bluuebunny/crossref_metadata_2025 huggingface dataset:
Hardware nanosecond‐precision timestamping for line‐rate packet capture
Authors: Huang Xiaoying
Published: January 2024

Cybersecurity events occur frequently. When it comes to investigating security threats, it is essential to offer a 100 percent accurate and packet‐level network history, which depends on packet capture with high precision packet timestamping. Many packet capture applications are developed based on data plane development kit (DPDK)—a set of libraries and drivers for fast packet processing. However, DPDK cannot give an accurate timestamp for every packet, and it is unable to truly reflect the order in which packets arrive at the network interface card. In addition, DPDK‐based applications cannot achieve zero packet loss when the packet is small such as 64 B for beyond 10 Gigabit Ethernet. Therefore, the authors proposed a new method based on Field‐Programmable Gate Array (FPGA) to solve this problem. The authors also develop a DPDK driver for FPGA devices to make the design compatible with all DPDK‐based applications. The proposed method performs timestamping at line‐rate for 10 Gigabit Ethernet traffic at 4 ns precision and 1 ns precision for 25 Gigabit, which greatly improves the accuracy of security incident retrospective analysis. Furthermore, the design can capture full‐size packets for any protocol with zero packet loss and can be applied to 40/100 Gigabit systems as well.
Multi‐dimensional evaluation and diagnostic methods for wind turbine power generation performance based on different influencing factors
Authors: Chen Qi , Wang Lin , Xie Shuzong , Zhan Yangyan , Wang Xin
Published: January 2024

The power generation performance of wind turbines has consistently been a paramount concern for wind power operators, maintainers, and manufacturers, as it directly determines the profitability of wind farms. However, due to the combined influence of complex environmental conditions within wind farms and inherent deficiencies in wind turbine design, significant variations in power generation performance persist among turbines of the same model. This discrepancy can be attributed to two crucial factors: site conditions and operational efficiency. To achieve more precise and systematic diagnostic work on the power generation performance of wind turbines, this paper focuses on three factors: air density, turbulence intensity, and yaw adaptability. Based on this, three evaluation and diagnosis methods are proposed, including a conversion method for air density based on two‐dimensional interpolation, a turbulence correction method based on the zero‐turbulence curve, and a yaw adaptability diagnosis method based on the convergence degree. Finally, the effectiveness of these proposed methods is verified through the analysis of actual wind field data.
EUS-guided hepaticogastrostomy versus percutaneous transhepatic biliary drainage after failed ERCP: A propensity score-matched analysis
Authors: Koutlas Nicholas J , Pawa Swati , Russell Greg , Ferris Taylor , Ponnatapura Janardhana , Pawa Rishi
Published: January 2024

Background and study aims Percutaneous transhepatic biliary drainage (PTBD) is the traditional second-line option after unsuccessful endoscopic retrograde cholangiopancreatography (ERCP). Endoscopic ultrasound-guided hepaticogastrostomy (EUS-HG) is a viable alternative to PTBD. Our study aimed to compare outcomes of EUS-HG and PTBD for benign and malignant biliary diseases following failed ERCP.

Patients and methods This single-center study retrospectively analyzed patients undergoing EUS-HG and PTBD for benign and malignant biliary disorders. A propensity score-matched analysis was performed using age, sex, and Charlson Comorbidity Index. The primary outcome was clinical success, which we defined as a decrease in total bilirubin by ≥ 50% at 2 weeks for malignant disease and resolution of the biliary disorder for benign disease.

Results In total, 41 patients underwent EUS-HG and 138 patients
underwent PTBD. After propensity score matching in a 1:2 ratio, 32 EUS-HG patients were
matched with 64 PTBD. Technical success was achieved in 29 of 32 (91%) for EUS-HG and 63 of 64
(98%) for PTBD (P=0.11). Clinical success was 100% for EUS-HG and
75% for PTBD (P=0.0021). EUS-HG was associated with a lower adverse
event rate (EUS-HG 13% vs. PTBD 58%, P <0.0001), shorter
procedure duration (median 60 vs. 115 minutes, P <0.0001),
shorter post-procedure length of stay (median 2 vs. 4 days, P
<0.0001), and fewer reinterventions (median 1 vs. 3, P
<0.0001).

Conclusions Our results suggest that EUS-HG is superior to PTBD in the treatment of benign and malignant biliary disorders after failed ERCP.
Adherence to quality indicators and best practices in surveillance endoscopy of Barrett’s esophagus: A video-based assessment
Authors: Enke Thomas , Keswani Rajesh , Triggs Joseph , Gannavarapu Bhargava , Mittal Chetan , Sinha Jasmine , Kwasny Mary J , Komanduri Srinadh
Published: January 2024

Background and study aims Adherence to quality indicators (QIs) and best practices (BPs) for endoscopic surveillance of Barrett’s esophagus (BE) is low based on clinical documentation which is an inaccurate representation of events occurring during procedures. This study aimed to assess adherence to measurable QI and BP using video evaluation.

