. We identified a pathogen of mosquito larvae from the field as a strain of
Chromobacterium haemolyticum
. Comparative genomic analyses and functional assays indicate this strain and other
Chromobacterium
are mosquitocidal but are also opportunistic pathogens of other animals. We also identify a critical role for diversity of the environmental microbiota in disease risk. Our study characterizes both the virulence mechanisms of a pathogen and the role of the environmental microbiota in disease risk to an aquatic animal of significant importance to human health.
Building a better model: abandon kitchen sink regression
Authors: Kuhle Stefan , Brown Mary Margaret , Stanojevic Sanja
Published: December 2023

This paper critically examines ‘kitchen sink regression’, a practice characterised by the manual or automated selection of variables for a multivariable regression model based on p values or model-based information criteria. We highlight the pitfalls of this method, using examples from perinatal/neonatal medicine, and propose more robust alternatives. The concept of directed acyclic graphs (DAGs) is introduced as a tool for describing and analysing causal relationships. We highlight five key issues with ‘kitchen sink regression’: (1) the disregard for the directionality of variable relationships, (2) the lack of a meaningful causal interpretation of effect estimates from these models, (3) the inflated alpha error rate due to multiple testing, (4) the risk of overfitting and model instability and (5) the disregard for content expertise in model building. We advocate for the use of DAGs to guide variable selection for models that aim to examine associations between a putative risk factor and an outcome and emphasise the need for a more thoughtful and informed use of regression models in medical research.
Child bereavement—what matters to the families. Part 1: Immediate and short-term communication and care
Authors: Johnston Shona Elizabeth , McAllister Suzanne , Norden Catriona , Keens Keta , Jones Katharine , Smith Gillian , Duncombe Rebecca , Barnett Laura , Krepska Amy
Published: December 2023

The death of a child is a complex and hugely significant time for a family and community. Sophisticated but sensitive management by clinicians can have both short-term and long-term impacts on how families process the death. There is a paucity of guidance for optimal child bereavement care. A description of the child death review process including key legalities is provided here, and other essential aspects such as memory making, cultural aspects and sibling involvement are explored. Useful agencies and resources are also detailed. We, as both clinicians and bereaved parents, can uniquely provide an overview of the logistics of managing such a challenging event and highlight important subtleties in communication. We attempt, using our own experiences, to provide a framework and best inform future practice.
Child bereavement—what matters to the families. Part 2: The long term
Authors: Johnston Shona Elizabeth , McAllister Suzanne , Norden Catriona , Keens Keta , Jones Katharine , Smith Gillian , Duncombe Rebecca , Barnett Laura , Krepska Amy
Published: December 2023

The death of a child is a devastating event. Families experience profound grief and loss immediately following the death, and this remains and evolves as time progresses. In this, the second in a series, we discuss the importance of longer term bereavement care and how continuing contact with healthcare can be navigated. As bereaved parents who are also doctors, we again share our experiences. The complex nature of parenting, supporting siblings or managing a pregnancy after loss are explored, and we look at the involvement of bereaved parents in developing bereavement services.
Surprise diagnosis of acquired von Willebrand syndrome in a patient previously thought to have type III von Willebrand disease: evaluation and periprocedural management
Authors: Zhou Katherine Ismei , Kapoor Sargam , Onwuemene Oluwatoyosi Adefunke
Published: December 2023

Acquired von Willebrand syndrome (AVWS) is a rare disorder that is characterised by an acquired deficiency of von Willebrand factor. AVWS was suspected in a patient with type III von Willebrand disease (VWD) who did not respond to factor replacement therapy. Given the crucial implications for management, we describe this patient’s clinical presentation, diagnosis and periprocedural management. To facilitate pericardiocentesis, periprocedural management included steroids, intravenous immunoglobulin and factor replacement therapy. In other patients with suspected immune-mediated AVWS, a similar approach may be effective. This case also highlights the importance of distinguishing AVWS from inherited VWD.
Intraocular pressure reduction and progression of highly myopic glaucoma: a 12-year follow-up cohort study
Authors: Shin Young In , Kim Young Kook , Jeoung Jin Wook , Park Ki Ho
Published: December 2023

Aims

To investigate any association between intraocular pressure (IOP) reduction amount and open-angle glaucoma (OAG) progression in highly myopic eyes and to determine the associated risk factors.

