bluuebunny/crossref_metadata_2025 huggingface dataset:
Theoretical Analysis of Workspace of a Hybrid Offset Joint
Authors: Peiyi Li , Hasiaoqier Han , Junwei Lin , Liheng Chen , Qingwen Wu , Zhenbang Xu
Published: November 2024

Offset joints are widely used in robotics, and literature has demonstrated that axial offset joints can expand the workspace. However, the hybrid offset joint, which incorporates offsets in three orthogonal directions (x, y, and z axes), provides a more flexible and comprehensive range of motion compared to traditional axial offset joints. Therefore, a comprehensive understanding of the workspace of hybrid offset joints with three-directional offsets is essential. First, through a parameter model, the interference motion of hybrid offset joints is studied, considering three different directional offsets and obtaining analytical expressions. Next, based on coordinate transformations, the workspace of this joint is investigated, resulting in corresponding theoretical formulas. In addition, the influence of offset amounts in various directions on the joint’s workspace is examined. Finally, the application of hybrid offset joints in parallel manipulators (PMs) is introduced, highlighting their practical engineering value. Through comparative analysis, it is found that lateral offsets on the x- and y-axes adjust the maximum rotation angles, while the z-axis offset expands the rotational range of these joints. Moreover, by increasing the limit rotation angle of the passive joint in a specific direction, the application of hybrid offset joints in PMs can impact the workspace. These findings offer valuable insights for the design of hybrid offset joints and their applications in robotics.
Alterations in Foot Positioning During Ankle Taping and Its Effects on Range of Motion and Jump Performance in Dancers
Authors: Anderson Eilish , Stanek Justin , McLoda Todd , Jagodinsky Adam , Heiman Benjamin
Published: November 2024

A closed basketweave ankle tape application is common throughout sports, yet less prevalent in the performing arts. This may be due to aesthetics and potential compromises to performance. The purpose of this study was to examine the effects of foot positioning (dorsiflexed or neutral/resting) during tape application on static range of motion (ROM), kinematic ROM, and jump ability while performing a maximum sauté jump. A randomized crossover cohort study design was used to evaluate ankle active ROM, kinematic ROM, and ground reaction force during a dance bipedal vertical jump. Results showed the application of tape caused significant differences in active ROM when compared with the no-tape condition. No significant differences in ground reaction force were found and inconsistent kinematic changes were found from the peak ROM data. Foot position during ankle taping does not appear to affect jump performance but does show similar active ROM restrictions, particularly in plantarflexion and inversion.
Sport- and Nonsport-Related Concussion Reporting Behaviors of Emerging Adults Participating in Organized Sport
Authors: Kerr Zachary Yukio , Pierce Megan N. , Register-Mihalik Johna , Ingram Brittany M.
Published: November 2024

This study examined concussion-related outcomes among emerging adults (18–24 years) who participated in organized sport and are at risk for both sport-related concussion (SRC) and non-SRC. An online survey on SRC/non-SRC history and reporting behaviors grouped a convenience sample of 146 individuals as: no concussion history, those with only SRCs, and those with ≥1 non-SRC (including those with and without SRCs). Participants also noted whether ≥1 concussions were sustained with medical presence or had delayed reporting to someone in authority (e.g., medical professional, coach, and parent). No differences by concussion history were observed. However, among those with both SRC and non-SRC (n = 20), there were higher odds of ≥1 SRC versus ≥1 non-SRC occurring with medical presence (McNemar odds ratio = 12.0, 95% confidence interval [1.6, 92.3]) and having delayed reporting (McNemar odds ratio = 5.0, 95% confidence interval [0.6, 42.8]). Findings highlight the need for multiple pathways to help at-risk individuals report and seek care for concussions.
The Effect of Step Frequency and Running Speed on the Coordination of the Pelvis and Thigh Segments During Running
Authors: Mesquita Raphael M. , Morin Jean-Benoit , Dewolf Arthur H.
Published: November 2024

This study investigates the specific influence of step frequency (SF) and speed on the coordination between pelvic and thigh movements. Eight recreational male runners ran at different SFs and speeds on an instrumented treadmill. The coordination between the pelvis and thigh segments was analyzed using modified vector coding in the sagittal and frontal planes (FPs). Our findings show that hip range of motion increases as a function of SF in the sagittal plane. Pelvic tilt plays a compensatory role in hip extension, particularly at lower SFs. In the FP, pelvic roll increased at lower SFs, whereas the thigh abduction angle was participant dependant. Coordination analysis showed that thigh movements dominated the sagittal plane motion, which was simplified at higher SF. At low SF, the pelvic movements were increased and anticipated, playing a more dominant role in explaining motion. In the FP, pelvic movements dominated the motion. The increase in pelvic motion at low SFs stretches the hip flexors further and for a longer period. The link between SF, pelvic motion, and the risks of running-related injuries in the sagittal and FP is considered. Understanding these could help athletes and sports professionals optimize performance and reduce injury risk.
Psychosocial Factors on Athlete Return to Sport Readiness After Anterior Cruciate Ligament Reconstruction: A Critically Appraised Topic
Authors: Robinson Kala , Kossman Melissa K.
Published: November 2024

