bluuebunny/crossref_metadata_2025 huggingface dataset:
Checking correctness in mathematical peer review
Authors: Greiffenhagen Christian
Published: September 2023

Mathematics is often treated as different from other disciplines, since arguments in the field rely on deductive proof rather than empirical evidence as in the natural sciences. A mathematical paper can therefore, at least in principle, be replicated simply by reading it. While this distinction is sometimes taken as the basis to claim that the results in mathematics are therefore certain, mathematicians themselves know that the published literature contains many mistakes. Reading a proof is not easy, and checking whether an argument constitutes a proof is surprisingly difficult. This article uses peer review of submissions to mathematics journals as a site where referees are explicitly concerned with checking whether a paper is correct and therefore could be published. Drawing on 95 qualitative interviews with mathematics journal editors, as well as a collection of more than 100 referee reports and other correspondence from peer review processes, this article establishes that while mathematicians acknowledge that peer review does not guarantee correctness, they still value it. For mathematicians, peer review ‘adds a bit of certainty’, especially in contrast to papers only submitted to preprint servers such as arXiv. Furthermore, during peer review there can be disagreements not just regarding the importance of a result, but also whether a particular argument constitutes a proof or not (in particular, whether there are substantial gaps in the proof). Finally, the mathematical community is seen as important when it comes to accepting arguments as proofs and assigning certainty to results. Publishing an argument in a peer-reviewed journal is often only the first step in having a result accepted. Results get accepted if they stand the test of time and are used by other mathematicians.
Spatio-Temporal Graph Neural Network for Traffic Prediction Based on Adaptive Neighborhood Selection
Authors: Sun HuanZhong , Tang XiangHong , Lu JianGuang , Liu FangJie
Published: September 2023

Traffic prediction is critical to intelligent transportation and smart cities. The prediction performance of many existing traffic prediction models is limited by the fixed original graph structure and inappropriate spatio-temporal dependency extraction. For this situation, this paper proposes a spatio-temporal graph neural network based on adaptive neighborhood selection (STGNN-ANS). To obtain more flexible graph structures, STGNN-ANS designs a neighbor selection mechanism to generate a new graph structure by filtering inappropriate neighbors. To further capture the spatio-temporal dependence of traffic data, a spatio-temporal serial module of STGNN-ANS adopts the bidirectional learning manner of bidirectional long short-term memory (BiLSTM) and the graph convolution network (GCN) enhanced by self-attention mechanism to reach excellent prediction accuracy in both short-range and long-range scenarios. In this paper, a new baseline comprehensive comparison metric (BCCM) is invented to cope with the complexity in the comparative analysis of large numbers of experimental results. Many experiments have been performed on four real-world traffic datasets, and the results show that the comprehensive prediction performance of STGNN-ANS is better than previous models.
Effects of curcumin and ursolic acid in prostate cancer: A systematic review
Authors: Besasie Benjamin D , Saha Achinto , DiGiovanni John , Liss Michael A
Published: September 2023

The major barriers to phytonutrients in prostate cancer therapy are non-specific mechanisms and bioavailability issues. Studies have pointed to a synergistic combination of curcumin (CURC) and ursolic acid (UA). We investigate this combination using a systematic review process to assess the most likely mechanistic pathway and human testing in prostate cancer. We used the PRISMA statement to screen titles, abstracts, and the full texts of relevant articles and performed a descriptive analysis of the literature reviewed for study inclusion and consensus of the manuscript. The most common molecular and cellular pathway from articles reporting on the pathways and effects of CURC ( n = 173) in prostate cancer was NF-κB ( n = 25, 14.5%). The most common molecular and cellular pathway from articles reporting on the pathways and effects of UA ( n = 24) in prostate cancer was caspase 3/caspase 9 ( n = 10, 41.6%). The three most common molecular and cellular pathway from articles reporting on the pathways and effects of both CURC and UA ( n = 193) in prostate cancer was NF-κB ( n = 28, 14.2%), Akt ( n = 22, 11.2%), and androgen ( n = 19, 9.6%). Therefore, we have identified the potential synergistic target pathways of curcumin and ursolic acid to involve NF-κB, Akt, androgen receptors, and apoptosis pathways. Our review highlights the limited human studies and specific effects in prostate cancer.
Managing the Chronically Ventilated Critically Ill Population
Authors: Chichra Astha , Tickoo Mayanka , Honiden Shyoko
Published: October 2023

Advances in intensive care over the past few decades have significantly improved the chances of survival for patients with acute critical illness. However, this progress has also led to a growing population of patients who are dependent on intensive care therapies, including prolonged mechanical ventilation (PMV), after the initial acute period of critical illness. These patients are referred to as the “chronically critically ill” (CCI). CCI is a syndrome characterized by prolonged mechanical ventilation, myoneuropathies, neuroendocrine disorders, nutritional deficiencies, cognitive and psychiatric issues, and increased susceptibility to infections. It is associated with high morbidity and mortality as well as a significant increase in healthcare costs. In this article, we will review disease burden, outcomes, psychiatric effects, nutritional and ventilator weaning strategies as well as the role of palliative care for CCI with a specific focus on those requiring PMV.
Implementation of Management Policy for Healthcare Facility to Respond COVID-19 Pandemic in West Java
Authors: Siagian Marion
Published: September 2023

