bluuebunny/crossref_metadata_2025_split huggingface dataset:
GBZ file format for pangenome graphs
Authors: Sirén Jouni , Paten Benedict 
Published: September 2022

AbstractMotivationPangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space efficiently.ResultsWe propose the GBZ file format based on data structures used in the Giraffe short-read aligner. The format provides good compression, and the files can be efficiently loaded into in-memory data structures. We provide compression and decompression tools and libraries for using GBZ graphs, and we show that they can be efficiently used on a variety of systems.Availability and implementationC++ and Rust implementations are available at https://github.com/jltsiren/gbwtgraph and https://github.com/jltsiren/gbwt-rs, respectively.Supplementary informationSupplementary data are available at Bioinformatics online.
Seeded binary segmentation: a general methodology for fast and optimal changepoint detection
Authors: Kovács S , Bühlmann P , Li H , Munk A 
Published: September 2022

Summary
We propose seeded binary segmentation for large-scale changepoint detection problems. We construct a deterministic set of background intervals, called seeded intervals, in which single changepoint candidates are searched for. The final selection of changepoints based on these candidates can be done in various ways, adapted to the problem at hand. The method is thus easy to adapt to many changepoint problems, ranging from univariate to high dimensional. Compared to recently popular random background intervals, seeded intervals lead to reproducibility and much faster computations. For the univariate Gaussian change in mean set-up, the methodology is shown to be asymptotically minimax optimal when paired with appropriate selection criteria. We demonstrate near-linear runtimes and competitive finite sample estimation performance. Furthermore, we illustrate the versatility of our method in high-dimensional settings.
A scoping review on the approaches for cannulation of reno-visceral target vessels during complex endovascular aortic repair
Authors: Grandi Alessandro , D’Oria Mario , Melloni Andrea , Calvagna Cristiano , Taglialavoro Jacopo , Chiesa Roberto , Lepidi Sandro , Bertoglio Luca 
Published: September 2022

Abstract

OBJECTIVES
The aim of this study was to assess the approaches to reno-visceral target vessels (TVs) cannulation during branched-fenestrated endovascular aortic repair, determine the evidence base that links these approaches to clinical outcomes and identify literature gaps.

METHODS
A scoping review following the PRISMA Protocols Extension for Scoping Reviews was performed. Available full-text studies published in English (PubMed, Cochrane and EMBASE databases; last queried, 31 June 2022) were systematically reviewed and analysed. Data were reported as descriptive narrative or tables, without any statistical analysis nor quality assessment.

RESULTS
Fourteen retrospective articles were included. Seven articles studied the use of upper extremity access (UEA) during branched-fenestrated endovascular aortic repair, 3 studied the use of steerable sheaths and 4 included both approaches. A left UEA was used in 757 patients (technical success: 99%, stroke rate: 1–3%) and a right UEA in 215 patients (technical success: 92–98%, stroke rate: 0–13%). Seven studies (1066 patients) described a surgical access only (technical success: 80–99%, stroke rate: 0–13%), while 3 studies (146 patients) described a percutaneous access only (technical success: 83–90%, stroke rate: 3%) and lastly 4 studies compared UEA versus use of steerable sheaths from the transfemoral approach (TFA) (UEA: 563 patients, technical success: 95–98%, stroke rate: 1–8%; TFA: 209 patients, technical success: 98–100%, stroke rate: 0–1%).

CONCLUSIONS
Both UEA and TFA as cannulation approaches were associated with high technical success and low perioperative complications. Currently, there is a paucity of high-quality data to provide definitive indication. Optimal UEA in terms of side (left versus right) and approach (surgical versus percutaneous) needs further study.
Rastelli conduit change with the Nuss procedure for relieving compression of extracardiac conduit
Authors: Yi Jung Hoon 
Published: September 2022

Abstract
When Rastelli conduit stenosis occurs concurrently with pectus excavatum, redo Rastelli operation alone may not be sufficient to solve the situation. Therefore, we performed 2 procedures simultaneously: right ventricle to pulmonary artery extracardiac conduit change and the Nuss procedure. The Nuss bar was removed after 4 years.
Who are the loss-averse farmers? Experimental evidence from structurally estimated risk preferences
Authors: Bonjean Isabelle 
Published: September 2022