Clinical Scenario: Anterior cruciate ligament (ACL) injuries are a common injury experienced by athletes and often involve lengthy and invasive treatments. Given the literature that exists supporting psychosocial response to injury, it is important to understand how these factors influence the recovery process ultimately influencing readiness to return to play. Clinical Question: What is the impact of psychosocial factors on athlete readiness to return to sport participation post-ACL reconstruction (ACLR)? Summary of Key Findings: All studies found that psychosocial factors, including athletic identity, motivation, anxiety, control, and fear, impacted perceived readiness to return to play. Several studies found various levels of influence in both a positive (eg, motivation and resilience) and negative (eg, fear and anxiety) direction. Furthermore, despite presenting more psychosocial barriers than physical, these factors do not appear to influence actual physical recovery. Clinical Bottom Line: Psychosocial factors have both direct and indirect effects, positive and negative, on an athlete’s perceived readiness to return to the play. ACLR rehabilitation protocols are well developed, well established, and known to be effective; however, athletes still do not feel ready to return, and there are physical and mental risks associated with that uncertainty. Therefore, psychosocial factors are important to include and prioritize as part of the ACLR recovery process to ensure athletes are physically and psychosocially ready to return to play. Strength of Recommendation: Grade B evidence exists that psychosocial factors positively and negatively impact physical recovery and perceptions of recovery on return-to-play post-ACLR.
Assessing the Knee Extensor’s Rate of Force Development Using a Fixed Handheld Dynamometer: An Inter- and Intrasession Reliability Study
Authors: Yona Tomer , Fischer Arielle G.
Published: November 2024

Context: The rate of force development (RFD), defined as the ability to rapidly generate muscle force, is commonly tested using an electromechanical dynamometer in isometric mode. However, these devices are expensive and not readily available. Therefore, this study aims to evaluate the interrater reliability of a ﬁxed handheld dynamometer to measure the knee extensors’ RFD and provide reference values using the proposed method. Design: This study used a cross-sectional study design. Methods: Using a fixed handheld dynamometer (microFET2) and a 3-dimensional-printed adapter, we evaluated the knee extensor muscles  in participants seated at the edge of a treatment bed. Each participant performed a standardized warm-up, followed by 3 maximal isometric knee extension trials. The outcome measures were peak force and early and late phase RFD (0–100 and 0–200 ms, respectively). The study consisted of 3 sessions: Visit one comprised of an initial session (session 1A) followed by a second session (session 1B) after 30 minutes for intrasession reliability; and visit two, conducted on week later, comprised the third session (session 2) for intersession reliability. Results: Fifty-one participants were enrolled in the study. The in-session intraclass correlation coefficient for the early phase RFD was .87 (95% CI, .74–.92) and .91 to .92 (95% CI, .87–.94) for the late phase. The between-session intraclass correlation coefficient for the early phase RFD was .83 to .86 (95% CI, .74–.91) and .87 to .90 (95% CI, .80–.94) for the late phase. Finally, the peak force’s intraclass correlation coefficient was .95 (95% CI, .92–.97) for the in-session and .91 to .92 (95% CI, .86–.95) for the between-session reliability. Conclusions: Our approach provides a reliable, cost-effective, and quick method to evaluate the knee extensor muscles’ RFD and peak force.
Bacterial interactions underpin worsening lung function in cystic fibrosis-associated infections
Authors: Rivett Damian W. , Hatfield Lauren R. , Gavillet Helen , Hardman Michelle , van der Gast Christopher
Published: November 2024

Chronic lung infections are the primary cause of morbidity and early mortality in cystic fibrosis (CF) and, as such, have been the subject of a great deal of research. Subsequently, they have become one of the key paradigms for polymicrobial infections. The literature, however, has traditionally focused on the presence of pathogens in isolation or univariate measures like number of species to predict decline of lung function and ignores large swathes of data. Here, we suggest that looking at the interactions between species identified by 16S rRNA gene sequencing, rather than at species singularly, could elucidate hitherto unknown properties of these complicated infections. To confirm this, pooled samples from studies conducted by our laboratory, sequenced using the same pipeline, were used to assess microbiome-wide associations to lung function. We found pathogenic interactions between species were limited to the most abundant species, which were composed of canonical CF pathogens (including
Pseudomonas
,
Staphylococcus
,
Stenotrophomonas
, and
Achromobacter
) and commensals. This observation is crucial for better understanding of polymicrobial infections and treatment of these conditions while providing a simple framework for expanding this research into other disease states. The adoption of ecological principles into infection science can provide better understanding and options to those suffering from chronic conditions. The statistical ecology approach presented here enables clear hypotheses from observational data that can be ratified through subsequent manipulative experimental studies. Moreover, it can also be used to support the design and construction of clinically relevant
in vitro
models of polymicrobial infections.

