bluuebunny/crossref_metadata_2025 huggingface dataset:
Economics and optimal investment policies of Attackers and Defenders in cybersecurity
Authors: Ebel Austin , Mitra Debasis
Published: November 2024

Our thesis is that economics and investment policies are vital factors in determining the outcome of cybersecurity conflicts. For our economic framework, we borrow from the pioneering work of Gordon and Loeb, in which the Defender optimally trades off investments for lower likelihood of its system breach. Our two-sided model has in addition an Attacker, assumed to be rational and also guided by economic considerations in its decision-making, to which the Defender responds. The model is a simplified adaptation of a model proposed during the Cold War for weapons deployment in the USA. Our model is a Stackelberg game and, from an analytic perspective, a Max–Min problem. The complexity of the analysis is due to the non-convexity of the objective function in the optimization. The Attacker’s possible actions add substantially to the risk to the Defender, and the Defender’s rational, risk-neutral optimal investments in general substantially exceed the optimal investments predicted by the one-sided Gordon–Loeb model. We obtain a succinct set of three decision types that categorize all of the Defender’s optimal investment decisions. Also, the Defender’s optimal decisions exhibit discontinuous behavior as the prior vulnerability of its system is varied. Results for two limiting cases of the model corresponding to an Extreme Attacker and an Extreme Defender are given. The analysis is supplemented by extensive numerical illustrations. The results from our model open several major avenues for future work.
Modified reconstruction procedure in subtotal esophagectomy with retrosternal gastric pull up to reduce anastomotic leakage: a propensity score-matched analysis
Authors: Okumura Tomoyuki , Miwa Takeshi , Murotani Kenta , Numata Yoshihisa , Watanabe Toru , Hashimoto Isaya , Kamiyama Koki , Tazawa Kenichi , Yamagishi Fuminori , Fujii Tsutomu
Published: November 2024

One risk factor for anastomotic leakage (AL) after esophagectomy with retrosternal gastric reconstruction is excessive compression of the gastric tube at the thoracic inlet. In this study, we evaluated the effect of our modified procedure to reduce AL by placing the esophagogastric anastomosis below the thoracic inlet. Between January 2008 and December 2022, 174 consecutive patients underwent subtotal esophagectomy with retrosternal gastric pull up, followed by circular stapler anastomosis in our hospitals. After January 2016, the gastric tube was pulled down to place the anastomosis below the suprasternal notch. Postoperative CT then measured the level of esophagogastric anastomosis (LEA). Comparing cases before and after revision (conventional group, n = 65 vs. test group, n = 109), AL was significantly reduced from 11 (16.9%) to 3 (2.8%) cases (P = 0.002). After propensity score matching, AL was observed in 14% (8/57) and 0% (0/57) cases in the conventional and test groups, respectively (P = 0.006). Smaller circular stapler size (P < 0.001), less intraoperative blood loss (P < 0.001), and lower LEA (P < 0.001) were observed in the test group than in the conventional group. Multivariate analysis revealed that anastomotic procedure (OR [95%CI], 0.01[0.00–0.46], P = 0.008), and body mass index (OR [95%CI], 6.92[1.10–135.01], P = 0.038) were the independent risk factors for the development of AL. Our modified procedure to avoid compression of the gastric tube at the thoracic inlet is suggested to noninvasively reduce the risk of AL in the subtotal esophagectomy with retrosternal reconstruction.
An eHealth intervention for patients with a low socioeconomic position during their waiting period preceding cardiac rehabilitation: a randomized feasibility study
Authors: Faber Jasper S , Kraal Jos J , ter Hoeve Nienke , Al-Dhahir Isra , Breeman Linda D , Chavannes Niels H , Evers Andrea W M , Bussmann Hans B J , Visch Valentijn T , van den Berg-Emons Rita J G
Published: November 2024

Aims

Cardiac rehabilitation (CR) shows lower effectiveness and higher dropouts among people with a low socioeconomic position (SEP) compared to those with a high SEP. This study evaluated an eHealth intervention aimed at supporting patients with a low SEP during their waiting period preceding CR.

Methods and results

Participants with a low SEP in their waiting period before CR were randomized into an intervention group, receiving guidance videos, patient narratives, and practical tips, or into a control group. We evaluated adherence (usage metrics), acceptance (modified Usefulness, Satisfaction, and Ease of use questionnaire), and changes in feelings of certainty and guidance between the waiting period’s start and end. Semi-structured interviews provided complementary insights. The study involved 41 participants [median interquartile range (IQR) age 62 (14) years; 33 males], with 21 participants allocated to the intervention group, using the eHealth intervention for a median (IQR) duration of 16 (10) days, using it on a median (IQR) of 100% (25) of these days, and viewing 88% of the available messages. Key adherence themes were daily routine compatibility and curiosity. Acceptance rates were 86% for usability, 67% for satisfaction, and 43% for usefulness. No significant effects on certainty and guidance were observed, but qualitative data suggested that the intervention helped to inform and set expectations.