This research describes organisation, interpretation and application of the legal policies in healthcare management as the response to the COVID-19 pandemic in West Java. This research used a descriptive method with a qualitative approach. Data collection was carried out with a study of documentation and forum group discussions. Data analysis technique employed the interactive model by Miles, M. B. (process of collecting, condensing, and presenting data, as well as drawing conclusions). In response to the COVID-19 pandemic in West Java, it was carried out by forming the Healthcare Facility Management Division under Acceleration Task Force. The policy was interpreted by establishing a plan to assess the requirements for additional capacity and healthcare workers by referring to the prediction of the increased number of patients using the SimCOVID model. Implementation of management policy for healthcare facilities in West Java has been carried out through organisation, interpretation, and application.
Advocacy and the Search for Truth in Management Scholarship: Can the Twain Ever Meet?
Authors: Wright Thomas A. , Emich Kyle , Pearce Jone L. , Ramoglou Stratos , Ashkanasy Neal , Bartunek Jean M. , Kunisch Sven , Denyer David , Foss Nicolai J. , Klein Peter G. , Town Sophia , Hollwitz John , Barney Chet E. , Harms Peter , Munyon Timothy P. , Seijts Gerard , Tsang Eric W.K.
Published: October 2023

Scholars have long debated the merits of advocacy-based research versus research considered from the quest for objective truth. Building upon reflections from multiple sources, a set of 11 brief reflections on three posed questions are presented. Tsang concludes our discussion with additional insights on how moving beyond the “interestingness” advocacy will be beneficial to the continued professional development of the management discipline.
The Impact of Ketamine for Treatment of Post-Traumatic Stress Disorder: A Systematic Review With Meta-Analyses
Authors: Sicignano Dakota J. , Kurschner Ryan , Weisman Nissen , Sedensky Ava , Hernandez Adrian V. , White C. Michael
Published: September 2023

Background:

Ketamine has been used in anesthesia, pain management, and major depressive disorder. It has recently been studied in patients with post-traumatic stress disorder (PTSD).

Objective:

To determine the impact of ketamine on PTSD symptomatology and depression scores.

Methods:

We conducted a literature search of Medline 1960 to May 20, 2023, and found 6 randomized controlled trials that met our inclusion criteria. We extracted data on the Clinician-Administered PTSD (CAPS), PTSD Checklist (PCL), or Montgomery-Asberg Depression Rating (MADRS) scales.

Results:

The use of ketamine significantly reduced CAPS scores (n = 5, MD: −10.63 [95% CI −14.95 to −6.32]), PCL scores (n = 3, MD: −6.13 [95% CI −8.61 to −3.64]), and MADRS scores (n = 3, MD: −6.33 [95% CI −8.97 to −3.69]) at the maximal follow-up times versus control. Significant benefits were found at day 1 and weeks 1, 2, and 4 for CAPS and PCL scores as well as MADRS scores at day 1, week 1, and week 4 for ketamine versus control. The time to PTSD relapse was prolonged in the patients receiving ketamine versus control (n = 2, 15.74 days [95% CI 3.57 to 29.91 days]). More dry mouth (n = 2, OR 5.85 [95% CI 1.32 to 25.95]), dizziness (n = 2, OR 3.83 [95% CI 1.28 to 11.41]), and blurred vision (n = 2, OR 7.57 [1.00 to 57.10]) occurred with ketamine than control therapy.

Conclusions and Relevance:

Ketamine modestly reduced PTSD and depression scores as early as 1 day of therapy, but the longevity of effect needs to be determined. Given similar magnitude of benefit with SSRIs and venlafaxine, ketamine would not supplant these traditional options for chronic use.
Tracking Needs-Based Community and Specialized Services of Young Adults and Their Parents Before and During a First Episode of Psychosis (FEP): Highlighting Intervention Trajectories in FEP
Authors: Morin Marie-Hélène , Proulx Maryse
Published: September 2023

Aim:

This article aims to document 10 service trajectories of young adults (YA) and their parents, informed by healthcare professionals (HP), before and during a first episode of psychosis (FEP).

Design:

Based on a crisis model perspective of the Life Course Theory (Elder; Elder and Shanahan) developed by Carpentier and White, and adapted to the current context to track community and specialized services trajectories. Thematic analysis was used to code responses to open-ended questions around the need for help and accessing services by young adults affected by a psychotic disorder, and their parents.

Setting:

In collaboration with FEP clinics, setting of choice by YA and their parents.

Participants:

5 YA, 12 parents, and 6 HP.

Results:

10 individual service trajectories grouped into 3 distinct types of trajectories (optimal, typical, and complex) based on grouping 5 similar characteristics, highlighting service access complexity and early intervention in FEP.