IMPORTANCE

Research studies have repeatedly demonstrated that chronic lung infection in cystic fibrosis is polymicrobial and consequently does not adhere to the single microbe-based Koch’s postulates. Despite the plethora of evidence, the role of the constituent taxa present is largely unknown. Here we demonstrate how an ecological modeling perspective on lung infection microbiota can tease out potential interactions that alter progression of disease. Using techniques akin to genome-wide association studies, we show and validate 22 taxa, present in the chronic respiratory disease associated with cystic fibrosis, which have significant interactions that are negatively associated with patient lung function, the majority of which are “non-pathogenic” organisms. This work highlights the need to understand the interactive landscapes of the microbiomes to fully appreciate the complexity and treat chronic lung infections. Furthermore, this presents testable hypotheses for manipulative experiments in model systems to elucidate key mechanisms to driving disease progression.
Complete genome sequence of
Weissella cibaria
strain CXO-01 isolated from Korean saliva
Authors: Jo HyungWoo , Lee Dong-Geol , Kim Hye-Been , Kim Jungeun , Kang Seunghyun , Mun Seyoung , Karm Myong-Hwan , Kim Hyun Jeong
Published: November 2024

We present the genome sequence of
Weissella cibaria
strain CXO-01, isolated from saliva from one Korean individual and kimchi. The genome consisted of one circular chromosome with a length of 2,371,631  bp, three circular plasmids of 20,579 bp, 4,818  bp, and 4,494 in size. Gene prediction revealed 2,305 genes, 2,157 coding DNA sequences.
Whole-genome sequence of
Ensifer aridi
strain RCAM05007 isolated from
Cyamopsis tetragonoloba
(L.) Taub. root nodule
Authors: Guro Polina , Kuznetsova Irina , Sazanova Anna , Belimov Andrey , Karlov Denis , Safronova Vera
Published: November 2024

We present the genome sequence of
Ensifer aridi
strain RCAM05007 obtained from long reads. The strain was isolated from the root nodule of
Cyamopsis tetragonoloba
(L.) Taub. plant inoculated with a soil sample from India. The assembly contains one chromosome and two megaplasmids totalling ~6.7 Mbp with 61.6% GC content.
Complete genome sequences of toxigenic
Clostridioides difficile
isolated from Australian feral horses
Authors: Hain-Saunders Natasza , Knight Daniel R. , Bruce Mieghan , Riley Thomas V.
Published: November 2024

Recent increases in community-associated
Clostridioides difficile
infections have highlighted the importance of monitoring toxigenic
C. difficile
from animal and environmental sources. We provide the complete circularized genomes of two toxigenic
C. difficile
strains isolated from feral horse faeces. Genome N64 (sequence type 964) consists of a single chromosome of 4,078,791 bp, while genome H251 (sequence type 963) comprises one chromosome (4,304,722 bp) and three plasmids (150,942 bp, 11,534 bp, and 9,074 bp).
Optimized methods for the targeted surveillance of extended-spectrum beta-lactamase-producing
Escherichia coli
in human stool
Authors: Gallichan Sarah , Forrest Sally , Picton-Barlow Esther , McKeown Claudia , Moore Maria , Heinz Eva , Feasey Nicholas A. , Lewis Joseph M. , Graf Fabrice E.
Published: November 2024

Understanding transmission pathways of important opportunistic, drug-resistant pathogens, such as extended-spectrum beta-lactamase (ESBL)-producing
Escherichia coli
, is essential to implementing targeted prevention strategies to interrupt transmission and reduce the number of infections. To link transmission of ESBL-producing
E. coli
(ESBL-EC) between two sources, single-nucleotide resolution of
E. coli
strains, as well as
E. coli
diversity within and between samples, is required. However, the microbiological methods to best track these pathogens are unclear. Here, we compared different steps in the microbiological workflow to determine the impact different pre-enrichment broths, pre-enrichment incubation times, selection in pre-enrichment, selective plating, and DNA extraction methods had on recovering ESBL-EC from human stool samples, with the aim to acquire high-quality DNA for sequencing and genomic epidemiology. We demonstrate that using a 4-h pre-enrichment in Buffered Peptone Water, plating on cefotaxime-supplemented MacConkey agar and extracting DNA using Lucigen MasterPure DNA Purification kit improves the recovery of ESBL-EC from human stool and produced high-quality DNA for whole-genome sequencing. We conclude that our optimized workflow can be applied for single-nucleotide variant analysis of an ESBL-EC from stool.

IMPORTANCE

Drug-resistant infections are increasingly difficult to treat with antibiotics. Preventing infections is thus highly beneficial. To do this, we need to understand how drug-resistant bacteria spread to take action to stop infection and transmission. This requires us to accurately trace these bacteria between different sources. In this study, we compared different laboratory methods to see which worked best for detecting extended-spectrum beta-lactamase (ESBL)-producing
E. coli
, a common cause of urinary tract or bloodstream infections, from human stool samples. We found that enriching stool in a nutrient broth for 4 h, then plating the bacterial suspension on antibiotic-selective MacConkey agar, and finally extracting DNA from the bacteria using a specific DNA purification kit resulted in improved recovery of ESBL
E. coli
and high-quality DNA. Sequencing multiple isolates from stool allowed us to distinguish unambiguously and at high resolution between different variants of ESBL
E. coli
present in stool.
Impact of hospital outpatients’ experiences of patient safety on fear of infection: a secondary analysis of national data
Authors: Kwon Hyunjeong , Lee Miseon
Published: November 2024

Introduction

Amid the COVID-19 pandemic, outpatients’ concerns about infection risk have increased. It is crucial to understand the factors that contribute to this fear of infection to promote patient safety and encourage outpatients to seek proper follow-up treatment without fear. This study aims to understand the relationship between outpatients’ experiences of patient safety and their fear of infection.

Design

This was a secondary analysis of national data from the Healthcare Service Experience Survey in 2020.