Conclusion

The study found the eHealth intervention feasible for cardiac patients with a low SEP, with good adherence, usability, and satisfaction. However, it showed no effect on feelings of certainty and guidance. Through further optimization of its content, the intervention holds promise to improve emotional resilience during the waiting period.

Registration

This trial is registered as follows: ‘Evaluation of a Preparatory eHealth Intervention to Support Cardiac Patients During Their Waiting Period (PReCARE)’ at ClinicalTrials.gov (NCT05698121, https://clinicaltrials.gov/study/NCT05698121).
Intensive care unit admissions following enhanced recovery video-assisted thoracoscopic surgery lobectomy
Authors: Visby Lasse , Secher Erik Lilja , Møller-Sørensen Hasse , Kehlet Henrik , Petersen René Horsleben
Published: November 2024

OBJECTIVES

Video-assisted thoracoscopic surgery (VATS) lobectomy combined with enhanced recovery after surgery (ERAS) protocols has improved postoperative outcomes, yet concerns persist regarding complications and readmissions. Limited research has explored intensive care unit (ICU) admissions and outcomes within this context. The goal of this study was to analyse ICU admissions following VATS lobectomy within an established ERAS protocol.

METHODS

Consecutive patients who underwent VATS lobectomy between 2018 and 2023 were included. Patient data were obtained from our prospective institutional database, while ICU data were extracted from electronic patient records.

RESULTS

Of 2099 patients included, 48 (2.3%) required ICU admission. The median age was 70 (interquartile range: 64–76) years, with ICU patients being older and predominantly male (73%). Overall 30-day mortality was 1.0% with an ICU mortality of 31%. Multiple logistic regression revealed significant associations between ICU admission and male gender (P ≤ 0.001), diabetes mellitus (P = 0.026), heart failure (P = 0.040) and diffusing capacity for carbon monoxide (0.013). Median time to ICU admission was 4 days (interquartile range: 2–10). Respiratory failure was the primary reason for ICU admission (60%). Severe surgical complications accounted for 8.3% of all ICU admissions.

CONCLUSIONS

In an ERAS setting, the incidence of ICU admissions following VATS lobectomy was 2.3%, with a mortality rate of 31%. Respiratory failure was the leading cause of ICU admission.
All-cause nursing home mortality rates have remained above pre-pandemic levels after accounting for decline in occupancy
Authors: Weiss Max , Normand Sharon-Lise T , Grabowski David C , Blacker Deborah , Newhouse Joseph P , Hsu John
Published: November 2024

During the initial year of the COVID-19 pandemic, a disproportionate share of COVID-19–related deaths occurred among nursing home residents. Initial estimates of all-cause mortality rates also spiked in early and late 2020 before falling to near or below historical rates by early 2021. During the first 3 years of the pandemic, the US nursing home resident population also decreased by 18% (239 000 fewer residents) compared with pre-pandemic levels. After accounting for these population changes, the all-cause nursing home mortality rate has remained above pre-pandemic levels through the middle of 2023. The peak was in December 2020 at 5692 deaths per 100 000 residents, which was 19% higher than estimates not accounting for the population decrease.
Standardizing social determinants of health data: a proposal for a comprehensive screening tool to address health equity a systematic review
Authors: Ganatra Sarju , Khadke Sumanth , Kumar Ashish , Khan Sadiya , Javed Zulqarnain , Nasir Khurram , Rajagopalan Sanjay , Wadhera Rishi K , Dani Sourbha S , Al-Kindi Sadeer
Published: November 2024

Social determinants of health (SDoH) significantly impacts health outcomes and disparities. While the Centers for Medicare and Medicaid Services has mandated hospitals to collect standardized SDoH data, existing tools lack key elements. This systematic review identified 78 studies and 20 screening tools addressing various SDoH domains. However, most tools were missing several key domains and lacked standardization. We propose a comprehensive tool meeting essential criteria: validated questions, brevity, actionability, cultural appropriateness, workflow integration, and community linkage. Our tool addresses gaps in available tools and incorporates standardized and validated questions to enable patient-centered screening for diverse social and environmental determinants of health. It uniquely includes detailed race/ethnicity data collection, housing characteristics, physical activity assessment, access to healthy food measures, and environmental exposure evaluation. The tool aims to provide actionable data for immediate interventions while informing broader population health strategies and policy initiatives. By offering a holistic assessment of SDoH across multiple domains, our tool enables standardized data collection, risk stratification, and focused initiatives to address health inequities at both individual and population levels. Further research is needed to develop evidence-based pathways for integrating SDoH data into real-world patient care workflows, improve risk prediction algorithms, address health-related social needs, and reduce disparities.
Endoscopic-assisted, minimally invasive versus sternotomy total arterial multivessel bypass grafting
Authors: Görtzen De Qing , Sampon Fleur , Timmermans Naomi , Ter Woorst Joost , Akca Ferdi
Published: November 2024

OBJECTIVES

This single-centre study compared the perioperative outcomes after total arterial multivessel revascularization through endoscopic-assisted, minimally invasive surgery compared to a conventional sternotomy approach.