AbstractEven though recognised to be of increasing importance, robust estimations of European farmers’ risk preferences are still scarce. Using an incentivised lab-in-the-field experiment with farmers, free of learning bias, this paper analyses the structurally derived parameters of risk preferences based on the cumulative prospect theory. The sector studied is the apple and pear sector in Flanders, Belgium. Farmers are found to be highly risk-averse and to distort probabilities by overweighting a small probability of desirable outcomes. However, there is no evidence of loss aversion on average, unlike previous studies. Moreover, investigating the heterogeneous effects shows that some farmers significantly differ from the representative agent by still being extremely loss-averse. The results of this piece of research prove the need to consider heterogeneity within and across sectors when assessing farmers’ risk preferences.
Linkage between electronic prescribing data and pharmacy claims records to determine primary adherence: the case of antihypertensive therapy in the Lisbon and Tagus Valley Region, Portugal
Authors: Coelho André 
Published: September 2022

AbstractBackgroundHypertension (HT) is highly prevalent and a major risk factor for cardiovascular disease. Over 42% of Portuguese adults have HT. Even though the benefits of antihypertensive (AHT) drugs have been demonstrated, HT control remains inadequate. One major reason is that patients often fail to take their medications as prescribed. This paper aims to determine primary adherence to AHT therapy in newly diagnosed and treated hypertensive patients in Primary Health Care (PHC) units of Lisbon and Tagus Valley Health Region.MethodsThis study reports data from a population-based, retrospective, cohort study from patients diagnosed with HT in PHC units of Lisbon and Tagus Valley Region from 1 January to 31 March 2011, with no prior use of AHT drugs. Primary adherence rate was expressed as number of claims records/total number of prescriptions records. Data were collected from SIARS for each patient during a 2-year period.ResultsOverall primary adherence rate was 58.5%, increasing with age. Rates were higher for men, living in the Lisbon Metropolitan Area and diagnosed with uncomplicated HT. Drugs acting on the renin–angiotensin system had the highest rates, increasing for fixed-dose combinations and diminishing with the increase of cost for the patient.ConclusionsOverall, almost 1 out of 2 prescribed AHT drugs were not dispensed. Until this study, little was known in Portugal about primary adherence. Our findings imply that the potential benefits of AHT therapy cannot be fully realized in this population.
Postsecular Pilgrimage in Malek Bennabi’s Lebbeik: pèlerinage de pauvres and Abdelkébir Khatibi’s Pèlerinage d’un artiste amoureux
Authors: Qadiri Sura 
Published: September 2022

Abstract
This paper explores representations of the Islamic pilgrimage to Mecca in two North African literary texts, Malek Bennabi’s Lebbeik (1947) and Abdelkébir Khatibi’s Pèlerinage d’un artiste amoureux (2003). It considers the divergent ways in which pilgrimage is used to explore the place of both literature and religion, as well as their interrelation, when it comes to working out ethics and values on individual and collective levels in Bennabi’s late-colonial Algeria, and Khatibi’s postcolonial Morocco. Drawing on Alain Badiou’s notion of the event as an occurrence that is retrospectively determined to have disrupted the status quo, and contrasting this with Derek Attridge’s idea of literature as a disruptive event with indeterminate outcomes, I consider the different ways in which both the pilgrimage and the narratives representing it can be seen as events, implicitly imparting reflections and even teachings on life and how to approach it in both texts.
Natural Regeneration Dynamics of Longleaf Pine Under Frequent, Low-Intensity Prescribed Fires in Southern Alabama, USA
Authors: Fan Zhaofei , Yang Shoayang , Kush John M , Narine Lana 
Published: September 2022