Setting and participants

A total of 4416 patients with experience using outpatient services in the past year were included in South Korea.

Primary and secondary outcome measures

Demographic characteristics, fear of infection and safety experiences were assessed in the original survey. Fear of infection served as the dependent variable, with safety experiences—specifically, patient identification, preinjection explanations, hand hygiene, proper use of injection supplies, skin disinfection and adverse drug reactions—as the independent variables.

Results

Approximately 14% of outpatients had a fear of infection when receiving medical care. The unadjusted model showed that all patient safety categories were determinants of fear of infection, and the multivariate logistic model identified hand hygiene and medication safety experiences as significant factors associated with fear of infection.

Conclusions

This study revealed that patient safety experiences are associated with fear of infection in outpatient settings. Improving healthcare professionals’ hand hygiene and managing adverse drug reactions are crucial for enhancing patient safety.
Population-level trends over a decade in geographical inequality for opportunity in access to maternal care services: a cross-sectional analysis from the National Family Health Surveys in India
Authors: Dandona Rakhi , Majumder Moutushi , Kumar G Anil
Published: November 2024

Objectives

The objective of this study is to examine the trends in geographical inequality of opportunity in maternal health services in India considering the Every Newborn Action Plan (ENAP) 2025 coverage targets.

Setting

India.

Participants

Women in the National Family Health Survey (NFHS)—NFHS-4 (2014–2015) and NFHS-5 (2019–2021).

Primary and secondary measures

District-level coverages of 4+antenatal care (ANC) visits, institutional delivery with skilled birth attendant, postnatal care (PNC) services within 48 hours of delivery, continuum of care (CoC) services for women with most recent live births were considered. Human Opportunity Index (HOI) documented the opportunities for equitable access to these services, ranging from 0 (high inequality) to 100 (universal access). HOI was compared between the survey rounds and wealth index (WI) quintiles that the women belonged to.

Results

Coverages of 4+ANC visits, institutional delivery, PNC and CoC in India increased by 22.8% (95% CI 22.1% to 23.5%), 12.6% (95% CI 12.2% to 12.9%), 28.5% (95% CI 28.0% to 29.0%) and 38.6% (95% CI 37.6% to 39.6%) between NFHS-4 and NFHS-5, respectively. The HOI for 4+ANC visits was 48.4 in NFHS-5, ranging from 11.3 to 92.4 in states and from 31.1 to 70.5 for WI I–V. The HOI for institutional delivery was 80.4 in NFHS-5, ranging from 37.4 to 99.7 in the states and from 21.0 to 100 for WI I–V. The HOI for PNC services was 73.5 in NFHS-5, ranging from 37.5 to 95.6 in the states and from 61.2 to 88.3 for WI I–V. The HOI for CoC was 37.1, ranging from 6.5 to 88.8 in the states and from 19.8 to 62.7 for WI I–V for CoC in NFHS-5.

Conclusion

Though significant improvements in the geographical inequity of maternal health services have been made in India, the geographical inequity for 4+ANC visits coverage lags significantly behind resulting in CoC coverage inequity to achieve the ENAP targets for these services.
Cost of delivering childhood RSV prevention interventions to the health system in Kenya: a prospective analysis
Authors: Baral Ranju , Otiang Elkanah , Odiyo Joseph , Nyawanda Bryan O , Nyiro Joyce U , Munywoki Patrick , Jalang'O Rose E , Pecenka Clint
Published: November 2024

Objectives

To evaluate the cost of delivering childhood respiratory syncytial virus (RSV) prevention interventions to the health system in Kenya.

Design

A prospective (cost projection) activity-based costing study.

Setting

Kenya, national introduction of interventions.

Participants

Not applicable.

Interventions

A single-dose RSV maternal vaccine and a single-dose, long-acting monoclonal antibody (mAb).

Primary and secondary outcome measures

Cost per eligible target population; cost per dose administered; non-commodity cost of delivery. Costs are reported in 2023 USD.

Results

RSV interventions are expected to be delivered using existing systems: maternal vaccine using the antenatal care platform and the mAb delivered similar to existing birth dose vaccines. Assuming a price of US$3 per dose (for both interventions) and baseline coverage rates averaging 50% for the maternal vaccine and 86% for the mAb, the estimated cost of delivering maternal vaccine was US$1.74 (financial) and US$6.60 (economic) per vaccinated woman, and the cost of delivering mAbs was US$1.56 (financial) and US$6.27 (economic) per vaccinated child. Excluding commodity cost, the cost of delivering maternal vaccine was US$1.32 (financial) and US$2.72 (economic) and that for mAb was US$1.23 (financial) and US$2.48 (economic). Cost differences between the two interventions are driven by the anticipated baseline coverage. Health worker training, service delivery and programme planning and coordination were major cost drivers.

Conclusion

This study presents the prospective cost of new RSV intervention introduction and delivery in low-income and middle-income country settings, which is largely unknown. Cost estimates incorporate anticipated health system strengthening activities needed to deliver the future RSV interventions. These cost estimates support country-level and global-level decision-makers evaluating implementation feasibility and intervention affordability.
Epidemiology and clinical characteristics of football injuries among academy players in Ghana
Authors: Kwakye Samuel Koranteng , Mostert Karien , Garnett Daniel , Masenge Andries
Published: November 2024

Objective

To determine the epidemiology and clinical characteristics of match and training injuries among football players at an academy in Ghana.