Methods

One hundred and thirty-one (131) eyes of 131 patients with highly myopic OAG, all of whom had received topical medications and been followed for 5 years or longer, were enrolled. Based on the IOP reduction percentage, patients were categorised into tertile groups, and subsequently, the upper-tertile and lower-tertile groups were compared for the cumulative probability of glaucoma progression. Kaplan-Meier survival analysis and log-rank testing were applied in the comparison, and multivariate analysis with Cox’s proportional hazard model, additionally, was performed to identify progression risk factors.

Results

Throughout the average 11.6±4.4 year follow-up on the 131 eyes (mean age, 41.2 years at initial visit; baseline IOP, 16.4 mm Hg), 72 eyes (55.0%) showed glaucoma progression. The upper-tertile group (IOP reduction percentage>23.7%) showed a high cumulative probability of non-progression relative to the lower-tertile group (IOP reduction percentage<11.0%; p=0.034), according to the Kaplan-Meier analysis. Presence of disc haemorrhage (DH; HR=2.189; p=0.032) was determined by the multivariate Cox’s proportional hazard model to be significantly associated with glaucoma progression. For progressors, the average rate of retinal nerve fibre layer thickness thinning was −0.88±0.74 µm/year, while the MD change was −0.42±0.36 dB/year.

Conclusions

Glaucoma progression is associated with amount of IOP reduction by topical medications in highly myopic eyes, and DH occurrence is a glaucoma progression risk factor.
Measurement of visual function in infantile nystagmus: a systematic review
Authors: Almagren Bader ,   Nystagmus UK Eye Research Group (NUKE), Dunn Matt J
Published: December 2023

Background/aims

Recent work has called into question the ability of visual acuity (VA) to accurately represent changes in visual function in infantile nystagmus (IN). This systematic review investigated factors affecting visual performance in IN, to guide development of suitable alternatives to VA.

Methods

Included studies used an experimental manipulation to assess changes in visual function in people with IN. Interventional studies, case series and case studies were excluded. Six databases were searched in August 2023. Selection, detection, attrition and measurement bias were assessed. Due to heterogeneous methodologies, narrative synthesis was undertaken.

Results

Eighteen relevant papers were identified, 11 of which complied with the review criteria. Articles were grouped according to the factor manipulated to evoke within-participant changes in performance (motion blur, psychological state, gaze angle or visual crowding). Optotype, image, grating and moving stimuli have been employed under varying lighting conditions and exposure duration.

Conclusion

Several factors affecting visual performance should be considered when assessing visual function in IN. While maximum VA is a useful metric, its measurement deliberately minimises nystagmus-specific factors such as changes in visual performance with gaze angle and the ‘slow to see’ phenomenon. Maximum VA can be measured using the null zone, providing unlimited viewing time, reducing stress/mental load and minimising visual crowding. Gaze-dependent functional vision space is a promising measure which quantifies the impact of the null zone but does not consider temporal vision. Although no complete measurement technique has yet been proven, this review provides insights to guide future work towards development of appropriate methods.
COVID-19 vaccination implementation in 52 African countries: trajectory and implications for future pandemic preparedness
Authors: Wariri Oghenebrume , Afolabi Muhammed Olanrewaju , Mukandavire Christinah , Saidu Yauba , Balogun Obe Destiny , Ndiaye Sidy , Okpo Emmanuel A , Nomhwange Terna , Uthman Olalekan A , Kampmann Beate
Published: December 2023

Introduction

To end the COVID-19 pandemic, the WHO set a goal in 2021 to fully vaccinate 70% of the global population by mid-2022. We projected the COVID-19 vaccination trajectory in 52 African countries and compared the projected to the ‘actual’ or ‘observed’ coverage as of December 2022. We also estimated the required vaccination speed needed to have attained the WHO 70% coverage target by December 2022.