Methods We performed a single center video-based retrospective review of surveillance endoscopies performed for BE ≥1 cm between March 1, 2018 and October 1, 2020. Adherence to QIs and BPs was assessed through video review and documentation. Videos were evaluated by five gastroenterologists. Interrater variability was determined using 10 videos before reviewing the remaining 128 videos. A generalized linear regression model was used to determine predictors of adherence to QIs and BPs.

Results There were 138 endoscopies reviewed. Inspection with virtual chromoendoscopy (VC) occurred in 75 cases (54%) on video review with documentation in 50 of these cases (67%). Adherence to the Seattle protocol (SP) occurred in 74 cases (54%) on video review with documentation in 28 of these cases (38%). Use of VC or the SP was documented but not observed on video review in 16 (12%) and 30 (22%) cases, respectively. Length of BE was associated with increased use of the Prague classification (odds ratio [OR] 1.21, 95% confidence interval [CI] 1.07–1.37) while years in practice was associated with a decreased likelihood of VC use (OR 0.93, 95% CI 0.88–0.99).

Conclusions This study validates prior data demonstrating poor adherence to QIs and BPs and highlights discrepancies between clinical documentation and events occurring during procedures.
Intercostal Nerve Cryoablation or Epidural Analgesia for Multimodal Pain Management after the Nuss Procedure: A Cohort Study
Authors: van Braak Hendrik , de Beer Sjoerd A. , de Jong Justin R. , Stevens Markus F. , Musters Gijsbert , Zwaveling Sander , Oomen Matthijs W. N. , der Made Wendeline Van , Krug Egbert , van Heurn L.W. Ernest
Published: January 2024

Background Nuss procedure for pectus excavatum is a minimally invasive, but painful procedure. Recently, intercostal nerve cryoablation has been introduced as a pain management technique.

Materials and Methods In this cohort study, we compared the efficacy of multimodal pain management strategies in children undergoing a Nuss procedure. The effectiveness of intercostal nerve cryoablation combined with patient-controlled systemic opioid analgesia (PCA) was compared with continuous epidural analgesia (CEA) combined with PCA. The study was conducted between January 2019 and July 2022. Primary outcome was length of stay (LOS), and secondary outcomes were operation room time, postoperative pain, opioid consumption, and gabapentin use.

Results Sixty-six consecutive patients were included, 33 patients in each group. The cryoablation group exhibited lower Numeric Rating Scale (NRS) pain scores on postoperative day 1 and 2 (p = 0.002, p = 0.001) and a shorter LOS (3 vs. 6 days (p < 0.001). Cryoablation resulted in less patients requiring opioids at discharge (30.3 vs. 97.0%; p < 0.001) and 1 week after surgery (6.1 vs. 45.4%; p < 0.001)). In the CEA group, gabapentin use was more prevalent (78.8 vs. 18.2%; p < 0.001) and the operation room time was shorter (119.4 vs. 135.0 minutes; p < .010). No neuropathic pain was reported.

Conclusions Intercostal nerve cryoablation is a superior analgesic method compared with CEA, with reduced LOS, opioid use, and NRS pain scores. The prophylactic use of gabapentin is redundant.
Retraction Note: A Spiritual View to the Huge Earthquake in Türkiye
Authors: Çaksen Hüseyin
Published: January 2024

Retraction

An investigation by the publisher found a number of articles, including this one, published in Journal of Child Science in Volume 13, Number 01, e62–e64, on May 04, 2023 (DOI: 10.1055/s-0043-1768636), with a number of concerns, including but not limited to undeclared conflicts of interest and manipulated peer review procedures. As a result, the publisher has retracted and removed this article.
User experiences with 360 brand videos: device experiences, presence, and creativity driving brand engagement
Authors: Butcher Luke , Sung Billy
Published: January 2024

Applications of 360 videos for brand storytelling and customer engagement are growing due to their immersive nature and novel sensory experiences, particularly when discovered through social media. These innovative digital media facilitate compelling experiences impacted by a user’s interaction with the medium and device, subsequently shaping how 360 videos achieve brand engagement. However, existing branding research ignores the user’s subjective experience of the device, does not consider how they assess the 360 brand video’s creativity, and typically examines brand outcomes that are not focal to brand managers for such a communication tool. To address these gaps, mediation analysis is undertaken for two distinct 360 brand videos experienced through a PC, Tablet, or VR device, incorporating psycho-physiological affective measures (arousal and pleasure). Findings highlight to brand managers the necessity to empirically assess the subjective experience a user has with the device and its influence on presence within the 360 video. We substantiate for the first time the mediating influence of the perceived creativity of a 360 brand video, and establish brand engagement outcomes relevant to how users respond to 360 videos.
Young democrats, critical citizens and protest voters: studying the profiles of movement party supporters
Authors: Santos Felipe G. , Mercea Dan
Published: January 2024