Methods

In this prospective observational study, we followed 80 youth and adult football players at a Ghanaian academy over a season of 39 weeks. Medical attention and time-loss injuries, as well as exposure times of players, were recorded by resident physiotherapists using a standardised injury surveillance form. The average weekly injury prevalence was calculated. Injury incidence rates were calculated per 1000 exposure hours, with significance indicated as 95% CIs.

Results

126 injuries were recorded during the season, with an average weekly injury prevalence of 4.1%. The overall injury incidence was 4.5 (95% CI 3.8 to 5.4) injuries per 1000 hours with under 14 (5.8 (3.3 to 10.2)/1000 hours) and under 18 players (5.7 (4.4 to 7.4)/1000 hours) recording a higher incidence than under 16 (5.1 (3.5 to 7.4)/1000 hours) and senior players (2.7 (1.9 to 3.9)/1000 hours). Match injury incidence was 13 times higher than training injury incidence (27.4 (21.5 to 34.9) vs 2.3 (1.8 to 3.0) injuries/1000 hours). Injuries to the lower extremities had the highest incidence (3.9 (2.1 to 7.2) injuries/1000 hours), with the knee being the most commonly injured site (n=30, 23.8%). The most common type of injury was a joint sprain (1.9 (1.5 to 2.5) injuries/1000 hours), and the most common injury mechanism was direct contact with another player (1.5 (1.1 to 2.0) injuries/1000 hours). Most injuries were moderately severe (2.0 (1.5 to 2.6) injuries/1000 hours).

Conclusion

Ghanaian academy football players have a substantial risk of sustaining injuries, especially among younger players. Further studies should focus on developing specific injury prevention programmes in under-researched football-playing populations.
Insurance coverage policies for infertility services in health insurance: a systematic review of global practices and disparities
Authors: Ahmadi Seyed Ahmad , Moeini Sajad , Ketabchi Ensieh , Veysi Sheikhrobat Mohammad , Shamsaei Monireh
Published: November 2024

Background

Infertility affects about 10% of the global population, imposing significant economic and psychosocial burdens. This systematic review examines disparities in insurance coverage for infertility services worldwide, assessing how these disparities affect access to care and fertility outcomes.

Methods

For this systematic review, scientific databases (PubMed, EMBASE, Web of Science and Scopus) were searched from the beginning of 1990 to 2022 to identify literature related to insurance coverage for infertility services by health insurance organisations worldwide. Two researchers screened titles and abstracts, extracted data from full-text articles and assessed their quality using the Joanna Briggs Institute Critical Appraisal Tool.

Results

11 studies, primarily from high-income countries, met the inclusion criteria. Findings show a substantial increase in access to infertility services in countries with comprehensive insurance policies, such as the USA, where Medicaid coverage led to a 27% increase in first births among women over 35 years. Disparities in coverage, particularly in advanced treatments such as assisted reproductive technology and in vitro fertilisation (IVF), were notable, with limited coverage in countries such as Japan. Low-income countries generally lack sufficient insurance policies, exacerbating access disparities.

Conclusion

Insurance coverage policies for infertility services are associated with improved fertility outcomes, especially through increased access to infertility services. However, coverage disparities remain, emphasising the need for comprehensive policies to reduce economic barriers and support equitable access across regions.
Human blood cell transcriptomics unveils dynamic systemic immune modulation along colorectal cancer progression
Authors: Martinez-Usatorre Amaia , Ciarloni Laura , Angelino Paolo , Wosika Victoria , Conforte Alessandra Jordano , Fonseca Costa Sara S , Durandau Eric , Monnier-Benoit Sylvain , Satizabal Hector Fabio , Despraz Jérémie , Perez-Uribe Andres , Delorenzi Mauro , Morgenthaler Stephan , Hashemi Brian , Hadadi Noushin , Hosseinian-Ehrensberger Sahar , Romero Pedro J
Published: November 2024

Background

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide. CRC deaths can be reduced with prevention and early diagnosis. Circulating tumor DNA-based liquid biopsies, are emerging tools for cancer detection. However, the tumor-signal-dependent nature of this approach results in low sensitivity in precancerous and early CRC stages. Here we propose the host immune response to the onset of cancer as an alternative approach for early detection of CRC.

Methods

We perform whole transcriptome analysis of peripheral blood mononuclear cells (PBMCs) isolated from individuals with CRC, precancerous lesions or negative colonoscopy in two independent cohorts using next-generation sequencing.

Results

We discover and validate novel early CRC RNA biomarkers. Taking into account, and adjusting for, the sensitivity of PBMCs transcriptomes to processing times, we report distinct transcriptomic changes in the periphery related to specific CRC stages. Activation of innate immunity is already detectable in the peripheral blood of individuals with pre-malignant advanced adenomas. This immune response is followed by signs of transient B-cell activation and sustained inhibition of T-cell responses along CRC progression, whereby at late stages, protumoral myeloid cells, wound healing and coagulation processes prevail. Moreover, some biomarkers show similar dysregulation in tumors and are implicated in known pathways of CRC pathophysiology.