Methods

We obtained publicly available, country-reported daily COVID-19 vaccination data, covering the initial 9 months following the deployment of vaccines. We used a deterministic compartmental Susceptible-Exposed-Infectious-Recovered-type model and fit the model to the number of COVID-19 cases and vaccination coverage in each African country using a Markov chain Monte Carlo approach within a Bayesian framework.

Findings

Only nine of the 52 African countries (Tunisia, Cabo Verde, Lesotho, Mozambique, Rwanda, Seychelles, Morocco, Botswana and Mauritius) were on track to achieve full COVID-19 vaccination coverage rates ranging from 72% to 97% by the end of December 2022, based on their progress after 9 months of vaccine deployment. Of the 52 countries, 26 (50%) achieved ‘actual’ or ‘observed’ vaccination coverage rates within ±10 percentage points of their projected vaccination coverage. Among the countries projected to achieve <30% by December 2022, nine of them (Chad, Niger, Nigeria, South Sudan, Tanzania, Somalia, Zambia, Sierra Leone and Côte d’Ivoire) achieved a higher observed coverage than the projected coverage, ranging from 12.3 percentage points in South Sudan to 35.7 percentage points above the projected coverage in Tanzania. Among the 52 countries, 83% (43 out of 52) needed to at least double their vaccination trajectory after 9 months of deployment to reach the 70% target by December 2022.

Conclusion

Our findings can guide countries in planning strategies for future global health emergencies and learning from each other, especially those that exceeded expectations and made significant progress towards the WHO’s 2022 COVID-19 vaccination target despite projected poor coverage rates.
The use of network meta-analysis in updating WHO living maternal and perinatal health recommendations
Authors: Williams Myfanwy J , Vogel Joshua P , Gallos Ioannis D , Ramson Jenny A , Chou Doris , Oladapo Olufemi T
Published: December 2023

Drawing on two recent examples of WHO living guidelines in maternal and perinatal health, this paper elucidates a pragmatic, stepwise approach to using network meta-analysis (NMA) in guideline development in the presence of multiple treatment options. NMA has important advantages. These include the ability to compare multiple interventions in a single coherent analysis, provide direct estimates of the relative effects of all available interventions, infer indirect effect estimates for interventions not directly compared and generate rankings of the available treatment options. It can be difficult to harness these advantages in the face of a lack of current guidance on using NMA evidence in guideline development, with several challenges emerging. Challenges include the choice of conceptual approach, the volume and complexity of the evidence, the contribution of treatment rankings, and the fact that the preferable treatment is not always obvious. This paper describes a layered approach to resolving these challenges, which supports systematic guideline decision-making and development of trustworthy clinical guidelines when multiple treatment options are available.
Third party monitoring for health in Afghanistan: the good, the bad and the ugly
Authors: Alba Sandra , Jacobs Eelco , Kleipool Elisabeth , Salehi Ahmad , Naeem Ahmad , Arab Sayed Rahim , Van Gurp Margo , Hamid Nasir , Manalai Partamin , Saeedzai Sayed Ataullah , Safi Sohrab , Paiman Farhad , Siddiqi Abdul Majeed , Gerretsen Barend , Gari Sara , Sondorp Egbert
Published: December 2023

Third party monitoring (TPM) is used in development programming to assess deliverables in a contract relationship between purchasers (donors or government) and providers (non-governmental organisations or non-state entities). In this paper, we draw from our experience as public health professionals involved in implementing and monitoring the Basic Package of Health Services (BPHS) and the Essential Package of Hospital Services (EPHS) as part of the SEHAT and Sehatmandi programs in Afghanistan between 2013 and 2021. We analyse our own TPM experience through the lens of the three parties involved: the Ministry of Public Health; the service providers implementing the BPHS/EPHS; and the TPM agency responsible for monitoring the implementation. Despite the highly challenging and fragile context, our findings suggest that the consistent investments and strategic vision of donor programmes in Afghanistan over the past decades have led to a functioning and robust system to monitor the BPHS/EPHS implementation in Afghanistan. To maximise the efficiency, effectiveness and impact of this system, it is important to promote local ownership and use of the data, to balance the need for comprehensive information with the risk of jamming processes, and to address political economy dynamics in pay-for-performance schemes. Our findings are likely to be emblematic of TPM issues in other sectors and other fragile and conflicted affected settings and offer a range of lessons learnt to inform the implementation of TPM schemes.
Influences of community engagement and health system strengthening for cholera control in cholera reporting countries
Authors: Baličević Stephanie Ayres , Elimian Kelly Osezele , King Carina , Diaconu Karin , Akande Oluwatosin Wuraola , Ihekweazu Vivianne , Trolle Hanna , Gaudenzi Giulia , Forsberg Birger , Alfven Tobias
Published: December 2023