The rise of movement parties in Europe has disrupted traditional notions of party politics, introducing new avenues for citizen engagement and political mobilisation. This paper provides a comprehensive analysis of the electorate of movement parties, using nationally representative survey data from six European countries. We identify four types of movement parties: green/left-libertarian, far-right, eclectic, and centrist, and examine the distinct profiles of their voters. The only common characteristic we find across movement party supporters is their belief in the influence of protests. We argue that green/left-libertarian voters embody a generational gap in political participation, as they utilise both electoral and non-electoral engagement to express their post-industrial demands. Far-right voters are distinguished by their discontent with the democratic system and political elites, following the pattern of what others have referred to as 'protest voters'. Meanwhile, centrist and eclectic voters embody the profile of 'critical citizens', who support the democratic system but are dissatisfied with its current functioning. While we see movement parties as a genuine innovation in the internal structuring of party organisations, our study calls into question the utility of this concept when seeking to understand the behaviour of their electorate. We emphasise the importance of recognising the diverse motivations behind movement party support, enriching our understanding of the changing dynamics of party politics in Europe.
Assembling international society
Authors: Naylor Tristen
Published: January 2024

Producing a means of conceptualising and analysing international society as an assemblage, this article reflects on Adam Watson’s Evolution of International Society and demonstrates how an assemblage theory approach allows us to undertake Watson’s general aims to engage in broad, comparative analyses of international societies historically and produce a history of contemporary international society, but without the problematic biases and omissions that plague the empirical dimensions of his work. Understanding international society as an assemblage affords an ability to see that the endurance of so much of Western European international society in contemporary, global international society is owing to its particular form of assemblage. As a highly adaptive form of assemblage, what changes there might be in the international domain tend to occur within the assemblage, as the assemblage’s form renders both a substantive change of the assemblage and the establishment of any rival assemblage unlikely.
Australia and the Ukraine crisis: deterring authoritarian expansionism
Authors: Lee Lavina
Published: January 2024

This paper seeks to explain Australia’s reaction to Russia’s invasion of Ukraine and how it has affected Australia’s strategic decisions in responding to Chinese aggression in the Indo-Pacific. Canberra’s responses are consistent with the ‘dependent ally’ and the ‘middle power’ traditions in Australian foreign policy. The paper argues that these responses are framed by assessments that a competition and struggle between a democratic and authoritarian bloc is occurring; authoritarian values and approaches are key causes of instability and disruption to the post-World War II liberal rules-based order; and should Moscow achieve its objectives in Ukraine and beyond, there is an increased possibility that Beijing will be tempted to use similar coercive measures against Taiwan and other nations. Canberra is consequently putting even more emphasis on the US-Australia alliance, and groupings such as AUKUS and the Quad as central to collective democratic action to constrain and deter contrary authoritarian behaviours in the Indo- Pacific.
Transdisciplinary learning trajectories: developing action and attitude in interplay
Authors: Horn Annemarie , Visser Marijke W. , Pittens Carina A. C. M. , Urias Eduardo , Zweekhorst Marjolein B. M. , van Dijk Gerda M.
Published: January 2024

Addressing complex societal challenges requires professionals capable of integrating multiple perspectives on problems and possible solutions. This requires crossing disciplinary boundaries and boundaries between science and society. Transdisciplinary approaches respond to this demand by deliberately integrating knowledge of different disciplinary specialists and societal actors for a joint framing and co-creation of new options for addressing societal challenges. There is, however, limited understanding of which assets transdisciplinary work requires and how students can be trained in these. We studied transdisciplinary learning in the context of a novel course in which students engaged in multi-actor agenda-setting and facilitated multi-actor dialog sessions at a community event. We found that with the support of teachers and a detailed script, and by acquiring knowledge and skills through theoretical learning and exercises, students were able to facilitate safe and structured multi-stakeholder dialog sessions. Shifts towards a more transdisciplinary attitude were sparked by eye-opening experiences in transdisciplinary encounters if students processed these critically and openly. Based on our findings we propose “Transdisciplinary Learning Trajectories” which conceptualizes transdisciplinary learning as developing the ability to engage in transdisciplinary action and developing towards a transdisciplinary attitude. Based on our findings, we argue for a combination of experiential and instruction approaches that support learning in both dimensions, simultaneously and in interplay.
Perceived risk of child mortality and fertility choices in climate-vulnerable regions of Bangladesh
Authors: Ahmed Khandaker Jafor , Atiqul Haq Shah Md
Published: January 2024