METHODS

In this retrospective, propensity score-matched (PSM) cohort study, a total of 740 patients were analysed [endoscopic coronary artery bypass grafting (Endo-CAB), N = 92; Sternotomy, N = 648]. After PSM (1:2 ratio), 73 Endo-CAB and 137 sternotomy patients were compared with an equal number of distal anastomoses (Endo-CAB 2.3 versus Sternotomy 2.4 anastomoses per patient, P = 0.082). We used ‘textbook outcome’ as a patient-orientated outcome measure, defined as the absence of 30-day mortality, re-exploration for bleeding, postoperative ischaemia, cardiac tamponade, cerebrovascular events, wound infection, new onset arrhythmias, pneumonia, placement of chest drains and prolonged hospital stay (>7 days).

RESULTS

Patients undergoing Endo-CAB had significantly more often a textbook outcome compared to the sternotomy group (78.1% vs 59.1%, P = 0.009). Endo-CAB patients had shorter hospital stay (4.0 vs 6.0 days, P < 0.001), less postoperative blood loss (360 vs 490 ml, P < 0.001) and a significant reduction of new onset postoperative atrial fibrillation (5.5% vs 17.5%, P = 0.015). Other postoperative outcomes were comparable for both groups.

CONCLUSIONS

Total arterial Endo-CAB demonstrates excellent postoperative outcomes compared to a sternotomy approach for multivessel coronary artery disease. These findings provide a strong basis for further expanding the multivessel Endo-CAB programme.
Implications of team submissions in open innovation contests
Authors: Candoğan Sıdıka Tunç , Korpeoglu C Gizem , Tang Christopher S
Published: November 2024

Accepted by: Aris Syntetos

Since the early aughts, open innovation platforms such as InnoCentive and HeroX have helped seekers (firms, SMEs, startups) develop and launch open innovation contests by inviting external (independent) solvers to submit their solutions. In an open innovation contest, an award is given to the top-quality submission, where the quality of each submission depends on two salient factors: (1) the costly effort(s) exerted by the solver(s); and (2) the random innovative shock(s) generated by the solver(s). Hence, highly novel contests are shock-driven, whereas less novel contests are effort-driven. In this paper, we examine if and when the platform (and the seekers) should encourage team submissions instead of individual submissions. We analyze a game-theoretic model of an open innovation contest associated with a decomposable problem and compare the equilibrium outcomes for two cases when solvers can make only (a) individual submissions and (b) team submissions. Solvers prefer team submissions due to free-riding and reduced competition (fewer submissions), which can afford them to reduce their effort(s). Consequently, team submissions may result in low-quality submissions, which are detrimental to the seekers. Even so, due to random shocks, we find team submissions are beneficial to the seekers when the seeker’s problem is less novel and the solver’s effort cost is sufficiently high. In addition, even when the seeker’s problem is highly novel, we find that team submissions can benefit the seekers when team submissions can attract sufficiently more external solvers to counteract the two negative effects associated with free-riding and reduced competition. Our results continue to hold when the reward level is endogenously determined.
BCS Post-Election Engagement and Strategy
Authors: Penketh Claire
Published: November 2024

Following the change of government, BCS, The Chartered Institute for IT, continues to play a crucial role in advancing technology policy, digital literacy and the professionalisation of the IT sector. Claire Penketh, BCS Senior Policy and Public Affairs Manager, reports.
Futurology
Authors: Lucas Matt
Published: November 2024

Matt Lucas FBCS CITP dives into the potential and pitfalls of the nondeterministic nature of quantum computing.
BCS Members Close the Digital Divide
Authors: Quek Freddie
Published: November 2024

Freddie Quek, Chair of the BCS Digital Divide Specialist Group, explores some impressive and important community initiatives by BCS members that focus on ending digital poverty.
Quantum to Overtake GPS Navigation
Authors: Cooper Martin
Published: November 2024

You'll never get lost again. A new quantum-based project intended to transform air, sea and road navigation has been announced.
Visualising VUCA to Ensure Survival
Authors: Vickery James
Published: November 2024

Data-driven signals can help organisations build resilience in the face of a range of existential threats from an increasingly turbulent operating environment. Dr James Vickery CITP explores and explains an innovative technique for understand these signals.
Does Current AI Represent a Dead End?
Authors: Boiten Eerke
Published: November 2024

Eerke Boiten, Professor of Cyber Security at De Montfort University Leicester, explains his belief that current AI should not be used for serious applications.
More Human Than Human?
Authors: Hall Jon
Published: November 2024

