bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of T2Bacteria in relationship to blood cultures - a retrospective comparative study
Authors: Yu David , Ekwall-Larson Anna , Özenci Volkan 
Published: August 2024

Abstract
Purpose
Blood culture (BC) is the gold standard for diagnosing blood stream infections (BSI) but is limited by long turnaround times (TAT) and low detection rate. The T2 Magnetic Resonance method (T2MR) offers a rapid, culture-independent alternative. The objective of this study was to compare the performance of the T2Bacteria assay to BCs in a real-world setting.

Methods
Retrospective comparative study consisting of T2Bacteria samples and BCs sampled within 72 h from the T2Bacteria sample. The primary outcome was detections by BC and T2Bacteria, respectively. The secondary outcome was difference in TAT.

Results
In total, 640 episodes were included, consisting of 640 T2Bacteria samples and 2,117 BCs. A median of three BCs was collected for each T2Bacteria sample. Overall positivity was 101 (15.8%) by either method. In 29 (28.7%) episodes, both T2Bacteria and BC were concordantly positive. In discordant episodes, 46/101 (45.5%) episodes were T2Bacteria positive/BC negative and 26/101 (25.7%) were T2Bacteria negative/BC positive (McNemar χ2, p < 0,05). In T2Bacteria positive/BC negative episodes, eight had growth of the same microorganism in a non-BC culture. Median (IQR) TAT for BC was 35 h and 30 min (25 h 50 min − 45 h 24 min), compared to 21 h and 3 min (17 h 6 min − 27 h 30 m) for T2Bacteria (p < 0.001), with longer delays for samplings occurring outside work hours.

Conclusions
The study highlights a high discordance between T2Bacteria and BC and suggests complementary roles of the methods in BSI diagnostics. Furthermore, it is crucial to improve TAT by reducing preanalytical delays.
The ties that bind: how trees can enhance agroecological transitions
Authors: Isaac Marney E. , Sinclair F. , Laroche G. , Olivier A. , Thapa A. 
Published: August 2024

AbstractAgricultural systems have a long history of responding to various economic and socio-political forces, including supply and demand, political preferences and power inequalities. Our current food system continues to respond to contemporary forces with a call for sustainable transformations in the face of increased pressure and competition over resources, severe consequences of climatic change, widespread degradation of land and water resources, and the accelerating loss of biodiversity. Both agroforestry and agroecology have evolved as approaches to agricultural management that focus on the application of ecological principles to achieve sustainable agriculture. Agroecological principles are designed to engage with the entire agrifood system, for instance identifying broad participation and involving a diversity of actors and knowledge systems. Agroecological approaches to production have significant historical and contemporary links to agroforestry approaches, but not all agroecology involves trees and not all agroforestry is in line with agroecological principles. Drawing on (1) a literature review, (2) case studies on the agroforestry and agroecology nexus presented at the 5th World Congress on Agroforestry (WCA), and (3) audience responses to statements presented at the Congress, we explore the two main ways that agroforestry and agroecology come together: agroforestry that encompasses agroecological principles and agroecological transitions that involve trees. We review the status of agroecology, the functions specific to agroforestry that can enhance the achievement of agroecological outcomes, the tensions between simple agroforestry systems and agroecology, and the larger potential of multidimensional sustainability of agroforestry with the inclusion of agroecological principles. We also present the level of agreement on four key statements about the agroforestry-agroecology nexus enumerated at the WCA. It is clear that some features of agroforestry operationalize agroecological principles that aim to transition away from monocultures and the use of environmentally disruptive agrochemicals, and toward strengthening biodiversity and resilience. Yet, much remains to be done to enhance agroecological principles more fully in framing agroforestry practices and to incorporate trees within agroecological practices. Pathways to strengthen the nexus of agroforestry and agroecology are proposed, which focus on the role of trees in multifunctionality and resilience and using agroecological principles related to knowledge sharing and equity to enrich agroforestry practices.
Decarbonised closed-loop supply chains resilience: examining the impact of COVID-19 toward risk mitigation by a fuzzy multi-layer decision-making framework
Authors: Amoozad Mahdiraji Hannan , Yaftiyan Fatemeh , Garza-Reyes Jose Arturo , Razavi Hajiagha Seyed Hossein , Kazancoglu Yigit 
Published: August 2024