The 2030 Global Task Force on Cholera Control Roadmap hinges on strengthening the implementation of multistranded cholera interventions, including community engagement and health system strengthening. However, a composite picture of specific facilitators and barriers for these interventions and any overlapping factors existing between the two, is lacking. Therefore, this study aims to address this shortcoming, focusing on cholera-reporting countries, which are disproportionately affected by cholera and may be cholera endemic. A scoping methodology was chosen to allow for iterative mapping, synthesis of the available research and to pinpoint research activity for global and local cholera policy-makers and shareholders. Using the Arksey and O’Malley framework for scoping reviews, we searched PubMed, Web of Science and CINAHL. Inclusion criteria included publication in English between 1990 and 2021 and cholera as the primary document focus in an epidemic or endemic setting. Data charting was completed through narrative descriptive and thematic analysis. Forty-four documents were included, with half relating to sub-Saharan African countries, 68% (30/44) to cholera endemic settings and 21% (9/44) to insecure settings. We identified four themes of facilitators and barriers to health systems strengthening: health system cooperation and agreement with external actors; maintaining functional capacity in the face of change; good governance, focused political will and sociopolitical influences on the cholera response and insecurity and targeted destruction. Community engagement had two themes: trust building in the health system and growing social cohesion. Insecurity and the community; cooperation and agreement; and sociopolitical influences on trust building were themes of factors acting at the interface between community engagement and health system. Given the decisive role of the community–health system interface for both sustained health system strengthening and community engagement, there is a need to advocate for conflict resolution, trust building and good governance for long-term cholera prevention and control in cholera reporting countries.
‘It was a joint plan we worked out together’. How the I-WOTCH programme enabled people with chronic non-malignant pain to taper their opioids: a process evaluation
Authors: Nichols Vivien P , Abraham Charles , Eldabe Sam , Sandhu Harbinder Kaur , Underwood Martin , Seers Kate
Published: December 2023

Background

The Improving the Wellbeing of people with Opioid Treated CHronic pain (I-WOTCH) randomised controlled trial found that a group-based educational intervention to support people using strong opioids for chronic non-malignant pain helped a significant proportion of people to stop or decrease opioid use with no increase in pain-related disability. We report a linked process evaluation of the group-based intervention evaluated in comparison to a usual-care control group that received a self-help booklet and relaxation CD.

Methods

We interviewed 18 intervention facilitators, and 20 intervention and 20 control participants who had chronic non-malignant pain and were recruited from general (family) practices in the UK. Quantitative data included change mechanism questions on the trial questionnaires which explored motivation, expectations and self-efficacy. Fidelity was assessed by listening to a sample of audio-recorded group sessions and nurse consultations. Quantitative and qualitative data were integrated using ‘follow a thread’ and a mixed-methods matrix.

Findings

Four overarching themes emerged: (1) the right time to taper, (2) the backdrop of a life with chronic pain, (3) needing support and (4) the benefits of being in a group. Delivery fidelity was good, adherence (83%) and competence (79%) across a range of intervention groups. Staff delivering the intervention found three typical responses to the intervention: resistance, open to trying and feeling it was not the right time. The group experience was important to those in the intervention arm. It provided people with a forum in which to learn about the current thinking about opioid usage and its effects. It also gave them examples of how feasible or personally relevant coming off opioids might be.

Conclusion

The process evaluation data showed that the I-WOTCH intervention was well delivered, well received and useful for most interviewees. Being ‘the right time’ to taper and having support throughout tapering, emerged as important factors within the context of living with chronic pain.