Conclusion:

This study is the first of its kind to examine the experiences of those who seek needs-based community and specialized services leading up to and during a FEP. Findings provide key insights related to early intervention in FEP and recommendations on improving access to such services in Quebec.
Maintaining and challenging conservative teaching and learning culture in conservatories: The need for holistic pedagogy in educational fields of tension
Authors: Almqvist Cecilia Ferm , Werner Ann
Published: September 2023

When the need of transforming and remixing music education is illuminated, fields of tensions in relation to the traditional master–apprentice model of teaching often appear. Binaries have been constructed and critiqued in research to describe tensions at various music educational levels. Some studies have also asked for a holistic, “both/and” holding. In higher music education (HME), the need for new approaches in research to understand how teaching and learning is developing are asked for. As a contribution, the overall aim of the article is to illuminate to what extent traditional culture norms and structures are maintained and challenged at three European conservatories. The specific aim is to map possible fields of tension surrounding approaches to teaching and related learning. The analysis in this article partly builds on understandings of culture and institutions, and partly on theories of relational pedagogy. To get access to how leaders, teachers, and students experience participating in the teaching and learning of conservatory cultures, an interview study was planned. The transcriptions were treated by a thematic analysis model. The analysis explored three themes that represent fields of tension: teaching in relation to established cultural structures, to create or not create new learning trajectories, and collaboration or competition—the educational culture. The fields of tension found through the analysis concern relations between the traditional conserved conservatory teaching and new open and diverse thoughts about and actions within in HME teaching. It becomes obvious that creating new learning trajectories should be a common issue, involving students and teachers, as well as leaders of conservatories, and that competition should be supported by collaboration. A consequence of such a pedagogical approach would be that differences between programs for diverse instruments could be balanced, and that all involved could learn from each other, which demands flexibility between individual and collaborative learning activities.
Conscientisation and Communities of Compost: Rethinking management pedagogy in an age of climate crises
Authors: Dallyn Sam , Checchi Marco , Prado Patricia , Munro Iain
Published: September 2023

The unprecedented scale of the climate crisis has led to a questioning of conventional approaches to sustainability in management education, centred around business case for sustainability narratives. Such critique gives rise to serious questions around how we approach teaching the universality of the climate crisis, species extinction and biodiversity loss differently. Working with Freire’s stress on the political role of the educator, action rooted in the concrete and the interconnections he establishes between pedagogy and political organisation, our contribution is to connect these interventions with Haraway’s call to stay ‘with the trouble’ and generate Communities of Compost – that is, collective more than human communities of multi-species flourishing. In doing so, we propose threading together ecocentric and political economy approaches in management education, to present an alternative to corporate sustainability solutionism and to politically rethink scalar mismatches – that is when problems and proposed ‘solutions’ to the climate crisis apply to different sets of relations. As a way of addressing this, we develop pedagogical practices around Haraway’s multi-species Communities of Compost and combine this with the political movement of La Via Campesina – focusing on its campaigns for agroecology and food sovereignty.
The travelogue cooking show in a sub-state nation: Representing Scotland in British food television
Authors: Knight Christine , Tominc Ana
Published: September 2023

Food television offers a new and unique lens on national identity, the Anglo-Scottish relationship, and their cultural representation in contemporary Britain. This article is based on the analysis of three British travelogue cooking shows, first broadcast between 1995 and 2011, about Scotland and its food. The programmes analysed exemplify and reinforce long-standing cultural constructions of the relationship between England and Scotland as sub-state nations of the United Kingdom, as well as illustrating and creating new national scripts, notably in relation to class and gender. These ‘homeland’ travelogue cooking shows consistently associate Scotland with a defined set of local and traditional foods, closely associated with a Romantic construction of Scotland, its history and landscape. However, the programmes also indicate wider changes in British and Scottish food culture during this period, including the rise of the local food movement and the increasing economic success and cultural confidence of the Scottish food and drink industry. The article highlights the role of celebrity chefs in the cultural construction of contemporary British sub-state national relationships.
Consociational politics as a mediating effect in strengthening ethnic unity among youth in Malaysian public universities
Authors: Wan Husin WN , Samsudin NI , Mujani WK , Zainurin SJ
Published: September 2023

This study analyses the role of consociational politics as a mediating effect in enhancing ethnic unity among youth in Malaysia, with reference to the university students, through educational policy, economic system and religious practice. The research focuses on ethnicity due to its persistent influence on election outcomes over the previous two decades. Besides, a significant number of voters choose to base their political choices on the party that resonate with their ethnic interests. For this study, it involved a survey of 373 students from two Malaysian public universities, namely University of Malaya and the National Defence University of Malaysia. The obtained data are subjected to descriptive analysis as well as structural equation modelling (SEM) analysis. The results indicate that all three domains are significant in strengthening ethnic unity among youth, and this finding has national significance since it demonstrates the efficacy of this strategy in safeguarding Malaysia's diverse population The study's findings demonstrate that the grand coalition, as a fundamental component of consociational politics, possesses the capacity to cultivate a political alliance comprising many ethnic groupings, ultimately earning the confidence of the broader populace, particularly the younger generation. This facilitates the ascendance of a politically diverse party with individuals from various ethnic backgrounds to take over governance of the nation. Hence, the successful promotion of racial peace among the youth in Malaysia can be attributed to the implementation of a consociational strategy within the country.
Experimental investigation on the hydro-acoustic characteristics of tandem cylinders with equal diameters
Authors: Bulut Sertaç , Ergin Selma
Published: September 2023