This research examined the influence of perceived child mortality risk on the fertility choices of married women in Bangladesh. Employing a cross-sectional survey conducted in four rural areas, categorized as either vulnerable or not vulnerable to extreme climate events, a total of 759 married women were surveyed through simple random sampling, while 25 women were selected for in-depth interviews through judgment sampling. The findings indicate that women in climate-vulnerable regions express a greater desire for additional children compared to those in non-vulnerable areas. Furthermore, women who perceive increased child mortality risk and have experienced past child loss show a stronger tendency towards wanting more offspring. The qualitative insights from the interviews shed light on the underlying motivations driving these preferences, emphasizing the significance of child replacement and seeking security against potential child loss. These empirical findings provide valuable insights into the complex dynamics between perceptions of child mortality and reproductive decision-making among women in Bangladesh. The implications of this study are crucial for policymakers and practitioners, as they can guide the development of targeted interventions and policies to address reproductive health challenges in climate-vulnerable areas. By acknowledging women’s perspectives and considering contextual factors, these strategies can effectively address the reproductive implications of climate vulnerability, empowering women to make informed decisions about their fertility and promoting improved reproductive outcomes and overall well-being in vulnerable communities.
Retail mix instruments influencing customer perceived value and customer engagement: a conceptual framework and research agenda
Authors: Senachai Prarawan , Julagasigorn Puthipong
Published: January 2024

COVID-19 has transformed customer behavior, notably in FMCG retailers. Although online stores grow, retail mix instruments remain essential for traditional shops, as these affect customer value perceptions and engagement. While previous studies suggest that customer value perceptions and engagement are linked, little is known about the effects of retail mix instruments on customer value perceptions and engagement. This study aims to fill this knowledge gap. In this study, the stimulus-organism-response (S-O-R) framework was used to propose the a priori conceptual framework, which was further employed in investigating the phenomena and the three concepts: the impact of retail mix instruments (S) on consumer value perceptions (O) and customer engagement (R). Interviews were conducted with 40 informants recruited by convenience sampling and snowballing techniques. They were Gen-X and Gen-Y and had experience visiting two FMCG retailers in Thailand. A thematic analysis was undertaken to analyze the obtained data. The a priori conceptual framework had been revised iteratively according to the emerging theme, resulting in a new conceptual framework containing descriptive details in terms of significant themes identified from the field data and potential relationships among the three concepts. Findings revealed 12 retail mix instruments and the effect of COVID-19, which were found to affect six types of customer value perceptions, resulting in four customer engagement behaviors. The proposed conceptual framework, the study’s primary theoretical contribution of the study, is used to guide potential future research agenda. To suggest how FMCG retailers may leverage the proposed conceptual framework to design strategies to promote customer engagement behaviors, an application of sales promotions is illustrated and suggests how to use sales promotion activities to induce customer value perception and their engagements.
Motivating student voter registration
Authors: Michelson Melissa R. , DeMora Stephanie L. , Hayes Sarah V. , Osorio Maricruz A. , Carter Lashonda Renee , Jackson Jasmine C.
Published: January 2024

College student voter turnout reflects the degree to which students are being taught to support and protect democracy, long a core mission of the U.S. higher education system. Yet, college student voter turnout is generally very low. In 2020–2021, campuses around the country participated in a coordinated program to increase college student voter registration during the COVID-19 pandemic. Using survey and focus group data collected in spring 2021, we find evidence of understudied barriers to student registration that continue to restrict the effectiveness of those efforts. Specifically, we find that students need help determining whether or how to choose a political party affiliation and whether to register with their campus address. Efforts to help students surmount these understudied challenges are a potentially powerful means of increasing youth registration and turnout. We also find that students operated as knowledge brokers, sharing with family members the information they were receiving on campus about how to register and vote using new virtual options offered due to the pandemic.
Green finance, social inclusion, and sustainable economic growth in OECD member countries
Authors: Han Jian , Gao HaiYan
Published: January 2024

The importance of fostering a thriving green economy is emphasized as a key strategy for mitigating the threats posed by climate change. This study aims to assess the influence of social inclusion and green finance on the sustainable growth of 31 Organization for Economic Co-operation and Development (OECD) nations between 2010 and 2021. The results obtained using the fully modified OLS (FMOLS) methodology indicate that social factors such as poverty reduction and social inclusion do not impact the green economic prosperity of OECD countries with an industry-focused economic structure. Furthermore, the expansion of green finance markets and the attraction of foreign direct investment with an environmental focus can contribute to the advancement of green development in OECD countries. As a recommendation, it is advisable for OECD nations to place greater emphasis on developing the green digital finance market, exploring blockchain-based green finance solutions, fostering green foreign direct investment, and promoting early warning economic systems.
Raymond Leslie Martin 1926–2020
Authors: Martin Lisandra L.
Published: January 2024