Trial registration number

ISRCTN49470934.
Best Evidence Topic report: does blood group type O decrease the risk of severe COVID-19 infection?
Authors: Alavi-Moghaddam Mostafa , Tajabadi Zohreh , Najafpour Sogand
Published: December 2023

A short-cut systematic review was conducted using a described protocol. The three-part question addressed was: In patients with COVID-19 infection, does blood group type O versus non-O blood groups lead to a lower risk of severe COVID-19 infection? MEDLINE, Embase, and Cochrane databases were searched for relevant evidence. Altogether, 238 papers were found using the search strategy developed. Seventeen provided the best evidence to answer the three-part question. The data on first author name, publication year, country of origin, study type, study sample size, participant’s gender, reported effect sizes, main findings and limitations were extracted from the relevant studies and listed in a table. Finally, 4 out of 17 studies revealed that having blood group type O may be associated with a lower risk of severe COVID-19 among patients with COVID-19 infection and the 13 remaining studies reported no significant relationship between having O blood group and risk of COVID-19 severity among the infected individuals. Of three systematic reviews and meta-analyses identified, none detected a protective effect of blood group type O. The clinical bottom line is that the best available evidence does not support the notion that blood group type O is protective against serious outcomes in COVID-19.
Abortion restrictions and medical residency applications
Authors: Mermin-Bunnell Kellen , Traub Ariana M , Wang Kelly , Aaron Bryan , King Louise Perkins , Kawwass Jennifer
Published: December 2023

Residency selection is a challenging process for medical students, one further complicated in the USA by the recentDobbs v Jackson Women’s Health Organization(Dobbs) decision over-ruling the federal right to abortion. We surveyed medical students to examine howDobbsis influencing the ideological, personal and professional factors they must reconcile when choosing where and how to complete residency.

Between 6 August and 22 October 2022, third-year and fourth-year US medical students applying to US residency programmes were surveyed through social media and direct outreach to medical schools. Analysis of quantitative and qualitative data from 494 responses was performed to assess downstream effects ofDobbson residency applicants’ family, health and career choices.

Most respondents said changes in abortion access would likely or very likely influence their decision regarding location of considered residency programme (76.9%), where to start a family (72.2%) and contraceptive planning for them or their partner (57.9%). Cis-gender females were more influenced byDobbsregarding where (5 (4, 5) p<0.001) and when (3 (3, 5) p<0.001) to start a family. In qualitative responses, medical trainees highlighted the importance of abortion access for their patients, themselves and their loved ones.

Medical trainees are incorporating state abortion access into their residency programme choices. Future physicians care about both the quality of care they will be able to provide and their own health. For personal and professional reasons, reproductive healthcare access is now a key factor in residency match decisions.
Improved naming in patients with Broca’s aphasia with tDCS
Authors: Bonilha Leonardo , Rorden Chris , Roth Rebecca , Sen Souvik , George Mark S , Fridriksson Julius
Published: December 2023

Background

Language impairment (aphasia) is a common neurological deficit after strokes. For individuals with chronic aphasia (beyond 6 months after the stroke), language improvements with speech therapy (ST) are often limited. Transcranial direct current stimulation (tDCS) is a promising approach to complement language recovery but interindividual variability in treatment response is common after tDCS, suggesting a possible relationship between tDCS and type of linguistic impairment (aphasia type).

Methods

This current study is a subgroup analysis of a randomised controlled phase II futility design clinical trial on tDCS in chronic post-stroke aphasia. All participants received ST coupled with tDCS (n=31) vs sham tDCS (n=39). Confrontation naming was tested at baseline, and 1, 4, and 24 weeks post-treatment.

Results

Broca’s aphasia was associated with maximal adjunctive benefit of tDCS, with an average improvement of 10 additional named items with tDCS+ST compared with ST alone at 4 weeks post-treatment. In comparison, tDCS was not associated with significant benefits for other aphasia typesF(1)=4.23,p=0.04. Among participants with Broca’s aphasia, preservation of the perilesional posterior inferior temporal cortex was associated with higher treatment benefit (R=0.35,p=0.03).