The investigation of the hydro-acoustic characteristics of tandem cylinders has a great importance because they occur in a variety of maritime applications that include submarines, offshore structures and seabed pipelines systems. Better understanding of the noise generation mechanism of tandem cylinders provides great contribution to reduce noise levels for many engineering applications. In this study, the hydro-acoustic characteristics of tandem cylinders with same diameter were experimentally investigated for five different distance ratios at Reynolds number of 1.6 × 104. The diameter of the front and rear cylinders used in hydro-acoustic experiments is 0.02 m. It is observed that the main peak spectrum becomes narrower as the distance ratio increases. The width of the main peak spectrum also decreases as the flow regime transition from the reattachment regime to the separation regime. An increase in the distance ratio is found to correspond to an increase in the main peak frequency. The maximum sound pressure level is observed to attain its peak value at the critical distance ratio of 3.0. Notably, the maximum sound pressure level exhibits a substantial increase of approximately 6 dB as the distance ratio increases from 1.5 to 3.0, followed by a subsequent decrease of approximately 1 dB between the distance ratios of 3.0 and 6.0.
Gender and Genre in Hannah Gadsby’s Nanette
Authors: Day Amber
Published: September 2023

This article argues that Hannah Gadsby’s 2018 Netflix stand-up special Nanette bundles a critique of the comedy industry and of gendered violence through genre transformations that expand the public sphere for survivor testimony. Though Gadsby was not the first to broach these topics in a public forum, she did so at a moment when audiences were primed to be newly receptive. While there was predictably some backlash from audience members who maintained that the special should not be considered comedy, there was also a fierce outpouring of enthusiasm. Nanette became a text with which one could publicly identify (or dis-identify), particularly around the framing of sexual violence and trauma, reminding us that we need popular cultural touchstones through which to shift the conversation. It may also be symptomatic of a widening of the range of perspectives and subject positions with which mainstream audiences are willing to sympathize.
Pregnant and lactating people’s strategies to mitigate the risk of cannabis consumption
Authors: Popoola Anuoluwa , Panday Janelle , Taneja Shipra , Greyson Devon , McDonald Sarah D. , Patel Tejal , Darling Elizabeth , Vanstone Meredith
Published: September 2023

Background:

Multiple studies have demonstrated that pregnant and lactating people who use cannabis perceive a variety of benefits from that use, offering some explanation of why rates of use continue to increase.

Objectives:

The aim of this study was to explore pregnant and lactating people’s perceptions of the risks of cannabis use and understand what steps, if any, they take to mitigate these risks.

Design:

Qualitative description.

Methods:

We analyzed semi-structured interviews with 52 Canadians who made the decision to start, stop, or continue using cannabis during pregnancy or lactation between 2019 and 2021. Data collection iterated with analysis. We used a conventional (inductive) approach to content analysis.

Results:

Perception of risk was found to be an essential component of decision-making about cannabis use. We identified a cycle of “risk identification,” “management,” and “observation” of effects. First, the pregnant or lactating person assesses the risks and weighs them against the perceived benefits of cannabis use. Second, they take action to minimize risks, with some choosing abstinence. Others, often those who were using cannabis to manage symptoms, continued cannabis use but devised a variety of other risk mitigation strategies such as, decreasing the amount or frequency of their use, changing the form of cannabis, and strategically timing their use with caregiving responsibilities. The final stage of the cycle involves seeking information about whether or not the initial perceived risk has manifested after implementing mitigation strategies, through observations and clinical information about the pregnancy or child.

Conclusion:

Participants consistently engaged in deliberation about the risks and benefits associated with their perinatal cannabis use. Nearly all implemented strategies intended to minimize risk. Our results highlight the need for more research to inform clear public health messaging about risk mitigation to minimize the potential harms of perinatal cannabis use. This work informs clinicians about patient-perceived risks and mitigation strategies which could in turn help inform shared decision-making conversations.
A narrative review of neuro-ophthalmologic disease in African Americans and Hispanics with multiple sclerosis
Authors: Tardo Lauren , Salter Amber , Truong-Le Melanie , Horton Lindsay , Blackburn Kyle M. , Sguigna Peter V.
Published: September 2023

Multiple sclerosis (MS) is the most common non-traumatic cause of disability in young people, with vision loss in the disease representing the second largest contributor to disability. In particular, African-American patients with MS are noted to have lower vision than their Caucasian counterparts. In this review, we examine the disparities in eye diseases in the MS population with our gaps in knowledge and discuss the underlying nature of pathological disparities.
Self-Management of Long-Term Physical Conditions During Emerging Adulthood: A Systematic Review
Authors: Mooney Orla , Lambert Veronica , Gallagher Pamela
Published: September 2023