In this column, Jon G. Hall explores how AI is well placed to help find solutions, but humans are still best placed for identifying the problems in the first place.
Being an Ethical Management Consultant
Authors: Jacobs Adam
Published: November 2024

Adam Jacobs MBCS CITP explores what it means to be an ethical management consultant, discussing why we should all do our best to do the right thing and how dilemmas can soon become PR disasters.
Crowdstrike and Kernel-Level Access
Authors: Harrison Anthony
Published: November 2024

Following the global CrowdStrike incident, Anthony Harrison FBCS takes a deep dive into how Microsoft's operating system integrates security software and asks whether there are technical lessons to be learned.
A Very Special Event: Bcswomen Lovelace Colloquium
Authors: Barikzai Safia , Dee Hannah
Published: November 2024

The BCS Lovelace Colloquium is an annual one-day conference for women and non-binary students of computing and related subjects. Dr Safia Barikzai and Dr Hannah Dee MBE discuss the storied event's history, significance and future.
The Triple Threat
Authors: Lovelock Christina
Published: November 2024

Christina Lovelock MBCS explains the importance of understanding technical, culture and security debt to develop and maintain a modern, efficient and secure business.
Scaling AI in the Business
Authors: Runciman Brian
Published: November 2024

As AI continues to garner column inches by the mile, Brian Runciman MBCS looks back at how AI seeped into the business arena from the perspective of BCS.
Adopting Automation
Authors: Major Danny
Published: November 2024

Danny Major FBCS looks at how enterprises can successfully adopt intelligent automation (IA).
Learning health system linchpins: information exchange and a common data model
Authors: Eisman Aaron S , Chen Elizabeth S , Wu Wen-Chih , Crowley Karen M , Aluthge Dilum P , Brown Katherine , Sarkar Indra Neil
Published: November 2024

Objective

To demonstrate the potential for a centrally managed health information exchange standardized to a common data model (HIE-CDM) to facilitate semantic data flow needed to support a learning health system (LHS).

Materials and Methods

The Rhode Island Quality Institute operates the Rhode Island (RI) statewide HIE, which aggregates RI health data for more than half of the state's population from 47 data partners. We standardized HIE data to the Observational Medical Outcomes Partnership (OMOP) CDM. Atherosclerotic cardiovascular disease (ASCVD) risk and primary prevention practices were selected to demonstrate LHS semantic data flow from 2013 to 2023.

Results

We calculated longitudinal 10-year ASCVD risk on 62,999 individuals. Nearly two-thirds had ASCVD risk factors from more than one data partner. This enabled granular tracking of individual ASCVD risk, primary prevention (ie, statin therapy), and incident disease. The population was on statins for fewer than half of the guideline-recommended days. We also found that individuals receiving care at Federally Qualified Health Centers were more likely to have unfavorable ASCVD risk profiles and more likely to be on statins. CDM transformation reduced data heterogeneity through a unified health record that adheres to defined terminologies per OMOP domain.

Discussion

We demonstrated the potential for an HIE-CDM to enable observational population health research. We also showed how to leverage existing health information technology infrastructure and health data best practices to break down LHS barriers.

Conclusion

HIE-CDM facilitates knowledge curation and health system intervention development at the individual, health system, and population levels.
Bayesian optimization for personalized dose-finding trials with combination therapies
Authors: Willard James , Golchi Shirin , Moodie Erica E M , Boulanger Bruno , Carlin Bradley P
Published: November 2024

Identification of optimal dose combinations in early-phase dose-finding trials is challenging, due to the trade-off between precisely estimating the many parameters required to flexibly model the possibly nonmonotonic dose-response surface, and the small sample sizes in early-phase trials. This difficulty is even more pertinent in the context of personalized dose-finding, where patient characteristics are used to identify tailored optimal dose combinations. To overcome these challenges, we propose the use of Bayesian optimization for finding optimal dose combinations in standard (one size fits all) and personalized multi-agent dose-finding trials. Bayesian optimization is a method for estimating the global optima of expensive-to-evaluate objective functions. The objective function is approximated by a surrogate model, commonly a Gaussian process, paired with a sequential design strategy to select the next point via an acquisition function. This work is motivated by an industry-sponsored problem, where the focus is on optimizing a dual-agent therapy in a setting featuring minimal toxicity. To compare the performance of the standard and personalized methods under this setting, simulation studies are performed for a variety of scenarios. Our study concludes that taking a personalized approach is highly beneficial in the presence of heterogeneity.
Internet-based treatment for provoked vulvodynia: factors associated with treatment outcomes
Authors: Hess Engström Andrea , Flink Ida , Kero Viktoria , Bohm-Starke Nina , Skalkidou Alkistis
Published: November 2024

Introduction

Previous research has indicated that internet-based Acceptance and Commitment Therapy (ACT) can reduce pain during intercourse and increase pain acceptance in individuals with provoked vulvodynia, but the factors associated with treatment outcomes remain unknown.