AbstractFrequent (≤3 y) prescribed burn has been conducted in the Escambia Experimental Forest in southern Alabama, USA, since 2001.The change in the density of new germinants (≤1 y) and older seedlings and saplings (&gt;1 y) of longleaf pine (Pinus palustris Mill.) from stands of varying conditions was quantified using the locally estimated scatterplot smoothing and spatial statistical methods. A relatively longer fire interval or time since last fire (TSLF) &gt; 600 days favored the recruitment of young seedlings. However, a short fire return interval or TSLF≤ 600 days promoted the recruitment of older seedlings and saplings. Large basal area (BA) and site index (SI) tended to diminish natural regeneration, whereas large quadratic mean diameter (QMD) and age were facilitative. The interactive effect of these factors indicated that a ratio of TSLF/BA of 60 to 120 and QMD/SI of 1.8 to 2.2 would maximize the recruitment of young seedlings. The recruitment of older seedlings and saplings increased linearly with QMD/SI but had no relationship with TSLF/BA. Recruitment was largely absent when QMD/SI was &lt;2.0. As a result, we recommend that QMD/SI be no greater than 2.0 and TSLF/BA range from 60 to 120 to regenerate longleaf pine naturally.
How Shading and Container Type Influence Ilex paraguariensis A.St.-Hil. Seedling Production
Authors: Siqueira Walter Letícia , Melo Moura Marks , Moreno Gabira Mônica , Saudade de Aguiar Natália , Stuepp Carlos André , Kratz Dagma 
Published: September 2022

Abstract
This study aimed to evaluate the influence of containers and shading on Ilex paraguariensis A.St.-Hil (yerba mate) seedling growth. We used a completely randomized design with a 3 × 2 factorial arrangement (containers × shading). We used PlantPaper®, Ellepot® (both biodegradable containers composed of cellulose fibers), and polypropylene tube containers and shaded (75% shading screen) and unshaded (without shading screen) greenhouse environments. We measured height and stem diameter every 30 days and shoot and root dry biomass 210 days after sowing. With these data, we calculated the total dry biomass, Dickson quality index, and height/diameter ratio. The unshaded environment increased yerba mate seedlings growth in height and stem diameter. In unshaded environments, seedlings produced in biodegradable containers had greater growth than those produced in polypropylene tubes. In the shaded environment, however, seedlings produced in polypropylene tubes had better growth. Despite the differences observed between treatments, all seedlings presented adequate growth during the nursery phase. We suggest the use of biodegradable containers to produce yerba mate seedlings in unshaded environments.
The future of fungi: threats and opportunities
Authors: Case Nicola T , Berman Judith , Blehert David S , Cramer Robert A , Cuomo Christina , Currie Cameron R , Ene Iuliana V , Fisher Matthew C , Fritz-Laylin Lillian K , Gerstein Aleeza C , Glass N Louise , Gow Neil A R , Gurr Sarah J , Hittinger Chris Todd , Hohl Tobias M , Iliev Iliyan D , James Timothy Y , Jin Hailing , Klein Bruce S , Kronstad James W , Lorch Jeffrey M , McGovern Victoria , Mitchell Aaron P , Segre Julia A , Shapiro Rebecca S , Sheppard Donald C , Sil Anita , Stajich Jason E , Stukenbrock Eva E , Taylor John W , Thompson Dawn , Wright Gerard D , Heitman Joseph , Cowen Leah E 
Published: September 2022

Abstract
The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.
Exploring Sectoral Reach in Age-Friendly Communities
Authors: Black Kathy , Oh Patricia 
Published: September 2022

Abstract

Background and Objectives
There is growing interest in better understanding the sectoral reach of age-friendly community practice. Action across a wide range of actors is central to achieving age-friendly societal change, according to the World Health Organization and required for governmental participation in its Global Network of Age-Friendly Cities and Communities. However, there is limited knowledge regarding the scope of sectoral reach by age-friendly communities.

Research Design and Methods
We used qualitative inquiry to assess sectoral efforts reported by American age-friendly communities that completed a 5-year cycle of participation (n = 40). We employed directed content analysis using a priori indicators by sectoral actors: public (i.e., government), private (i.e., business), and civil society, including nonprofit organizations and volunteers. We classify sectoral actions by type (i.e., intersectoral and multisectoral) and by clustered domain community foci (i.e., built, social, and service).