The aim of this mixed-studies systematic review was to synthesise existing research to identify if the five features of emerging adulthood (identity exploration; instability; self-focus; feeling in-between; possibilities) were evident in the self-management of long-term physical conditions by emerging adults (aged 18 – 29 years old). Five databases were systematically searched. Thirty papers met the eligibility criteria and were included. The synthesis identified that the five features of emerging adulthood are present in the self-management strategies and tasks of emerging adults living with long-term physical conditions. Due to numerous transitions, that characterise this unstable developmental period, emerging adults encounter specific self-management challenges. However, a greater understanding of the extent to which each of the five features are present and the challenges posed to the self-management of a long-term physical condition in emerging adults is required. This will inform targeted self-management supports and interventions in the future.
Post-disaster mobilities of Muslim typhoon survivors: How gendered religious preferences and discrimination shape socio-spatial exclusions in Catholic-majority Cagayan de Oro, Philippines
Authors: Gibb Christine
Published: September 2023

Natural hazards don’t care who you worship. However, the evacuation camps, transitional housing sites and relocation sites aimed at helping disaster survivors do. Empirically, this paper explains a puzzle in which Muslim survivors of Typhoon Sendong in the Philippines were all but absent in official post-disaster spaces of this Catholic-majority country. Based on qualitative interviews, focus groups and site visits, I identify two exclusionary mechanisms: (1) prejudices, preferences and practicalities, and (2) socio-spatial design of official post-disaster spaces. This paper argues that by studying Muslim survivors’ post-disaster mobilities, we see that discrimination along the lines of religion, as it plays out in everyday gendered religious socio-spatial practices, repels survivors from accessing evacuation camps and other post-disaster spaces. This is important for two related reasons. One, these humanitarian spaces claim to be inclusive yet, in practice, deter would-be migrants on the basis of religion. Two, religiously-informed gender relations shape the politics of disaster recovery processes, which further exacerbate inequities post-disaster.
Racial capitalism and self-organized houseless encampments: (En)countering banishment in Portland and Miami
Authors: Farrington Alex
Published: September 2023

In this paper, I contribute to the literature on self-organized houseless encampments in the United States in two ways. First, I draw on Roy’s concept of racial banishment to examine the relationship between encampments and American racial capitalism. Second, I extend Caldeira’s theory of peripheral urbanization – originally developed to describe urban informality in the Global South – to encampments in the United States. Doing so highlights how encampment residents and local government interact with one another through transversal logics. I show how both these frameworks – racial banishment and peripheral urbanization – can help us understand the creation of two self-organized houseless encampments: Dignity Village in Portland and Umoja Village in Miami. In each city, I describe how these encampments not only encountered, but also countered various forms of banishment through creative means.
Pediatric leukemia and maternal occupational exposure to anticancer drugs: the Japan Environment and Children’s Study
Authors: Yamamoto Shunsuke , Sanefuji Masafumi , Suzuki Maya , Sonoda Yuri , Hamada Norio , Kato Wakako , Ono Hiroaki , Oba Utako , Nakashima Kentaro , Ochiai Masayuki , Kusuhara Koichi , Koga Yuhki , Ohga Shouichi
Published: October 2023

Occupational exposure to medical agents and ionizing radiation has been suggested as a possible risk factor for childhood cancer. However, the relationship between such exposure and pediatric malignant neoplasms has not yet been comprehensively studied. This cohort study aimed to investigate the association between parental occupational exposure to hazardous medical agents or ionizing radiation and the risk of childhood cancer in offspring. Data from a large birth cohort in Japan, which included 104 062 fetuses, were analyzed. The primary outcome was the development of leukemia or brain tumors diagnosed by community physicians during the first 3 years after birth. Exposure factors were medical agents, including anticancer agents, ionizing radiation, and anesthetics, handled by mothers during pregnancy or by fathers for 3 months before conception. The incidence of leukemia, but not of brain tumors, was higher in mothers exposed to anticancer drugs. Multivariable regression analysis showed that maternal exposure to anticancer drugs was associated with an increased risk of leukemia in offspring older than 1 year (adjusted relative risk, 7.99 [95% confidence interval, 1.98-32.3]). Detailed information obtained from medical certificates of patients with identified leukemia revealed no infant leukemia but acute lymphoblastic leukemias in the exposed group. Our findings suggest that maternal occupational exposure to anticancer drugs may be a potential risk factor for acute lymphoblastic leukemia in offspring older than 1 year. Effective prevention methods may be necessary to prevent maternal exposure to anticancer drugs and to reduce the risk of childhood malignant neoplasms.
Predicting tumour content of liquid biopsies from cell-free DNA
Authors: Cardner Mathias , Marass Francesco , Gedvilaite Erika , Yang Julie L. , Tsui Dana W. Y. , Beerenwinkel Niko
Published: September 2023

Background

Liquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-free DNA (cfDNA) fragment lengths has been shown to differ between healthy subjects and cancer patients, whereby the distributional shift correlates with the sample’s tumour content. These fragmentomic data have not yet been utilised to directly quantify the proportion of tumour-derived cfDNA in a liquid biopsy.