AbstractToday's primary challenges in supply chains (SCs) include considerable greenhouse gas emissions, waste, and disruptions. Addressing these requires the examination of three interconnected SC paradigms, i.e. decarbonisation, resilience, and Closed-Loop SCs (CLSCs). This paper seeks to investigate and assess the criteria for decarbonised resilient CLSCs, as influenced by the global pandemic, specifically within the context of Iran's small and medium pharmaceutical enterprises, employing a mixed-method approach. Initially, a Systematic Literature Review was employed to identify a categorised list of decarbonised resilient CLSC criteria by determining the impact of COVID-19 on SCs. Afterwards, the list was indigenised via the fuzzy-Delphi method. Two popular Fuzzy Multi-Criteria Decision-Making methods, i.e. fuzzy Decision-Making Trial and Evaluation Laboratory and fuzzy Interpretive Structural Modelling-Matrix-based Multiplication Applied to a Classification (MICMAC), were then employed to investigate the finalised criteria. This paper has innovatively enhanced these methods by incorporating a multi-scenario analysis approach. The findings indicate that technological advancements, issues related to market and communication, and raw material markets significantly affect other criteria. Transportation and logistics are also crucial in reducing lead times, waste, and CO2 emissions. Two countermeasures are recommended for senior managers, i.e. (i) the identification and application of suitable basic and advanced technologies across each SC process and (ii) engaging in a coevolutionary process beginning with SMEs' cooperation and collaboration towards their co-creation. The importance of regulatory bodies was also emphasised in devising effective policies to improve the markets for raw materials and finished products.
Fragmentation of care in breast cancer: greater than the sum of its parts
Authors: Freeman Hadley D. , Burke Linnea C. , Humphrey Ja’Neil G. , Wilbers Ashley J. , Vora Halley , Khorfan Rhami , Solomon Naveenraj L. , Namm Jukes P. , Ji Liang , Lum Sharon S. 
Published: August 2024

Abstract
Introduction
Fragmentation of care (FC, the receipt of care at > 1 institution) has been shown to negatively impact cancer outcomes. Given the multimodal nature of breast cancer treatment, we sought to identify factors associated with FC and its effects on survival of breast cancer patients.

Methods
A retrospective analysis was performed of surgically treated, stage I–III breast cancer patients in the 2004–2020 National Cancer Database, excluding neoadjuvant therapy recipients. Patients were stratified into two groups: FC or non-FC care. Treatment delay was defined as definitive surgery > 60 days after diagnosis. Multivariable logistic regression was performed to identify factors predictive of FC, and survival was compared using Kaplan–Meier and multivariable Cox proportional hazards methods.

Results
Of the 531,644 patients identified, 340,297 (64.0%) received FC. After adjustment, FC (OR 1.27, 95% CI 1.25–1.29) was independently associated with treatment delay. Factors predictive of FC included Hispanic ethnicity (OR 1.04, 95% CI: 1.01–1.07), treatment at comprehensive community cancer programs (OR 1.06, 95% CI: 1.03–1.08) and integrated network cancer programs (OR 1.55, 95% CI: 1.51–1.59), AJCC stage II (OR 1.06, 95% CI 1.05–1.07) and stage III tumors (OR 1.06, 95% CI: 1.02–1.10), and HR + /HER2 + tumors (OR 1.05, 95% CI: 1.02–1.07). Treatment delay was independently associated with increased risk of mortality (HR 1.23, 95% CI 1.20–1.26), whereas FC (HR 0.87, 95% CI 0.86–0.88) showed survival benefit.