Ray Martin (1926–2020) was a talented and successful academic and leader, who won numerous awards and made discoveries that changed fundamental knowledge of the sub-discipline of physical inorganic chemistry. His journey over more than 90 years is one that demonstrates that he was one of nature’s gentlemen, who enjoyed sports, arts and people. He was passionate about science and discovery, and through a series of chance events, had a peripatetic life moving from academic positions, to industry, management, a vice chancellorship at Monash University, and then scientific advisor to the Australian Federal Government. Throughout this journey, he always made strong friendships, was an exceptional teacher and outstanding mentor—he was a quiet achiever.
Pedagogical decisions in the teaching of segmentals and suprasegmentals
Authors: Gordon Joshua , Darcy Isabelle
Published: January 2024

This short article summarizes the pedagogical decisions behind the implementation of treatment in our 2022 study
(Gordon & Darcy, 2022). In this study, we provided explicit pronunciation
instruction to three groups of first-semester English-as-a-foreign-language (EFL) classes at a small university in Costa Rica. We
included a group trained on suprasegmental features and connected speech (Suprasegmental Group), a second group that received
instruction on vowels and consonants (Segmental Group), and a third group that received a combination of segmentals and
suprasegmentals as in the other two groups (Mixed Group). We collected speech samples in a pretest and a posttest, which were
rated by a group of L1-English speakers for comprehensibility, fluency, and accentedness. In this article, we provide details
about the selection of content, materials development, and the implementation of instruction in the three experimental groups in
our study.
Effects of Fc glycosylation on the activity of WNT mimetic agonistic antibodies
Authors: Chen Hui , Lee Sung-Jin , Ouyang Brian , Suen Nicholas , Ye Jay , Lu Chenggang , Li Yang
Published: January 2024

Monoclonal antibodies have been explored in a broad range of applications including receptor agonism. Given the importance of receptor conformation in signaling, the agonistic activity of antibodies that engage these receptors are influenced by many parameters. Tetravalent bispecific antibodies that target the frizzled and lipoprotein receptor-related protein receptors and subsequently activate WNT (“Wingless-related integration site” or “Wingless and Int-1” or “Wingless-Int”) signaling have been constructed. Because WNT activation stimulates stem cell proliferation and tissue regeneration, immune effector functions should be eliminated from therapeutic antibodies targeting this pathway. Here, we report an unexpected effect of Fc glycosylation on the agonistic activity of WNT mimetic antibodies. Our findings underscore the importance of antibody format, geometry and epitope in agonistic antibody design, and highlight the need to establish appropriate early discovery screening strategies to identify hits for further optimization.
Effects of study design parameters on estimates of bee abundance and richness in agroecosystems: a meta-analysis
Authors: Levenson Hannah K , Metz Bradley N , Tarpy David R
Published: January 2024

Pollinators are critical for agricultural production and food security, leading to many ongoing surveys of pollinators (especially bees) in crop and adjacent landscapes. These surveys have become increasingly important to better understand the community of potential pollinators, quantify relative insect abundance, and secure crop ecosystem services. However, as some bee populations are declining, there is a need to align and improve bee survey efforts, so that they can best meet research and conservation goals, particularly in light of the logistical and financial constraints of conducting such studies. Here, we mined the existing literature on bee surveys in or around agricultural lands to better understand how sampling methods can be optimized to maximize estimates of 2 key measures of bee communities (abundance and richness). After reviewing 72 papers spanning 20 yr of publication, we found that study duration, number of sites, sampling time, and sampling method most significantly influenced abundance, while the number of trips per year and collection method significantly influenced richness. Our analysis helps to derive thresholds, priorities, and recommendations that can be applied to future studies describing bee communities in agroecosystems.
What are the priorities for research of older people living in their own home, including those living with frailty? A systematic review and content analysis of studies reporting older people’s priorities and unmet needs
Authors: Graham Liz , Brundle Caroline , Harrison Nicola , Andre Deirdre , Clegg Andrew , Forster Anne , Spilsbury Karen
Published: January 2024

Background

There is limited evidence regarding the needs of older people, including those living with frailty, to inform research priority setting.

Objectives

This systematic review aimed to identify the range of research priorities of community-dwelling older people living in their own home, including those living with frailty.

Methods

Included studies were from economically developed countries and designed to identify the priorities for research or unmet needs of community-dwelling older people. Studies were excluded if they described priorities relating to specific health conditions. Medline, Embase, PsycInfo and CINAHL were searched (January 2010–June 2022), alongside grey literature. Study quality was assessed, but studies were not excluded on the basis of quality. A bespoke data extraction form was used and content analysis undertaken to synthesise findings.

Results

Seventy-five reports were included. Seven explicitly aimed to identify the priorities or unmet needs of frail older people; 68 did not specify frailty as a characteristic. Study designs varied, including priority setting exercises, surveys, interviews, focus groups and literature reviews. Identified priorities and unmet needs were organised into themes: prevention and management, improving health and care service provision, improving daily life, meeting carers’ needs and planning ahead.