Conclusions

The strong systemic immune modulation triggered during CRC progression leads to previously unnoticed alterations detectable in PBMCs, paving the way for the development of an early CRC screening blood test, incorporating 226 validated biomarkers identified through immunotranscriptomics.
Towards distributed facilitation in research teams: an example from itDf
Authors: Cronin Orla
Published: November 2024

This essay argues that facilitation is a valuable tool for research teams. It suggests that an external facilitator is particularly helpful for more complex gatherings, and that for smaller or more routine gatherings, building skills within teams to enable the distribution of facilitation across team members is a viable alternative to hiring an external facilitator. Distributed facilitation is a way of supporting internal facilitators by helping to mitigate the time and effort it takes them to manage both process and content.
Prevalence of medial tibial stress syndrome in the British Armed Forces: a population-based study
Authors: Farquharson Emma , Roberts A J , Warland A I , Parnis N , O’Connell N E
Published: November 2024

Introduction

Medial tibial stress syndrome (MTSS) is common in the Armed Forces due to the physical demands placed on service personnel (SP). There are no large studies reporting the extent to which MTSS affects the Armed Forces. A retrospective cross-sectional study design was used to report the annual prevalence of MTSS in the British Armed Forces and in training units and healthcare utilisation.

Methods

Secondary data were sourced from the electronic medical records for all SP with MTSS (20 257) between 1 January 2010 and 31 December 2018. Prevalence was calculated annually across the Armed Forces and in recruits. Healthcare utilisation (number of contacts and days under the care of a healthcare professional) was reported according to characteristics of SP (sex, age, ethnicity, service branch, body composition measurement and medical discharge).

Results

Over 9 years, 20 257 SP were seen for MTSS. Prevalence of MTSS decreased across the Armed Forces, from 2.19% (95% CI 2.12 to 2.26) in 2013 to 1.61% (95% CI 1.55 to 1.68) in 2018. The prevalence of MTSS was 2.7 times higher in recruits, affecting 4.34% (95% CI 4.00 to 4.69) in 2018. In 2018, the prevalence in female recruits was over four times higher (7.03%, 95% CI 5.74 to 8.32) than trained female SP (1.60%, 95% CI 1.39 to 1.81) and higher than male recruits (4%, 95% CI 3.65 to 4.35). Comparing service branches, royal marines had the least healthcare input (median contacts (IQR): 3 (1–7.5)) over the least number of days (median days (IQR): 17 (0–154)), with the royal air force receiving the most (median contacts (IQR): 5 (2–13)) over the greatest number of days (median days (IQR): 76 (4–349)).

Conclusion

The prevalence of MTSS has reduced; however, it remains high in subsections of the Armed Forces, particularly in female recruits. There is a large variation in the amount and duration of healthcare input SP received for MTSS.
Biomechanical determinants of rheumatoid arthritis severity and excess cardiovascular disease: common origins of two complex diseases
Authors: Oakley Stephen Philip , Stott Samantha , Gill Kerri , Weston Lyanne
Published: November 2024

Objectives

The determinants of rheumatoid arthritis (RA) severity and excess cardiovascular disease (CVD) are incompletely understood. Biomechanical factors are known to influence RA severity. Articular stiffness correlates with arterial and skin stiffness. This study explored the hypothesis that constitutional stiffness is a common determinant of RA severity and excess CVD.

Methods

Fifty-eight patients with anti-CCP antibody (ACPA) positive RA and 57 controls were enrolled noting age, sex, body mass index, alcohol and tobacco exposure, Shared Epitope status and in RA disease duration, disease activity, ACPA titre and radiographic damage. Severe RA was defined as radiographic progression >1.3 mSharp points/year or requiring biological disease-modifying antirheumatic drugs (bDMARDs). Articular stiffness (Beighton Score and right 5th metacarpophalangeal (MCP) joint stress–strain responses), carotid-femoral pulse wave velocity and skin extensibility (percent increase distance two dots with manual traction dorsum right hand) were assessed.

Results

Right 5th MCP stiffness correlated with Beighton Score and with arterial and skin stiffness. High radiographic rate was associated with greater MCP articular (t test p 0.014), arterial (p 0.044) and, in RA <5 years duration, greater skin stiffness (p 0.002) with similar trends in subjects requiring bDMARDs. In RA, arterial stiffness correlated with age (ß p<0.005), articular (ß p<0.001) and skin stiffness (ß p 0.037) and inversely with alcohol consumption (p 0.035).

Conclusions

Articular, arterial and skin stiffness correlated with each other and with RA severity. As skin is not affected by RA, this association suggests that constitutional stiffness might be a common determinant of RA and CVD. Prospective studies of at-risk preclinical and early RA are required to determine if this relationship is causal.