Aim

This study aimed to investigate factors associated with changes in pain acceptance following an internet treatment based on ACT.

Methods

This exploratory study used data from the EMBLA study, a multicenter randomized controlled trial that investigated the effects of internet-based ACT for provoked vulvodynia. The examined factors included sociodemographics, medical history, pain and sexual behavior, and psychosocial characteristics. Linear regression analysis was employed to assess the association of these factors with pain acceptance, including interaction effects. Results were adjusted for multiple testing using Bonferroni correction.

Outcomes

The outcome measure was pain acceptance assessed on the scale Chronic Pain Questionnaire–Revised, which comprises two sub-scales: activity engagement and pain willingness.

Results

Before adjustment, greater improvement in overall pain acceptance and the subscale activity engagement was seen participants in the intervention group who had a history of physical violence or sexual assault. Increased time spent on the treatment platform per week was also associated with greater improvement in pain acceptance. Participants who reported gastrointestinal problems before the internet-based treatment showed better treatment outcomes in activity engagement. Previous contact with a psychologist or counselor was associated with less improvement in activity engagement. The intervention was less effective on the subscale pain willingness with increased age and for those reporting urinary problems. No associations remained statistically significant after adjustment for multiple testing.

Clinical implications

Previous exposure to violence and sexual assault, concomitant gastrointestinal or urinary problems, and adherence to treatment should be further investigated in larger studies on factors associated with treatment outcomes after internet treatment based on ACT, especially regarding pain.

Strengths and limitations

This was a novel and exploratory study and provides information for researchers in future investigations of how individual characteristics may influence treatment outcomes. A range of variables were explored in the models, underscoring the importance of future studies to strengthen the findings. One limitation concerns the sample size, which was fairly small considering the nature of the study.

Conclusion

After correcting for multiple testing, no factors were found to be statistically associated with changes in pain acceptance after the treatment.
Nitrogen at the crossroads of light: integration of light signalling and plant nitrogen metabolism
Authors: Sathee Lekshmy , R Suriyaprakash , Barman Dipankar , Adavi Sandeep B , Jha Shailendra K , Chinnusamy Viswanathan
Published: November 2024

Plants have developed complex mechanisms to perceive, transduce, and respond to environmental signals, such as light, which are essential for acquiring and allocating resources, including nitrogen (N). This review delves into the complex interaction between light signals and N metabolism, emphasizing light-mediated regulation of N uptake and assimilation. Firstly, we examine the details of light-mediated regulation of N uptake and assimilation, focusing on the light-responsive activity of nitrate reductase (NR) and nitrate transporters. Secondly, we discuss the influence of light on N-dependent developmental plasticity, elucidating how N availability regulates crucial developmental transitions such as flowering time, shoot branching, and root growth, as well as how light modulates these processes. Additionally, we consider the molecular interaction between light and N signalling, focusing on photoreceptors and transcription factors such as HY5, which are necessary for N uptake and assimilation under varying light conditions. A recent understanding of the nitrate signalling and perception of low N is also highlighted. The in silico transcriptome analysis suggests a reprogramming of N signalling genes by shade, and identifies NLP7, bZIP1, CPK30, CBL1, LBD37, LBD38, and HRS1 as crucial molecular regulators integrating light-regulated N metabolism.
Betaine lipids overproduced in seed plants are not imported into plastid membranes and promote endomembrane expansion
Authors: Salomon Sarah , Schilling Marion , Albrieux Catherine , Si Larbi Grégory , Jouneau Pierre-Henri , Roy Sylvaine , Falconet Denis , Michaud Morgane , Jouhet Juliette
Published: November 2024

Plants and algae have to adapt to environmental changes and face various stresses that negatively affect their growth and development. One common stress is phosphate (Pi) deficiency, which is often present in the environment at limiting levels. In response to Pi deficiency, these organisms increase Pi uptake and remobilize intracellular Pi. Phospholipids are degraded to provide Pi and are replaced by non-phosphorus lipids, such as glycolipids or betaine lipids. During evolution, seed plants lost the ability to synthesize betaine lipids. By expressing Bta1 genes, which are involved in the synthesis of diacylglyceryl-N,N,N-trimethyl-homoserine (DGTS), from different species, we showed that DGTS can be produced in seed plants. In Arabidopsis, expression of BTA1 under a phosphate starvation-inducible promoter resulted in limited DGTS production without having any impact on plant growth or lipid remodelling. In transient expression systems in Nicotiana benthamiana, leaves were able to accumulate DGTS to up to 30% of their glycerolipid content at a slight expense to galactolipid and phospholipid production. At the subcellular level, we showed that DGTS is absent from plastids and seems to be enriched in endomembranes, inducing endoplasmic reticulum membrane proliferation. Finally, the DGTS synthesis pathway seems to compete with phosphatidylcholine (PC) synthesis via the Kennedy pathway but does not appear to be derived from the PC diacylglycerol backbone and therefore does not interfere with the eukaryotic pathway involved in galactolipid synthesis.
The abundance of regulatory T cell subsets is associated with the clinical outcomes of sarcoidosis
Authors: Kusaka Katsuhide , Miyazaki Yusuke , Nakayamada Shingo , Kubo Satoshi , Miyagawa Ippei , Satoh-Kanda Yurie , Todoroki Yasuyuki , Ueno Masanobu , Tanaka Yoshiya
Published: November 2024

Objectives

Some patients with sarcoidosis achieve spontaneous remission, whereas others repeatedly experience relapse. We examined differences in the clinical course of active sarcoidosis according to peripheral blood immunophenotypes before treatment.