Discussion

Many priority areas were raised by older people, carers and health/care professionals, but few were identified explicitly by/for frail older people. An overarching need was identified for tailored, collaborative provision of care and support.

Conclusion

Review findings provide a valuable resource for researchers and health/care staff wishing to focus their research or service provision on areas of importance for older people.
Implementation of clopidogrel pharmacogenetic clinical decision support for a preemptive return of results program
Authors: Aquilante Christina L , Trinkley Katy E , Lee Yee Ming , Crooks Kristy R , Hearst Emily C , Heckman Simeon M , Hess Kaitlyn W , Kudron Elizabeth L , Martin James L , Swartz Carolyn T , Kao David P
Published: January 2024

Purpose

To describe our experiences implementing and iterating CYP2C19 genotype–guided clopidogrel pharmacogenetic clinical decision support (CDS) tools over time in the setting of a large health system–wide, preemptive pharmacogenomics program.

Clopidogrel-treated patients who are genetically predicted cytochrome P450 isozyme 2C19 (CYP2C19) intermediate or poor metabolizers have an increased risk of atherothrombotic events, some of which can be life-threatening. The Clinical Pharmacogenetics Implementation Consortium provides guidance for the use of clopidogrel based on CYP2C19 genotype in patients with cardiovascular and cerebrovascular diseases. Our multidisciplinary team implemented an automated, interruptive alert that fires when clopidogrel is ordered or refilled for biobank participants with structured CYP2C19 intermediate or poor metabolizer genomic indicators in the electronic health record. The implementation began with a narrow cardiovascular indication and setting and was then scaled in 4 primary dimensions: (1) clinical indication; (2) availability across health-system locations; (3) care venue (e.g., inpatient vs outpatient); and (4) provider groups (eg, cardiology and neurology). We iterated our approach over time based on evolving clinical evidence and proactive strategies to optimize CDS maintenance and sustainability. A key facilitator of expansion was socialization of the broader pharmacogenomics initiative among our academic medical center community, accompanied by clinician acceptance of pharmacogenetic alerts in practice.

Conclusion

A multidisciplinary collaboration is recommended to facilitate the use of CYP2C19 genotype–guided antiplatelet therapy in patients with cardiovascular and cerebrovascular diseases. Evolving clopidogrel pharmacogenetic evidence necessitates thoughtful iteration of implementation efforts and strategies to optimize long-term maintenance and sustainability.
Patterns ofGrewia(Malvaceae) diversity across geographical scales in Africa and Madagascar
Authors: Karimi Nisa , Hanes Margaret M
Published: January 2024

Background and Aims

Quantifying spatial species richness is useful to describe biodiversity patterns across broad geographical areas, especially in large, poorly known plant groups. We explore patterns and predictors of species richness across Africa in one such group, the palaeotropical genus Grewia L. (Malvaceae).

Methods

Grewia species richness was quantified by extracting herbarium records from GBIF and Tropicos and creating geographical grids at varying spatial scales. We assessed predictors of species richness using spatial regression models with 30 environmental variables. We explored species co-occurrence in Madagascar at finer resolutions using Schoener’s index and compared species range sizes and International Union for Conservation of Nature status among ecoregions. Lastly, we derived a trait matrix for a subset of species found in Madagascar to characterize morphological diversity across space.

Key Results

Grewia species occur in 50 countries in Africa, with the highest number of species in Madagascar (93, with 80 species endemic). Species richness is highest in Madagascar, with ≤23 Grewia species in a grid cell, followed by coastal Tanzania/Kenya (≤13 species) and northern South Africa and central Angola (11 species each). Across Africa, higher species richness was predicted by variables related to aridity. In Madagascar, a greater range in environmental variables best predicted species richness, consistent with geographical grid cells of highest species richness occurring near biome/ecoregion transitions. In Madagascar, we also observe increasing dissimilarity in species composition with increasing geographical distance.

Conclusions

The spatial patterns and underlying environmental predictors that we uncover in Grewia represent an important step in our understanding of plant distribution and diversity patterns across Africa. Madagascar boasts nearly twice the Grewia species richness of the second most species-rich country in Africa, which might be explained by complex topography and environmental conditions across small spatial scales.
Correction of Rectus Abdominis Diastasis: A Prospective Comparative Study Between a New Suturable Polypropylene Mesh vs Polypropylene Standard Suture Plication
Authors: Marangi Giovanni Francesco , Gratteri Marco , Savani Luca , Porso Daniela , Cimmino Andrea , Arcari Lucrezia , Romano Fara Desiree , Segreto Francesco , Mirra Carlo , Persichetti Paolo
Published: January 2024

Background

Duramesh (Mesh Suture Inc., Chicago, IL) is a new suturing concept, combining the principles of mesh with the precision, flexibility, and versatility of a suture, suitable also for abdominal rectus diastasis (ARD) correction.