Trials registration number

ACTRN12617000170325.
Effect of aquatic worms and straw amendments on the geotechnical and biogeochemical properties of oil sands tailings
Authors: Kuznetsov Petr , Balaberda Amy-lynne , Pardo Miguel de Lucas , Ulrich Ania
Published: November 2024

Aquatic Oliogochaete worms ( Lumbriculus variegatus) combined with straw led to improved geotechnical properties of fluid fine tailings (FFT) and thickened tailings (TT) in large-scale column studies. Gravity settling caused 19.9% and 20.6% consolidation of FFT and TT over 125 and 127 days, while the addition of straw and worms increased consolidation to 22.0%–24.3% for FFT and 28.1%–28.9% for TT. Solids content and yield stress were up to 1.1x and 6.6x higher in straw and worm columns, with greatest improvements seen in the top tailings layers where worm tunnels were visually observed. Surviving worms were only found in one column, suggesting the worms provide benefits extending past their depth of penetration and lifespan. The addition of straw stimulated methanogenic activity, decreasing pH, increasing alkalinity, and creating strictly anaerobic conditions (−300 mV), which may have impacted the survivability of the worms but provided another bioconsolidation pathway.
The effect of structural enrichment and increased water flow on the opportunity for domestication selection in hatchery-reared steelhead (Oncorhynchus mykiss)
Authors: Obley Miriam B. , Milston-Clements Ruth H. , Krajcik Jennifer A. , Blouin Michael S.
Published: November 2024

Hatchery-reared salmon often have lower fitness in the wild than wild fish, a difference that appears to result from rapid adaptation to the hatchery environment. Size at release is heritable and positively correlated with survival at sea. Therefore, selection should favor traits that promote fast growth in the hatchery even if those traits are maladaptive in the wild. Modifying hatchery conditions to reduce the variation in size among families should decrease the opportunity for selection. Using a mix of 15 full-sibling families of winter run steelhead ( Oncorhynchus mykiss), we tested two modifications designed to benefit the normally slower-growing fish: (1) the addition of structure to rearing tanks and (2) increased water flow. Neither treatment substantially changed the variance in size at release relative to controls. Furthermore, there was a very high correlation among family mean size across all environments. We conclude that simple changes to the hatchery environment such as those tested here cannot overcome the large family effects and are unlikely to substantially reduce the opportunity for selection on size at release.
Non-minimally coupled teleparallel scalar field reconstruction of matter bounce scenario
Authors: Tripathy S. K. , Pal Sasmita , Mishra B.
Published: November 2024

Teleparallel description of gravity theories where the gravity is mediated through the tetrad field and consequent torsion provide an alternative route to explain the late time cosmic speed up issue. Generalisation of the teleparallel gravity theory with different functional forms of the torsion scalar T leads to f(T) gravity. The role of scalar field played in addressing issues in cosmology and astrophysics has developed an interest in the inclusion of a scalar field along with an interaction potential in the action. Such a generalised gravity theory is dubbed as $$f(T,\phi )$$

f
(
T
,
ϕ
)

theory. We have explored such a gravity theory to reconstruct the interaction potential of the scalar field required for an extended matter bounce scenario. The cosmological implications of the reconstructed scalar field potential are studied considering two viable and well known functional forms of $$f(T,\phi )$$

f
(
T
,
ϕ
)

. The energy conditions of these model are discussed to assess the viability of the cosmological models.
Anisotropic extension of the Kohler–Chao–Tikekar cosmological solution with like Wyman IIa complexity factor
Authors: Siza B. , Andrade J. , Santana D. , Naseer Tayyab
Published: November 2024

We construct a new stellar compact object model in the regime of anisotropic pressure using the framework of gravitational decoupling via minimal geometric deformation, with the particularity that the seed solution used is the known Kohler–Chao–Tikekar cosmological solution. As an extra condition to close the Einstein’s field equations resulting for this construction, we use a generalised complexity factor for self-gravitating spheres to the well-known Wyman IIa solution. The resulting model fulfils the fundamental physical acceptability stellar conditions for a compactness factor of a pulsar SMC X-1. The stability of the model is also investigated.
Review of Long-Term Sequelae and Management in Paediatric Lower Limb Replantation
Authors: HO Xin Nee , LIAO Janice Chin-Yi , PUHAINDRAN Mark E. , CHONG Alphonsus K. S.
Published: November 2024

Major limb amputation in a child is a rare but devastating injury associated with significant psychosocial and financial burden. This, combined with the higher growth and remodelling potential despite segmental limb loss, decreases the threshold for replantation in children. Advances in microsurgical techniques and a better understanding of such injuries have led to lower limb replantation becoming a feasible option, with good long-term functional outcomes, even in bilateral amputations. However, long-term sequelae such as limb length discrepancy (LLD) are common, and patients are often subject to multiple surgical interventions. We present a case of replantation in a 2-year-old child following traumatic right below knee amputation, followed up over a period of 5 years. After multiple surgeries, the patient gained good functional recovery and sensibility of the replanted limb. We reviewed and discussed the management of subsequent long-term sequelae, including LLD, lower limb contractures and valgus deformity.

Level of Evidence: Level V (Therapeutic)
Detecting Refactoring Commits in Machine Learning Python Projects: A Machine Learning-Based Approach
Authors: Noei Shayan , Li Heng , Zou Ying
Published: November 2024