Results

We used statistical learning to predict tumour content from Fourier and wavelet transforms of cfDNA length distributions in samples from 118 cancer patients. The model was validated on an independent dilution series of patient plasma.

Conclusions

This proof of concept suggests that our fragmentomic methodology could be useful for predicting tumour content in liquid biopsies.
DGDTA: dynamic graph attention network for predicting drug–target binding affinity
Authors: Zhai Haixia , Hou Hongli , Luo Junwei , Liu Xiaoyan , Wu Zhengjiang , Wang Junfeng
Published: September 2023

Background

Obtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins and drugs still need to be further analyzed. Recently, deep learning has been successfully used in many fields. Hence, designing a more effective deep learning method for predicting DTA remains attractive.

Results

Dynamic graph DTA (DGDTA), which uses a dynamic graph attention network combined with a bidirectional long short-term memory (Bi-LSTM) network to predict DTA is proposed in this paper. DGDTA adopts drug compound as input according to its corresponding simplified molecular input line entry system (SMILES) and protein amino acid sequence. First, each drug is considered a graph of interactions between atoms and edges, and dynamic attention scores are used to consider which atoms and edges in the drug are most important for predicting DTA. Then, Bi-LSTM is used to better extract the contextual information features of protein amino acid sequences. Finally, after combining the obtained drug and protein feature vectors, the DTA is predicted by a fully connected layer. The source code is available from GitHub athttps://github.com/luojunwei/DGDTA.

Conclusions

The experimental results show that DGDTA can predict DTA more accurately than some other methods.
Reference-based genome compression using the longest matched substrings with parallelization consideration
Authors: Lu Zhiwen , Guo Lu , Chen Jianhua , Wang Rongshu
Published: September 2023

Background

A large number of researchers have devoted to accelerating the speed of genome sequencing and reducing the cost of genome sequencing for decades, and they have made great strides in both areas, making it easier for researchers to study and analyze genome data. However, how to efficiently store and transmit the vast amount of genome data generated by high-throughput sequencing technologies has become a challenge for data compression researchers. Therefore, the research of genome data compression algorithms to facilitate the efficient representation of genome data has gradually attracted the attention of these researchers. Meanwhile, considering that the current computing devices have multiple cores, how to make full use of the advantages of the computing devices and improve the efficiency of parallel processing is also an important direction for designing genome compression algorithms.

Results

We proposed an algorithm (LMSRGC) based on reference genome sequences, which uses the suffix array (SA) and the longest common prefix (LCP) array to find the longest matched substrings (LMS) for the compression of genome data in FASTA format. The proposed algorithm utilizes the characteristics of SA and the LCP array to select all appropriate LMSs between the genome sequence to be compressed and the reference genome sequence and then utilizes LMSs to compress the target genome sequence. To speed up the operation of the algorithm, we use GPUs to parallelize the construction of SA, while using multiple threads to parallelize the creation of the LCP array and the filtering of LMSs.

Conclusions

Experiment results demonstrate that our algorithm is competitive with the current state-of-the-art algorithms in compression ratio and compression time.
Time course of changes in the transcriptome during russet induction in apple fruit
Authors: Straube Jannis , Suvarna Shreya , Chen Yun-Hao , Khanal Bishnu P. , Knoche Moritz , Debener Thomas
Published: September 2023

Background

Russeting is a major problem in many fruit crops. Russeting is caused by environmental factors such as wounding or moisture exposure of the fruit surface. Despite extensive research, the molecular sequence that triggers russet initiation remains unclear. Here, we present high-resolution transcriptomic data by controlled russet induction at very early stages of fruit development. During Phase I, a patch of the fruit surface is exposed to surface moisture. For Phase II, moisture exposure is terminated, and the formerly exposed surface remains dry. We targeted differentially expressed transcripts as soon as 24 h after russet induction.

Results

During moisture exposure (Phase I) of ‘Pinova’ apple, transcripts associated with the cell cycle, cell wall, and cuticle synthesis (SHN3) decrease, while those related to abiotic stress increase. NAC35 and MYB17 were the earliest induced genes during Phase I. They are therefore linked to the initial processes of cuticle microcracking. After moisture removal (Phase II), the expression of genes related to meristematic activity increased (WOX4 within 24 h, MYB84 within 48 h). Genes related to lignin synthesis (MYB52) and suberin synthesis (MYB93, WRKY56) were upregulated within 3 d after moisture removal. WOX4 and AP2B3 are the earliest differentially expressed genes induced in Phase II. They are therefore linked to early events in periderm formation. The expression profiles were consistent between two different seasons and mirrored differences in russet susceptibility in a comparison of cultivars. Furthermore, expression profiles during Phase II of moisture induction were largely identical to those following wounding.