Objectives

This prospective research aimed to compare mesh with the standard polypropylene suture plication for rectus diastasis repair with regard to safety (infection, seroma, hematoma, surgical wound dehiscence, and fistula rates and hospital stay); effectiveness (ARD recurrence by ultrasound sonography, palpability of the muscular suture, surgical time, and postoperative pain evaluation); and satisfaction of the patients based on the BODY-Q, a patient-reported outcome measure.

Methods

Sixty-five of the initial 70 patients who underwent rectus diastasis repair with a 6-month follow-up were randomly divided into 2 groups, comprising 33 patients treated with Duramesh and 32 patients treated with standard 0 polypropylene suture plication. Data regarding infection, seroma, hematoma, surgical wound dehiscence, and fistula rates; hospital stay; ARD recurrence; palpability of the muscular suture; surgical time; postoperative pain evaluation (measured by visual analog scale, or VAS); and the BODY-Q were analyzed by Prism 9 (GraphPad Software Inc., San Diego, CA).

Results

No significant differences were reported between the 2 groups with regard to infection, seroma, hematoma, surgical wound dehiscence, and fistula rates and hospital stay. The mesh decreased the time required to perform plication compared with standard polypropylene detached sutures. No statistically significant differences were found with respect to the VAS and BODY-Q data.

Conclusions

Duramesh 0 application for rectus diastasis repair is safe and effective without compromising aesthetic improvement when compared with standard 0 polypropylene plication.

Level of Evidence: 2
Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep
Authors: Liu Teng , Fang Zhaoyu , Li Xin , Zhang Lining , Cao Dong-Sheng , Li Min , Yin Mingzhu
Published: January 2024

Motivation

Spatial clustering is essential and challenging for spatial transcriptomics’ data analysis to unravel tissue microenvironment and biological function. Graph neural networks are promising to address gene expression profiles and spatial location information in spatial transcriptomics to generate latent representations. However, choosing an appropriate graph deep learning module and graph neural network necessitates further exploration and investigation.

Results

In this article, we present GRAPHDeep to assemble a spatial clustering framework for heterogeneous spatial transcriptomics data. Through integrating 2 graph deep learning modules and 20 graph neural networks, the most appropriate combination is decided for each dataset. The constructed spatial clustering method is compared with state-of-the-art algorithms to demonstrate its effectiveness and superiority. The significant new findings include: (i) the number of genes or proteins of spatial omics data is quite crucial in spatial clustering algorithms; (ii) the variational graph autoencoder is more suitable for spatial clustering tasks than deep graph infomax module; (iii) UniMP, SAGE, SuperGAT, GATv2, GCN, and TAG are the recommended graph neural networks for spatial clustering tasks; and (iv) the used graph neural network in the existent spatial clustering frameworks is not the best candidate. This study could be regarded as desirable guidance for choosing an appropriate graph neural network for spatial clustering.

Availability and implementation

The source code of GRAPHDeep is available at https://github.com/narutoten520/GRAPHDeep. The studied spatial omics data are available at https://zenodo.org/record/8141084.
DESpace: spatially variable gene detection via differential expression testing of spatial clusters
Authors: Cai Peiying , Robinson Mark D , Tiberi Simone
Published: January 2024

Motivation

Spatially resolved transcriptomics (SRT) enables scientists to investigate spatial context of mRNA abundance, including identifying spatially variable genes (SVGs), i.e. genes whose expression varies across the tissue. Although several methods have been proposed for this task, native SVG tools cannot jointly model biological replicates, or identify the key areas of the tissue affected by spatial variability.

Results

Here, we introduce DESpace, a framework, based on an original application of existing methods, to discover SVGs. In particular, our approach inputs all types of SRT data, summarizes spatial information via spatial clusters, and identifies spatially variable genes by performing differential gene expression testing between clusters. Furthermore, our framework can identify (and test) the main cluster of the tissue affected by spatial variability; this allows scientists to investigate spatial expression changes in specific areas of interest. Additionally, DESpace enables joint modeling of multiple samples (i.e. biological replicates); compared to inference based on individual samples, this approach increases statistical power, and targets SVGs with consistent spatial patterns across replicates. Overall, in our benchmarks, DESpace displays good true positive rates, controls for false positive and false discovery rates, and is computationally efficient.