Conclusions

These results indicate that adjuvant tDCS can enhance ST to treat naming in Broca’s aphasia, and this may guide intervention approaches in future studies.
Empowering the next generation: integrating adolescents into the Reproductive Justice movement
Authors: Brisson Julien , Withers Mellissa
Published: December 2023

This article explores the ethical implications of mandatory parental consent requirements for adolescents seeking sexual and reproductive health services (SRHS). Using a Reproductive Justice framework, which identifies systemic barriers to accessing healthcare services, we examine ageism as a potential factor restricting adolescents' access to SRHS. While the Reproductive Justice framework has addressed systemic issues like racism and ableism in healthcare, ageism involving adolescents has been less explored. The article challenges the pertinence of mandatory parental consent requirements—as a potential barrier—for adolescents’ access to SRHS. We argue that in the specific context of SRHS (contraceptives, abortion, testing and treatment of sexually transmitted infections), adolescents’ autonomy (self-determination) should be respected if they request to access those services independently. From a global health perspective, adolescents have a low prevalence and uneven access to SRHS. To address the issue, we propose the integration of adolescence into the Reproductive Justice movement to empower them through education on how to access the SRHS they need.
Ethical guidelines for antiracism work in medicine: lessons from the antiracist healing collaborative
Authors: Legha Rupinder , Mabeza Russyan Mark
Published: December 2023

An explosion of antiracism in medicine efforts have transpired since 2020. However, no ethical guidelines exist to guide them. This oversight is concerning because the racism and white supremacy rife within medicine can easily thwart them. This article addresses this gap by highlighting ethical guidelines for antiracism work in medicine. We present nine core tenets derived from our experience forming the Antiracist Healing Collaborative (AHC), a medical student-led initiative committed to developing bold and disruptive antiracist medical education content. Our lessons developing and implementing these tenets can guide other antiracism in medicine collaborations striving to promote liberation and healing, rather than recapitulating the racism and white supremacy culture embedded within medicine. We close by reflecting on how these tenets have steadied our recent decision to draw AHC to a close. They have allowed us to honour what we achieved together, strengthen the relationship that formed the foundation for our activism and bolster the shared antiracism mission that will guide our individual journeys moving forwards. The first of their kind, our ethical guidelines for antiracism work in medicine can facilitate greater recognition of the risks embedded in anti-oppression work transpiring in academic settings.
Electronic tagging and tracking aquatic animals to understand a world increasingly shaped by a changing climate and extreme weather events
Authors: Lennox Robert J. , Afonso Pedro , Birnie-Gauvin Kim , Dahlmo Lotte S. , Nilsen Cecilie I. , Arlinghaus Robert , Cooke Steven J. , Souza Allan T. , Jarić Ivan , Prchalová Marie , Říha Milan , Westrelin Samuel , Twardek William , Aspillaga Eneko , Kraft Sebastian , Šmejkal Marek , Baktoft Henrik , Brodin Tomas , Hellström Gustav , Villegas-Ríos David , Vollset Knut Wiik , Adam Timo , Sortland Lene K. , Bertram Michael G. , Crossa Marcelo , Vogel Emma F. , Gillies Natasha , Reubens Jan
Published: December 2023

Despite great promise for understanding the impacts and extent of climate change and extreme weather events on aquatic animals, their species, and ecological communities, it is surprising that electronic tagging and tracking tools, like biotelemetry and biologging, have not been extensively used to understand climate change or develop and evaluate potential interventions that may help adapt to its impacts. In this review, we provide an overview of methodologies and study designs that leverage available electronic tracking tools to investigate aspects of climate change and extreme weather events in aquatic ecosystems. Key interventions to protect aquatic life from the impacts of climate change, including habitat restoration, protected areas, conservation translocations, mitigations against interactive effects of climate change, and simulation of future scenarios, can all be greatly facilitated by using electronic tagging and tracking. We anticipate that adopting animal tracking to identify phenotypes, species, or ecosystems that are vulnerable or resilient to climate change will help in applying management interventions such as fisheries management, habitat restoration, invasive species control, or enhancement measures that prevent extinction and strengthen the resilience of communities against the most damaging effects of climate change. Given the scalability and increasing accessibility of animal tracking tools for researchers, tracking individual organisms will hopefully also facilitate research into effective solutions and interventions against the most extreme and acute impacts on species, populations, and ecosystems.
Complexity growth of BTZ black hole in massive gravity with a null string
Authors: Zhou Yu-Ting
Published: December 2023