Conclusions

The combination of a unique controlled russet induction technique with high-resolution transcriptomic data allowed for the very first time to analyse the formation of cuticular microcracks and periderm in apple fruit immediately after the onset of triggering factors. This data provides valuable insights into the spatial-temporal dynamics of russeting, including the synthesis of cuticles, dedifferentiation of cells, and impregnation of cell walls with suberin and lignin.
Sequential regression and simulation: a method for estimating causal effects from heterogeneous clinical trials without a common control group
Authors: Rudrapatna Vivek A. , Ravindranath Vignesh G. , Arneson Douglas V. , Mosenia Arman , Butte Atul J. , Wang Shan
Published: October 2023

Background

The advent of clinical trial data sharing platforms has created opportunities for making new discoveries and answering important questions using already collected data. However, existing methods for meta-analyzing these data require the presence of shared control groups across studies, significantly limiting the number of questions that can be confidently addressed. We sought to develop a method for meta-analyzing potentially heterogeneous clinical trials even in the absence of a common control group.

Methods

This work was conducted within the context of a broader effort to study comparative efficacy in Crohn’s disease. Following a search of clnicaltrials.gov we obtained access to the individual participant data from nine trials of FDA-approved treatments in Crohn’s Disease (N = 3392). We developed a method involving sequences of regression and simulation to separately model the placebo- and drug-attributable effects, and to simulate head-to-head trials against an appropriately normalized background. We validated this method by comparing the outcome of a simulated trial comparing the efficacies of adalimumab and ustekinumab against the recently published results of SEAVUE, an actual head-to-head trial of these drugs. This study was pre-registered on PROSPERO (#157,827) prior to the completion of SEAVUE.

Results

Using our method of sequential regression and simulation, we compared the week eight outcomes of two virtual cohorts subject to the same patient selection criteria as SEAVUE and treated with adalimumab or ustekinumab. Our primary analysis replicated the corresponding published results from SEAVUE (p = 0.9). This finding proved stable under multiple sensitivity analyses.

Conclusions

This new method may help reduce the bias of individual participant data meta-analyses, expand the scope of what can be learned from these already-collected data, and reduce the costs of obtaining high-quality evidence to guide patient care.
Implementation of interprofessional quality circles on deprescribing in Swiss nursing homes: an observational study
Authors: Mena Stephanie , Moullin Joanna C. , Schneider Marie , Niquille Anne
Published: October 2023

Background

Polypharmacy and potentially inappropriate medications (PIMs) are still frequent among older adults in nursing homes. Deprescribing is an intervention that has been shown to be effective in reducing their use. However, the implementation of deprescribing in clinical practice has not yet been widely evaluated. The Quality Circle Deprescribing Module (QC-DeMo) intervention has been trialled through an effectiveness-implementation hybrid type 2 design. The intervention consists of a quality circle workshop session between healthcare professionals HCPs (physicians, nurses, and pharmacists) within a nursing home, in which they define a consensus to deprescribe specific PIMs classes. The aim of this study was to evaluate the implementation of the QC-DeMo intervention in nursing homes.

Methods

This observational study focuses on the implementation part of the QC-DeMo trial. Implementation was based on the Framework for Implementation of Pharmacy Services (FISpH). Questionnaires at baseline and follow-up were used to evaluate reach, adoption, implementation effectiveness, fidelity, implementation, maintenance and the implementation strategies. Other data were collected from the QC-DeMo trial and routine data collected as part of the integrated pharmacy service where the QC-Demo trial was embedded. Implementation strategies included training of pharmacists, integration of the intervention into an existing quality circle dynamic and definition of tailored strategies to operationalise the consensus by each nursing home.

Results

The QC-DeMo intervention was successfully implemented in 26 nursing homes in terms of reach, fidelity, adoption, implementation and implementation effectiveness. However, the intervention was found to be implemented with low maintenance as none of the nursing homes repeated the intervention after the trial. Implementation strategies were well received by HCPs: training was adequate according to pharmacists. Pre-existing quality circle dynamic facilitated interprofessional collaboration as involvement and support of each HCP was rated as high. HCPs recognized a specific and important role for each HCP in the deprescribing process. The most relevant tailored strategies to implement the consensus defined by each nursing home were identification of the patients by the pharmacist and a systematic review of medication’s patients.

Conclusions

The implementation of a Quality Circle on Deprescribing is feasible but its maintenance in practice remains challenging. This study explores multiple implementation outcomes to better inform future implementation efforts of these types of interventions.

Trial registration

ClinicalTrials.gov (NCT03688542), registered on 26.09.2018.
Characterization of patients admitted to specialized geriatric acute care hospital units with the German version of the Standardized Evaluation and Intervention for Seniors at Risk (SEISAR) screening-instrument: a cross-sectional study
Authors: Wirth Rainer , Verdon J. , Frohnhofen H. , Djukic M. , Meisel M. , Musolf M. , Zinke A. , Heppner H. J. , Jamour M. , Denkinger M. , Trampisch U. S.
Published: September 2023

Background

The Standardized Evaluation and Intervention for Seniors at Risk (SEISAR) screening tool records major geriatric problems, originally applied in the emergency department. Particularly, the distinction of compensated and uncompensated problems is an interesting and new approach. Therefore, we translated the SEISAR in German language and used it to characterize patients in specialized geriatric hospital wards in Germany and to gather initial experience regarding its usability and practicability.