Availability and implementation

DESpace is freely distributed as a Bioconductor R package at https://bioconductor.org/packages/DESpace.
scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution
Authors: Chen Zeyu , Miao Yuxin , Tan Zhiyuan , Hu Qifan , Wu Yanhong , Li Xinqi , Guo Wenbo , Gu Jin
Published: January 2024

Single-cell RNA-seq (scRNA-seq) is a powerful technique for decoding the complex cellular compositions in the tumor microenvironment (TME). As previous studies have defined many meaningful cell subtypes in several tumor types, there is a great need to computationally transfer these labels to new datasets. Also, different studies used different approaches or criteria to define the cell subtypes for the same major cell lineages. The relationships between the cell subtypes defined in different studies should be carefully evaluated. In this updated package scCancer2, designed for integrative tumor scRNA-seq data analysis, we developed a supervised machine learning framework to annotate TME cells with annotated cell subtypes from 15 scRNA-seq datasets with 594 samples in total. Based on the trained classifiers, we quantitatively constructed the similarity maps between the cell subtypes defined in different references by testing on all the 15 datasets. Secondly, to improve the identification of malignant cells, we designed a classifier by integrating large-scale pan-cancer TCGA bulk gene expression datasets and scRNA-seq datasets (10 cancer types, 175 samples, 663 857 cells). This classifier shows robust performances when no internal confidential reference cells are available. Thirdly, scCancer2 integrated a module to process the spatial transcriptomic data and analyze the spatial features of TME.

Availability and implementation

The package and user documentation are available at http://lifeome.net/software/sccancer2/ and https://doi.org/10.5281/zenodo.10477296.
Many-core algorithms for high-dimensional gradients on phylogenetic trees
Authors: Gangavarapu Karthik , Ji Xiang , Baele Guy , Fourment Mathieu , Lemey Philippe , Matsen Frederick A , Suchard Marc A
Published: January 2024

Motivation

Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations.

Results

We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable.

Availability and implementation

We provide an implementation of our GPU algorithms in BEAGLE v4.0.0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).
A note on minimax robustness of designs against correlated or heteroscedastic responses
Authors: Wiens D P
Published: January 2024

We present a result according to which certain functions of covariance matrices are maximized at scalar multiples of the identity matrix. This is used to show that experimental designs that are optimal under an assumption of independent, homoscedastic responses can be minimax robust, in broad classes of alternate covariance structures. In particular, it can justify the common practice of disregarding possible dependence, or heteroscedasticity, at the design stage of an experiment.
LT and SOX9 expression are associated with gene sets that distinguish Merkel cell polyomavirus (MCPyV)-positive and MCPyV-negative Merkel cell carcinoma
Authors: Torre-Castro Juan , Rodríguez Marta , Alonso-Alonso Ruth , Mendoza Cembranos María Dolores , Díaz-Alejo Jesús Frutos , Rebollo-González Marcos , Borregón Jennifer , Nájera Botello Laura , Mahillo-Fernández Ignacio , Samimi Mathab , Kervarrec Thibault , Requena Luis , Piris Miguel Ángel
Published: January 2024

Background

Merkel cell carcinoma (MCC) is an aggressive malignant neuroendocrine tumour. There are two subsets of MCC, one related to Merkel cell polyomavirus (MCPyV) and the other to ultraviolet radiation (UVR). MCPyV-positive and MCPyV-negative MCCs have been considered to be different tumours, as the former harbour few DNA mutations and are not related to UVR, and the latter usually arise in sun-exposed areas and may be found in conjunction with other keratinocytic tumours, mostly squamous cell carcinomas. Two viral oncoproteins, large T antigen (LT; coded by MCPyV_gp3) and small T antigen (sT; coded by MCPyV_gp4), promote different carcinogenic pathways.

Objectives

To determine which genes are differentially expressed in MCPyV-positive and MCPyV-negative MCC; to describe the mutational burden and the most frequently mutated genes in both MCC subtypes; and to identify the clinical and molecular factors that may be related to patient survival.

Methods

Ninety-two patients with a diagnosis of MCC were identified from the medical databases of participating centres. To study gene expression, a customized panel of 172 genes was developed. Gene expression profiling was performed with nCounter technology. For mutational studies, a customized panel of 26 genes was designed. Somatic single nucleotide variants (SNVs) were identified following the GATK Best Practices workflow for somatic mutations.

Results

The expression of LT enabled the series to be divided into two groups (LT positive, n = 55; LT negative, n = 37). Genes differentially expressed in LT-negative patients were related to epithelial differentiation, especially SOX9, or proliferation and the cell cycle (MYC, CDK6), among others. Congruently, LT displayed lower expression in SOX9-positive patients, and differentially expressed genes in SOX9-positive patients were related to epithelial/squamous differentiation. In LT-positive patients, the mean SNV frequency was 4.3; in LT-negative patients it was 10 (P = 0.03). On multivariate survival analysis, the expression of SNAI1 [hazard ratio (HR) 1.046, 95% confidence interval (CI) 1.007–1.086; P = 0.02] and CDK6 (HR 1.049, 95% CI 1.020–1.080; P = 0.001) were identified as risk factors.

Conclusions

Tumours with weak LT expression tend to co-express genes related to squamous differentiation and the cell cycle, and to have a higher mutational burden. These findings are congruent with those of earlier studies.