Methods

This retrospective study compared peripheral blood immunophenotypes between patients with active sarcoidosis (n = 28) and healthy control subjects (n = 10). Patients with sarcoidosis were divided into the spontaneous remission group without treatment (n = 9), the non-relapsed group after treatment (n = 13), and the relapsed group after treatment (n = 6) and were compared for peripheral blood immunophenotypes and background characteristics at baseline.

Results

Patients with sarcoidosis showed increases in activated T helper (Th) 1 cells, activated Th17 cells, and regulatory T (Treg) cell subsets. The proportion of effector Treg cells was highest in the spontaneous remission group, and the proportion of non-suppressive Treg cells was highest in the relapsed group. No differences were observed in the proportions of other CD4+ T cell subsets. The cut-off values for predicting spontaneous remission and relapse were calculated for the effector Treg/non-suppressive Treg ratio. As a result, A ratio ≥1.469 predicted spontaneous remission (75%), while ≤0.722 predicted relapse (66.7%).

Conclusion

Effector and non-suppressive Treg cell proportions before treatment may predict spontaneous remission and relapse in active sarcoidosis.
Collaborative Music Therapy and Speech-Language Pathology for Pediatric Acquired Communication Impairments: A Phenomenological International Perspective
Authors: Burns James , Keaveney Cecilia , Nieto Natalia , O’Connor Rebecca , Moss Hilary
Published: November 2024

The partnership between music therapy and speech-language pathology is gaining recognition as an effective approach in the rehabilitation of young children with acquired communication impairments (ACIs). Yet, there remains a notable gap in understanding the distinctive contributions and challenges inherent in this collaborative practice. This study explored the perspectives of music therapists (MTs) and speech-language pathologists (SLPs) regarding the unique role of this collaborative effort, the elements of successful collaboration, and the methods implemented by clinicians to evaluate outcomes. Semi-structured interviews were conducted with nine pairs of MTs and SLPs in rehabilitation facilities across seven countries. These interviews were analyzed thematically using Van Manen’s approach to hermeneutic phenomenology. Three themes arose from the data: (a) the role of collaborative music therapy and speech-language pathology, (b) building blocks of successful collaboration, and (c) evaluating collaborative practices. This collaboration fosters a unified strategy aimed at achieving shared language and communication goals. By combining their distinct expertise, MTs and SLPs can address the complex and varied needs of children with ACIs more effectively. However, further research is essential to comprehensively understand the functional outcomes arising from such collaborative endeavors in pediatric ACIs. This is crucial for validating the efficacy and significance of this approach in bolstering language and communication skills and advocating for its wider integration within rehabilitation services.
GTO: a comprehensive gene therapy omnibus
Authors: Meng Xuehang , Du Yujia , Liu Chang , Zhai Zhaoyu , Pan Jianbo
Published: November 2024

Gene therapy, which involves the delivery of genetic material into cells to correct an underlying genetic problem, has emerged as a promising approach for treating various conditions. To promote research in this rapidly evolving field, we developed the Gene Therapy Omnibus (GTO) (http://www.inbirg.com/gto/), a comprehensive resource containing detailed clinical trial data and molecular information related to gene therapy. The GTO includes 6333 clinical trial records and 3466 transcriptome profiles, with information on 614 altered genes and 22 types of gene therapy, including DNA therapies, RNA therapies and genetically-modified cell therapies. For each gene therapy product in a clinical trial, detailed information, such as altered gene name, structural components, indication, vector information, phase of the clinical trial, clinical outcomes and adverse effects, is provided when available. Additionally, 345 comparison datasets, including 29 single-cell RNA-sequencing datasets comprising information on both gene therapy and control samples, were established. Differential gene expression and downstream functional enrichment analyses were performed through standardized pipelines to elucidate the molecular alterations induced by gene therapy. The user-friendly interface of the GTO supports efficient data retrieval, visualization and analysis, making it an invaluable resource for researchers and clinicians performing clinical research on gene therapy and the underlying mechanisms.
The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters
Authors: Udwary Daniel W , Doering Drew T , Foster Bryce , Smirnova Tatyana , Kautsar Satria A , Mouncey Nigel J
Published: November 2024