In this paper, we investigate the complexity growth of the tensionless limit of string in the neutral BTZ black hole horizon in massive gravity. When the string approaches the horizon, we observe a novel phenomenon for the Nambu–Goto action growth that produces significant difference from tensile string geometry. The string’s tension is then suggested to partially contribute to the growth of the action. We also argue a potential proposal that reconstructs the complexity from the renormalization group (RG) flow.
Visual Noise Cancellation: Exploring Visual Discomfort and Opportunities for Vision Augmentations
Authors: Hong Junlei , Langlotz Tobias , Sutton Jonathan , Regenbrecht Holger
Published: December 2023

Acoustic noise control or cancellation (ANC) is a commonplace component of modern audio headphones. ANC aims to actively mitigate disturbing environmental noise for a quieter and improved listening experience. ANC is digitally controlling frequency and amplitude characteristics of sound. Much less explored is visual noise and active visual noise control, which we address here. We first explore visual noise and scenarios in which visual noise arises based on findings from four workshops we conducted. We then introduce the concept of visual noise cancellation (VNC) and how it can be used to reduce identified effects of visual noise. In addition, we developed head-worn demonstration prototypes to practically explore the concept of active VNC with selected scenarios in a user study. Finally, we discuss the application of VNC, including vision augmentations that moderate the user’s view of the environment to address perceptual needs and to provide augmented reality content.
Using Voice and Biofeedback to Predict User Engagement during Product Feedback Interviews
Authors: Ferrari Alessio , Huichapa Thaide , Spoletini Paola , Novielli Nicole , Fucci Davide , Girardi Daniela
Published: December 2023

Capturing users’ engagement is crucial for gathering feedback about the features of a software product. In a market-driven context, current approaches to collecting and analyzing users’ feedback are based on techniques leveraging information extracted from product reviews and social media. These approaches are hardly applicable in contexts where online feedback is limited, as for the majority of apps, and software in general. In such cases, companies need to resort to face-to-face interviews to get feedback on their products. In this article, we propose to utilize biometric data, in terms of physiological and voice features, to complement product feedback interviews with information about the engagement of the user on product-relevant topics. We evaluate our approach by interviewing users while gathering their physiological data (i.e.,
biofeedback
) using an Empatica E4 wristband, and capturing their voice through the default audio-recorder of a common laptop. Our results show that we can predict users’ engagement by training supervised machine learning algorithms on biofeedback and voice data, and that voice features alone can be sufficiently effective. The best configurations evaluated achieve an average F1 ∼ 70% in terms of classification performance, and use voice features only. This work is one of the first studies in requirements engineering in which biometrics are used to identify emotions. Furthermore, this is one of the first studies in software engineering that considers voice analysis. The usage of voice features can be particularly helpful for emotion-aware feedback collection in remote communication, either performed by human analysts or voice-based chatbots, and can also be exploited to support the analysis of meetings in software engineering research.
What Learning Strategies are Used by Programming Students? A Qualitative Study Grounded on the Self-regulation of Learning Theory
Authors: Silva Leonardo , Mendes António , Gomes Anabela , Fortes Gabriel
Published: December 2023