Methods

The tool was translated by three independent specialists in geriatric medicine and backtranslated for quality-assurance by a non-medical English native speaker. In a second step, 8 acute care geriatric hospital departments used the translated version to characterize all consecutive patients admitted over a period of one month between December 2019 and May 2020 at time of admission.

Results

Most of the 756 patients (78%) lived in an own apartment or house prior to hospital admission. Participants had on average 4 compensated and 6 uncompensated problems, a Barthel-Index of 40 pts. on admission with a median increase of 15 points during hospital stay, and a median length of stay of 16 days in the geriatric hospital department.

Conclusion

SEISAR is an interesting standardized brief comprehensive geriatric assessment tool for the identification of compensated and uncompensated health problems in older persons. The data of this study highlights the number, variability, and complexity of geriatric problems in patients treated in specialized acute care geriatric hospital wards in Germany.

Trial registration

German Clinical trial register (DRKS-ID: DRKS00031354 on 27.02.2023).
PB-LNet: a model for predicting pathological subtypes of pulmonary nodules on CT images
Authors: Zhang Yuchong , Qu Hui , Tian Yumeng , Na Fangjian , Yan Jinshan , Wu Ying , Cui Xiaoyu , Li Zhi , Zhao Mingfang
Published: October 2023

Objective

To investigate the correlation between CT imaging features and pathological subtypes of pulmonary nodules and construct a prediction model using deep learning.

Methods

We collected information of patients with pulmonary nodules treated by surgery and the reference standard for diagnosis was post-operative pathology. After using elastic distortion for data augmentation, the CT images were divided into a training set, a validation set and a test set in a ratio of 6:2:2. We used PB-LNet to analyze the nodules in pre-operative CT and predict their pathological subtypes. Accuracy was used as the model evaluation index and Class Activation Map was applied to interpreting the results. Comparative experiments with other models were carried out to achieve the best results. Finally, images from the test set without data augmentation were analyzed to judge the clinical utility.

Results

Four hundred seventy-seven patients were included and the nodules were divided into six groups: benign lesions, precursor glandular lesions, minimally invasive adenocarcinoma, invasive adenocarcinoma Grade 1, Grade 2 and Grade 3. The accuracy of the test set was 0.84. Class Activation Map confirmed that PB-LNet classified the nodules mainly based on the lungs in CT images, which is in line with the actual situation in clinical practice. In comparative experiments, PB-LNet obtained the highest accuracy. Finally, 96 images from the test set without data augmentation were analyzed and the accuracy was 0.89.

Conclusions

In classifying CT images of lung nodules into six categories based on pathological subtypes, PB-LNet demonstrates satisfactory accuracy without the need of delineating nodules, while the results are interpretable. A high level of accuracy was also obtained when validating on real data, therefore demonstrates its usefulness in clinical practice.
Risk of venous thromboembolism in patients undergoing gastric cancer surgery: a systematic review and meta-analysis
Authors: Xiang Lin , Jin Shuai , Yu Yang , Wang Dengfeng , Chen Hao
Published: October 2023

Background

Venous thromboembolism (VTE) is a common postoperative complication in patients undergoing surgery for gastric cancer (GC). Although VTE incidence may vary among cancers, guidelines rarely stratify preventive methods for postoperative VTE by cancer type. The risk of VTE in patients undergoing surgery for GC remains unclear.

Methods

A systematic review and meta-analysis was undertaken to determine the risk of VTE after GC surgery and discuss the clinical value of pharmacological thromboprophylaxis in these cases. Medline, Embase, Web of Science, and Cochrane Library databases were searched for articles published from their inception to September 2022.

Results

Overall, 13 studies (111,936 patients) were included. The overall 1-month incidence of VTE, deep vein thrombosis (DVT), and pulmonary embolism (PE) after GC surgery was 1.8% (95% CI, 0.8–3.1%; I²=98.5%), 1.2% (95% CI, 0.5–2.1%; I²=96.1%), and 0.4% (95% CI, 0.1–1.1%; I²=96.3%), respectively. The prevalence of postoperative VTE was comparable between Asian and Western populations (1.8% vs. 1.8%; P > 0.05). Compared with mechanical prophylaxis alone, mechanical plus pharmacological prophylaxis was associated with a significantly lower 1-month rate of postoperative VTE and DVT (0.6% vs. 2.9% and 0.6% vs. 2.8%, respectively; all P < 0.05), but not PE (P > 0.05). The 1-month postoperative incidence of VTE was not significantly different between laparoscopic and open surgery (1.8% vs. 4.3%, P > 0.05).

Conclusion

Patients undergoing GC surgery do not have a high risk of VTE. The incidence of VTE after GC surgery is not significantly different between Eastern and Western patients. Mechanical plus pharmacological prophylaxis is more effective than mechanical prophylaxis alone in postoperative VTE prevention. The VTE risk is comparable between open and laparoscopic surgery for GC.