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.
Combining neural networks with galaxy light subtraction for discovering strong lenses in the Hyper Suprime-Cam Subaru Strategic Program
Authors: Ishida Yuichiro , Wong Kenneth C , Jaelani Anton T , More Anupreeta
Published: November 2024

Galaxy-scale strong gravitational lenses are valuable objects for a variety of astrophysical and cosmological applications. Strong lensing galaxies are rare, so efficient search methods, such as convolutional neural networks (CNNs), are often used on large imaging datasets. In this work, we apply a new technique to improve the performance of supervised neural networks by subtracting the central (lensing) galaxy light from both the training and test datasets. We use multiband imaging data from the Hyper Suprime-Cam Subaru Strategic Program as our training and test datasets. By subtracting the lensing galaxy light, we increase the contrast of the lensed source compared to the original imaging data. We also apply the light subtraction to non-lenses in order to compare them to the light-subtracted lenses. Residual features resulting from poor light subtraction can adversely affect the performance of networks trained on the subtracted images alone. We find that combining the light-subtracted images with the original $gri$-band images for training and classification can overcome this and improve the overall classification accuracy. We find the area under the receiver operating characteristic curve can be improved to 0.841 using the combination of the fiducial images and light-subtracted images, compared to 0.808 for the fiducial imaging dataset alone. This may be a promising technique for improving future lens searches using CNNs.
Mitochondrial Splicing Efficiency Is Lower in Holoparasites Than in Free-Living Plants
Authors: Garcia Laura E , Sanchez-Puerta M Virginia
Published: November 2024

Mitochondria play a crucial role in eukaryotic organisms, housing their own genome with genes vital for oxidative phosphorylation. Coordination between nuclear and mitochondrial genomes is pivotal for organelle gene expression. Splicing, editing and processing of mitochondrial transcripts are regulated by nuclear-encoded factors. Splicing efficiency (SEf) of the many group II introns present in plant mitochondrial genes is critical for mitochondrial function since a splicing defect or splicing deficiency can severely impact plant growth and development. This study investigates SEf in free-living and holoparasitic plants, focusing on 25 group II introns from 15 angiosperm species. Our comparative analyses reveal distinctive splicing patterns with holoparasites exhibiting significantly lower SEf, potentially linked to their unique evolutionary trajectory. Given the preponderance of horizontal gene transfer (HGT) in parasitic plants, we investigated the effect of HGT on SEf, such as the presence of foreign introns or foreign nuclear-encoded splicing factors. Contrary to expectations, the SEf reductions do not correlate with HGT events, suggesting that other factors are at play, such as the loss of photosynthesis or the transition to a holoparasitic lifestyle. The findings of this study broaden our understanding of the molecular evolution in parasitic plants and shed light on the multifaceted factors influencing organelle gene expression.
Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants
Authors: Wang Xutong , Duan Jingbo , Clark Chancelor B , Feng Wanjie , Ma Jianxin
Published: November 2024

Alternative transcription initiation (ATI) appears to be a ubiquitous regulatory mechanism of gene expression in eukaryotes. However, the extent to which it affects the products of gene expression and how it evolves and is regulated remain unknown. Here, we report genome-wide identification and analysis of transcription start sites (TSSs) in various soybean (Glycine max) tissues using a survey of transcription initiation at promoter elements with high-throughput sequencing (STRIPE-seq). We defined 193,579 TSS clusters/regions (TSRs) in 37,911 annotated genes, with 56.5% located in canonical regulatory regions and 43.5% from start codons to 3′ untranslated regions, which were responsible for changes in open reading frames of 24,131 genes. Strikingly, 6,845 genes underwent ATI within coding sequences (CDSs). These CDS-TSRs were tissue-specific, did not have TATA-boxes typical of canonical promoters, and were embedded in nucleosome-free regions flanked by nucleosomes with enhanced levels of histone marks potentially associated with intragenic transcriptional initiation, suggesting that ATI within CDSs was epigenetically tuned and associated with tissue-specific functions. Overall, duplicated genes possessed more TSRs, exhibited lower degrees of tissue specificity, and underwent stronger purifying selection than singletons. This study highlights the significance of ATI and the genomic and epigenomic factors shaping the distribution of ATI in CDSs in a paleopolyploid eukaryote.
How reliance on Spanish-language social media predicts beliefs in false political narratives amongst Latinos
Authors: Abrajano Marisa , Garcia Marianna , Pope Aaron , Vidigal Robert , Tucker Joshua A , Nagler Jonathan
Published: November 2024