Results
Our study identifies the extent and types of sectoral actors and actions reported by age-friendly communities with the greatest efforts reported in the public sector, and while similarly distributed across all the domains, slightly more efforts were noted in the built environment. We also found greater intersectoral efforts (i.e., explicitly working toward shared goals) than multisectoral (i.e., not necessarily in collaboration on shared goals), particularly across government.

Discussion and Implications
While our study substantiates the breadth of actions toward age-friendly change, additional research is needed to examine the ways in which the public and other sectoral actions are further linked to outcomes in communities in the United States and in other countries.
Ulcer Size After Induction Therapy Performs Better Than Symptom Assessment for Prediction of One Year Endoscopic Remission in Crohn’s Disease: A Post Hoc Analysis
Authors: Pray Cara , Wong Emily C L , Aruljothy Achuthan , Dulai Parambir S , Marshall John K , Reinisch Walter , Narula Neeraj 
Published: September 2022

Abstract

Background
We evaluated whether postinduction ulcer size and patient-reported outcome (PRO) severity are associated with the achievement of 1-year endoscopic remission (ER) in patients with Crohn’s disease (CD).

Methods
This post hoc analysis combined data from several clinical trials including 283 patients with baseline ulcers ≥5 mm with repeat endoscopy after ustekinumab or adalimumab induction therapy. Patient-reported outcomes including stool frequency (SF) and abdominal pain (AP) were measured by the Crohn’s Disease Activity Index. Thresholds of SF ≥4 and/or AP ≥2 indicated moderately to severely active CD. Endoscopic remission was defined as Simple Endoscopic Score for CD (SES-CD) &lt;3. Multivariate logistic regression models adjusted for confounders (including disease duration and treatment allocation) evaluated the relationships between postinduction ulcer size, PRO symptoms, and achievement of 1-year ER.

Results
Among the 131 CD patients who continued to have ulcers ≥5 mm after induction therapy, 48 (36.6%) achieved 1-year ER. Patients with postinduction ulcers ≥5 mm were approximately 5 times less likely to achieve 1-year ER than the 152 individuals who had small or no postinduction ulcers (odds ratio [OR], 0.20; 95% CI, 0.08-0.51, P = .001). In patients with ulcers ≥5 mm after induction, postinduction PRO scores (including PRO2 and PRO3) did not predict 1-year ER.

Conclusions
Crohn’s disease patients with ulcers ≥5 mm after induction therapy are less likely to achieve 1-year ER. Postinduction PRO severity does not offer additional prognostic information. This may suggest that objective measures of disease such as endoscopic ulcer size should be considered over symptom assessments for determining clinical response to therapy and utilized in trials for maintenance therapy.
Sex differences in childhood cancer risk among children with major birth defects: a Nordic population-based nested case-control study
Authors: Daltveit Dagrun Slettebø , Klungsøyr Kari , Engeland Anders , Ekbom Anders , Gissler Mika , Glimelius Ingrid , Grotmol Tom , Madanat-Harjuoja Laura , Ording Anne Gulbech , Sørensen Henrik Toft , Troisi Rebecca , Bjørge Tone 
Published: September 2022

Abstract

Background
Childhood cancer is more common among children with birth defects, suggesting a common aetiology. Whether this association differs by sex is unclear.

Methods
We performed a population-based nested case-control study using nationwide health registries in four Nordic countries. We included 21 898 cancer cases (0–19 years) and 218 980 matched population controls, born 1967–2014. Associations between childhood cancer and major birth defects were calculated as odds ratios (ORs) with 95% confidence intervals (CIs) using logistic regression models. Effect modification was evaluated using a counterfactual framework to estimate confidence intervals and P-values for the natural indirect effects.