Refactoring aims to improve the quality of software without altering its functional behaviors. Understanding developers’ refactoring activities is essential to improve software maintainability. The use of machine learning (ML) libraries and frameworks in software systems has significantly increased in recent years, making the maximization of their maintainability crucial. Due to the data-driven nature of ML libraries and frameworks, they often undergo a different development process compared to traditional projects. As a result, they may experience various types of refactoring, such as those related to the data. The state-of-the-art refactoring detection tools have not been tested in the ML technical domain, and they are not specifically designed to detect ML-specific refactoring types (e.g., data manipulation) in ML projects; therefore, they may not adequately find all potential refactoring operations, specifically the ML-specific refactoring operations. Furthermore, a vast number of ML libraries and frameworks are written in Python, which has limited tooling support for refactoring detection. PyRef, a rule-based and state-of-the-art tool for Python refactoring detection, can identify 11 types of refactoring operations with relatively high precision. In contrast, for other languages such as Java, state-of-the-art tools are capable of detecting a much more comprehensive list of refactorings. For example, Rminer can detect 99 types of refactoring for Java projects. Inspired by previous work that leverages commit messages to detect refactoring, we introduce MLRefScanner, a prototype tool that applies ML techniques to detect refactoring commits in ML Python projects. MLRefScanner detects commits involving both ML-specific refactoring operations and additional refactoring operations beyond the scope of state-of-the-art refactoring detection tools. To demonstrate the effectiveness of our approach, we evaluate MLRefScanner on 199 ML open source libraries and frameworks and compare MLRefScanner against other refactoring detection tools for Python projects. Our findings show that MLRefScanner outperforms existing tools in detecting refactoring-related commits, achieving an overall precision of 94% and recall of 82% for identifying refactoring-related commits. MLRefScanner can identify commits with ML-specific and additional refactoring operations compared to state-of-the-art refactoring detection tools. When combining MLRefScanner with PyRef, we can further increase the precision and recall to 95% and 99%, respectively. MLRefScanner provides a valuable contribution to the Python ML community, as it allows ML developers to detect refactoring-related commits more effectively in their ML Python projects. Our study sheds light on the promising direction of leveraging machine learning techniques to detect refactoring activities for other programming languages or technical domains where the commonly used rule-based refactoring detection approaches are not sufficient.
Learning Knowledge-diverse Experts for Long-tailed Graph Classification
Authors: Mao Zhengyang , Ju Wei , Yi Siyu , Wang Yifan , Xiao Zhiping , Long Qingqing , Yin Nan , Liu Xinwang , Zhang Ming
Published: November 2024

Graph neural networks (GNNs)
have shown remarkable success in graph-level classification tasks. However, most of the existing GNN-based studies are based on balanced datasets, while many real-world datasets exhibit long-tailed distributions. In such datasets, the tail classes receive limited attention during training, leading to prediction bias and degraded performance. To address this issue, a range of long-tailed learning strategies have been proposed, such as data re-balancing and transfer learning. However, these approaches encounter several challenges, including insufficient representation capacity for tail classes and their evaluation solely on uniform test data, limiting their capacity to handle unknown class distributions. To tackle these challenges, we introduce a novel framework, namely
Knowledge-diverse Experts (KDEX)
for long-tailed graph classification. Our KDEX leverages a dynamic memory module to enable the transfer of knowledge from head to tail, which improves the representation ability of the tail. To deal with unknown test distributions, KDEX introduces a knowledge-diverse expert training approach to train experts with different capacities in managing various test distributions. Moreover, we train the hierarchical router in a self-supervised manner to dynamically aggregate each knowledge-diverse expert during testing. Experimental results on multiple benchmarks reveal that our KDEX outperforms current baselines in both standard and test-agnostic long-tailed graph classification.
Fantastic Circuits and Where to Find Them—A Holistic ILP Formulation for Model-Based Hardware Design
Authors: Fiege Nicolai , Zipf Peter
Published: November 2024

The end of Moore’s law and Dennard scaling emphasizes the need for application-specific computing architectures to achieve high resource and energy efficiency and real-time performance. The concept of a silicon compiler remains an enduring aspiration for design time reduction. In order to generate hardware implementations at register transfer level from behavioral descriptions, design automation tools must address challenging and interdependent problems, including allocation, scheduling, and binding. Additionally, manual intervention by the user is necessary to balance the
resources vs. performance tradeoff
via, for example, function inlining or loop unrolling/pipelining. Existing approaches typically solve these problems sequentially, compromising optimality in favor of simplicity and runtime. Here we show how to model the whole model-based design flow as one holistic integer linear programming (ILP) formulation aiming at consistently deriving the optimal microarchitecture for any given application. Incorporating clock gating minimizes the number of useless operations with negligible resource overhead (if any), while always guaranteeing optimal throughput. The unified nature of the proposed ILP model enables implementations unmatched by state-of-the-art approaches in terms of resource efficiency and measured power consumption. These results facilitate a streamlined design flow for highly optimized embedded systems in the context of model-based design.
RASopathies in Cardiac Disease
Authors: Chennappan Saravanakkumar , Kontaridis Maria Irene
Published: November 2024

RASopathies are a group of clinically overlapping autosomal dominant disorders caused primarily by mutations in genes that reside along the canonical Ras–mitogen-activated protein kinase signaling cascade. Though individually rare, collectively, these disorders constitute one of the largest families of congenital disorders worldwide, particularly for infantile hypertrophic cardiomyopathy. Significantly, despite almost five decades of RASopathy research, therapeutic options remain limited and focused primarily on treating symptoms rather than disease etiology. Targeting the genes causal to these disorders, and the nodal pathways critical for their regulation, however, has been challenging. In this review, we highlight these challenges, particularly with respect to congenital heart defects and cardiac diseases and discuss limitations and future directions for approaches to new therapeutic strategies.