False political narratives are nearly inescapable on social media in the United States. They are a particularly acute problem for Latinos, and especially for those who rely on Spanish-language social media for news and information. Studies have shown that Latinos are vulnerable to misinformation because they rely more heavily on social media and messaging platforms than non-Hispanic whites. Moreover, fact-checking algorithms are not as robust in Spanish as they are in English, and social media platforms put far more effort into combating misinformation on English-language media than Spanish-language media, which compounds the likelihood of being exposed to misinformation. As a result, we expect that Latinos who use Spanish-language social media to be more likely to believe in false political narratives when compared with Latinos who primarily rely on English-language social media for news. To test this expectation, we fielded the largest online survey to date of social media usage and belief in political misinformation of Latinos. Our study, fielded in the months leading up to and following the 2022 midterm elections, examines a variety of false political narratives that were circulating in both Spanish and English on social media. We find that social media reliance for news predicts one’s belief in false political stories, and that Latinos who use Spanish-language social media have a higher probability of believing in false political narratives, compared with Latinos using English-language social media.
Online Graded Motor Imagery Is Effective in Women Diagnosed With Pelvic Pain: A Randomized Controlled Trial
Authors: Lopez-Brull Aida , Perez-Dominguez Borja , Plaza-Carrasco Maria , Blasco-Ortiz Cristina , Navarro-Ribera Blanca , Casaña Jose , Mohedo Esther Diaz , Nahon Irmina
Published: November 2024

Objective

Effective therapeutic strategies are crucial for managing genito-pelvic pain/penetration disorder (GPPPD), a condition presenting challenges for both patients and health care providers. This study aims to assess the effectiveness of an online graded motor imagery (GMI) program in alleviating pain intensity and improving sexual function in women diagnosed with GPPPD.

Methods

Eighty-seven women were randomly assigned to either an online GMI group or a control group. The online GMI protocol involved engaging participants in 2-week segments of left/right judgment exercises, mental simulation of movements, and gradual exposure therapy. After 6 weeks, we assessed pain intensity and sexual function. The control group gained access to the program upon study completion.

Results

The online GMI group demonstrated a significant reduction in pain intensity, coupled with improvements in sexual function. Notably, participants with enhanced movement imagery abilities experienced greater improvements, while those with negative beliefs and thoughts regarding vaginal penetration showed lower sexual function scores.

Conclusion

An online GMI program is effective in alleviating the pain burden faced by women dealing with GPPPD.

Impact

Effectively addressing pelvic pain in patients remains a daunting challenge for physical therapists. Therefore, implementing efficient and easily accessible strategies is crucial. The incorporation of GMI intervention proves to be an effective approach for improving both pain and sexual functioning in women with GPPPD.
A Dynamic Model of Authoritarian Social Control
Authors: Lagunoff Roger
Published: November 2024

Authoritarian regimes often use targeted social control—unequal application of the law to limit expressive freedom and enforce social conformity. At the same time, their methods appear less draconian than in the past. In this model, an authority structures punishments and rewards to compel adherence to its preferred norm. The authority’s commitment is time-limited and depends on imperfectly informative signals of a citizen’s behaviour. Given two citizens with the same observed behaviour, the authority imposes harsher punishments on the poorer and/or ex ante dissident individual. Lighter punishments are imposed on the wealthier citizen to prevent “over-compliance”. Wealth inequality increases over time. Some citizens become prosperous “lackeys” while others become destitute from confiscation. In stable regimes with high state capacity, the authority reduces punishments and/or increases rewards to allow citizens to accumulate wealth, leading to social conformity and balanced growth in the long run. In unstable regimes with low capacity, the citizenry splits into groups of wealthy lackeys and destitute proles.
The diffusion of industrial robots in Europe: regional or country effect?
Authors: Nuccio Massimiliano , Guerzoni Marco , Cappelli Riccardo , Geuna Aldo
Published: November 2024

The paper investigates whether the penetration of advanced manufacturing technologies can be better explained at the regional or national level. If regional effects prevail, policy actions would focus on local investments, while if country effects make regional covariates redundant, they should be redirected to more structural reform of the national systems of innovation. In this respect, the contribution is 2-fold. First, data on acquisitions of industrial robots in the five largest European economies are rescaled at regional levels to draw a clear picture of winners and losers in the robotics race after the 2008 financial crisis. Second, we explain differential of growth rates in robot adoption with (1) traditional measures of industrial variety, (2) an unsupervised machine learning approach classifying a region’s industry profile (3) usual determinants of innovation and, thereafter test the robustness of the results when country effects are added. As the main result, we highlight a process of regional convergence in which country-fixed effects hold greater explanatory power, although related variety and the number of skilled people are statistically significant regional explanatory factors. We do not discover a specific industry mix associated with the rise of adoption, but we highlight the one associated with its decline.
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
Authors: Nanduri Sravani , Black Allison , Bedford Trevor , Huddleston John
Published: November 2024

Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis, multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS embeddings accurately represented pairwise genetic distances including the intermediate placement of recombinant SARS-CoV-2 lineages between parental lineages. Clusters from t-SNE embeddings accurately recapitulated known phylogenetic clades, H3N2 reassortment groups, and SARS-CoV-2 recombinant lineages. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.