Self-regulation of learning (SRL) is an essential ability for academic success in multiple educational contexts, including programming education. However, understanding how students regulate themselves during programming learning is still limited. This exploratory research aimed to investigate the regulatory strategies externalized by 51 students enrolled in an introductory programming course. The objective was to identify the SRL strategies used by these students during multiple phases of the learning process and compare the SRL behavior of high and low-performers. The following research questions guided this investigation: (RQ1) What regulation of learning strategies are used by programming students?; and (RQ2) How do the SRL strategies used by high and low-performing students differ?. The findings demonstrate that learning to program involves complex psychological resources (e.g., cognition, metacognition, behavior, motivation, and emotion) and that students present heterogeneity in their SRL repertoire. In addition, high and low-performing students showed significant differences in how they regulate, which can contribute to understanding the factors that may contribute to learning programming. Lastly, we argue that for analyzing SRL strategies, it is necessary to consider the specificities of programming education, which motivated the development of a conceptual framework to describe the identified strategies and regulatory phases in this learning domain.
Data-Driven Causal Effect Estimation Based on Graphical Causal Modelling: A Survey
Authors: Cheng Debo , Li Jiuyong , Liu Lin , Liu Jixue , Le Thuc Duy
Published: December 2023

In many fields of scientific research and real-world applications, unbiased estimation of causal effects from non-experimental data is crucial for understanding the mechanism underlying the data and for decision-making on effective responses or interventions. A great deal of research has been conducted to address this challenging problem from different angles. For estimating causal effect in observational data, assumptions such as Markov condition, faithfulness, and causal sufficiency are always made. Under the assumptions, full knowledge, such as a set of covariates or an underlying causal graph, is typically required. A practical challenge is that in many applications, no such full knowledge or only some partial knowledge is available. In recent years, research has emerged to use search strategies based on graphical causal modelling to discover useful knowledge from data for causal effect estimation, with some mild assumptions, and has shown promise in tackling the practical challenge. In this survey, we review these data-driven methods on causal effect estimation for a single treatment with a single outcome of interest and focus on the challenges faced by data-driven causal effect estimation. We concisely summarise the basic concepts and theories that are essential for data-driven causal effect estimation using graphical causal modelling but are scattered around the literature. We identify and discuss the challenges faced by data-driven causal effect estimation and characterise the existing methods by their assumptions and the approaches to tackling the challenges. We analyse the strengths and limitations of the different types of methods and present an empirical evaluation to support the discussions. We hope this review will motivate more researchers to design better data-driven methods based on graphical causal modelling for the challenging problem of causal effect estimation.
A Survey of Generative Adversarial Networks for Synthesizing Structured Electronic Health Records
Authors: Ghosheh Ghadeer O. , Li Jin , Zhu Tingting
Published: December 2023

Electronic Health Records (EHRs) are a valuable asset to facilitate clinical research and point of care applications; however, many challenges such as data privacy concerns impede its optimal utilization. Deep generative models, particularly Generative Adversarial Networks (GANs), show great promise in generating synthetic EHR data by learning underlying data distributions while achieving excellent performance and addressing these challenges. This work aims to survey the major developments in various applications of GANs for EHRs and provides an overview of the proposed methodologies. For this purpose, we combine perspectives from healthcare applications and machine learning techniques in terms of source datasets and the fidelity and privacy evaluation of the generated synthetic datasets. We also compile a list of the metrics and datasets used by the reviewed works, which can be utilized as benchmarks for future research in the field. We conclude by discussing challenges in GANs for EHRs development and proposing recommended practices. We hope that this work motivates novel research development directions in the intersection of healthcare and machine learning.
CMAF: Cross-Modal Augmentation via Fusion for Underwater Acoustic Image Recognition
Authors: Yang Shih-Wei , Shen Li-Hsiang , Shuai Hong-Han , Feng Kai-Ten
Published: December 2023

Underwater image recognition is crucial for underwater detection applications. Fish classification has been one of the emerging research areas in recent years. Existing image classification models usually classify data collected from terrestrial environments. However, existing image classification models trained with terrestrial data are unsuitable for underwater images, as identifying underwater data is challenging due to their incomplete and noisy features. To address this, we propose a cross-modal augmentation via fusion (
CMAF
) framework for acoustic-based fish image classification. Our approach involves separating the process into two branches: visual modality and sonar signal modality, where the latter provides a complementary character feature. We augment the visual modality, design an attention-based fusion module, and adopt a masking-based training strategy with a mask-based focal loss to improve the learning of local features and address the class imbalance problem. Our proposed method outperforms the state-of-the-art methods. Our source code is available at
https://github.com/WilkinsYang/CMAF
.