Results
Birth defects were present for 5.1% (1117/21 898) of childhood cancer cases and 2.2% (4873/218 980) of controls; OR of cancer was higher for chromosomal (OR = 10, 95% CI = 8.6–12) than for non-chromosomal defects (OR = 1.9, 95% CI = 1.8–2.1), strongest between genetic syndromes/microdeletion and renal tumours, Down syndrome and leukaemia, and nervous system defects and central nervous system tumours. The association between birth defects and cancer was stronger among females (OR = 2.8, 95% CI = 2.6–3.1) than males (OR = 2.1, 95% CI = 1.9–2.2, Pinteraction &lt;0.001). Male sex was an independent risk factor for childhood cancer, but very little of the overall association between sex and childhood cancer was mediated through birth defects (4.8%, PNIE &lt;0.001), although more at younger ages (10% below years and 28% below 1 year).

Conclusions
The birth defect–cancer associations were generally stronger among females than males. Birth defects did not act as a strong mediator for the modest differences in childhood cancer risk by sex, suggesting that other biological pathways are involved.
Association Between Inflammatory Cytokines, Executive Function, and Substance Use in Patients With Opioid Use Disorder and Amphetamine-Type Stimulants Use Disorder
Authors: Wang Tzu-Yun , Lu Ru-Band , Lee Sheng-Yu , Chang Yun-Hsuan , Chen Shiou-Lan , Tsai Tsung-Yu , Tseng Huai-Hsuan , Chen Po See , Chen Kao Chin , Yang Yen Kuang , Hong Jau-Shyong 
Published: September 2022

Abstract

Background
Long-term opioid and amphetamine-type stimulants (ATS) abuse may affect immunological function and impair executive function. We aimed to determine whether biomarkers of inflammation and executive function were associated with substance use in individuals with opioid use disorder (OUD) and ATS use disorder (ATSUD). The interactions between these biomarkers were also explored.

Methods
We assessed plasma cytokines [tumor necrosis factor (TNF)-α, C-reactive protein (CRP), interleukin (IL)-8, IL-6, transforming growth factor (TGF)-β1, brain-derived neurotrophic factor (BDNF), and executive function in terms of the Wisconsin Card Sorting Test (WCST) and Continuous Performance Test (CPT) in OUD and ATSUD patients and healthy controls (HC). OUD and ATSUD patients were followed for 12 weeks, and their urine morphine and amphetamine tests, cytokine levels, and executive function were repeatedly measured.

Results
We enrolled 483 patients and 145 HC. Plasma TNF-α, CRP, IL-8, IL-6, and BDNF levels and most subscale scores on the WCST and CPT significantly differed between OUD and ATSUD patients and HC. Increased TNF-α levels and more perseveration error on the WCST were significantly associated with more urine drug-positive results and less abstinence. Plasma IL-6 and CRP levels were significantly negatively correlated with WCST and CPT performance.

Conclusion
OUD and ATSUD patients had more inflammation and worse executive function than HC. Inflammatory markers and WCST performance were associated with their urinary drug results, and higher inflammation was associated with poor executive function. Studies on regulating the inflammatory process and enhancing executive function in OUD and ATSUD are warranted.
From Truth Commission to Truth Project: The Evolution of Mississippi’s Incomplete Truth Commission, 2005–2010
Authors: Whitlinger Claire 
Published: September 2022

ABSTRACT∞
Just months after the Mississippi Truth Commission’s public launch in 2009, organizers abandoned the Commission despite sufficient funding and growing public support, deciding instead to pursue a statewide oral history project. This study explores why, offering insight into an understudied phenomenon: incomplete truth commissions. Drawing on ethnographic observations, archival documents and interviews with local practitioners, this study highlights several reasons that local organizers changed course. In addition to a shifting cultural context, the Mississippi Truth Commission faced several cognitive challenges. First, local audiences struggled to comprehend the structure and scope of the truth commission model, leading to ‘Transitional Justice 101,’ a perpetual, and ultimately unsuccessful, public education program. Second, local organizers’ visit to South Africa in 2009 cast doubt on the efficacy of truth commissions and caused them to question the metaphoric logic that had constructed Mississippi’s history of racial violence as analogous to South Africa’s, providing implicit justification for the Commission until that point. Thus, alongside economic and political resources, this research suggests that cognitive resources are a critical, and often overlooked, component of truth commissions’ infrastructure. Findings also indicate that incomplete truth commissions can be leveraged to support alternative truth-seeking processes that may be more advantageous in stable democracies.