Conclusions
While treatment delay negatively impacts survival in breast cancer patients, our findings suggest FC could be a marker for multispecialty care that may mitigate some of these effects.
A phase I safety and efficacy clinical trial of plocabulin and gemcitabine in patients with advanced solid tumors
Authors: Ghalib Mohammad H. , Pulla Mariano Provencio , De Miguel Luken Maria J. , de Juan Virginia Calvo , Chaudhary Imran , Hammami M Bakri , Vikash Sindhu , Maitra Radhashree , Martinez Sara , Kahatt Carmen , Extremera Sonia , Fudio Salvador , Goel Sanjay 
Published: August 2024

Summary
Plocabulin (Plo) induces depolymerization of tubulin fibers with disorganization and fragmentation of the microtubule network leading to mitosis. Plo combined with gemcitabine (Gem) showed synergistic anti-tumor activity in preclinical studies. This phase I trial evaluated the safety, pharmacokinetics (PK) and efficacy of Plo 10-min infusion plus Gem on Day 1 and 8 every 3-week in patients with advanced solid tumors. Fifty-seven patients were enrolled into 8 dose levels (DLs); 74%: females; 74%: ECOG performance status 1; median age: 62 years; median number of prior lines of therapy:3. Dose-limiting toxicities (DLT) in Cycle 1 were grade (G) 3 intestinal obstruction at the maximum tolerated dose (MTD), G3 peripheral sensory neuropathy (PSN), G3 abdominal pain, and G4 thrombocytopenia (1 patient each). The highest DL (DL8: Plo 10.5 mg/m2/Gem 1000 mg/m2) was the MTD. Accrual into DL7 (Plo 10.0 mg/m2/Gem 1000 mg/m2) was stopped before it was formally defined as the recommended dose (RD). Most common treatment-related adverse events (AEs) were fatigue (56%), nausea (55%), diarrhea (31%); G3/4 hematologic toxicities comprised anemia (35%), neutropenia (27%) and thrombocytopenia (17%). No treatment-related deaths occurred. PK parameters for Gem or dFdU at all DLs were in line with reference values from the literature. Six of 46 evaluable pts were responders (overall response rate:13%). Of note, 2 partial responses (PR) and 2 stable disease (SD) ≥ 4 months occurred among 13 pts with ovarian cancer. The combination of Plo and Gem is well tolerated. The MTD was Plo 10.5 mg/m2/Gem 1000 mg/m2. No PK drug-drug interaction was found. The most encouraging outcome occurred in ovarian cancer patients.
On the acceptance by code reviewers of candidate security patches suggested by Automated Program Repair tools
Authors: Papotti Aurora , Paramitha Ranindya , Massacci Fabio 
Published: August 2024

Abstract
Objective
We investigated whether (possibly wrong) security patches suggested by Automated Program Repairs (APR) for real world projects are recognized by human reviewers. We also investigated whether knowing that a patch was produced by an allegedly specialized tool does change the decision of human reviewers.

Method
We perform an experiment with $$n= 72$$

n
=
72

Master students in Computer Science. In the first phase, using a balanced design, we propose to human reviewers a combination of patches proposed by APR tools for different vulnerabilities and ask reviewers to adopt or reject the proposed patches. In the second phase, we tell participants that some of the proposed patches were generated by security-specialized tools (even if the tool was actually a ‘normal’ APR tool) and measure whether the human reviewers would change their decision to adopt or reject a patch.

Results
It is easier to identify wrong patches than correct patches, and correct patches are not confused with partially correct patches. Also patches from APR Security tools are adopted more often than patches suggested by generic APR tools but there is not enough evidence to verify if ‘bogus’ security claims are distinguishable from ‘true security’ claims. Finally, the number of switches to the patches suggested by security tool is significantly higher after the security information is revealed irrespective of correctness.

Limitations
The experiment was conducted in an academic setting, and focused on a limited sample of popular APR tools and popular vulnerability types.
Verifying the Generalization of Deep Learning to Out-of-Distribution Domains
Authors: Amir Guy , Maayan Osher , Zelazny Tom , Katz Guy , Schapira Michael 
Published: August 2024

AbstractDeep neural networks (DNNs) play a crucial role in the field of machine learning, demonstrating state-of-the-art performance across various application domains. However, despite their success, DNN-based models may occasionally exhibit challenges withgeneralization, i.e., may fail to handle inputs that were not encountered during training. This limitation is a significant challenge when it comes to deploying deep learning for safety-critical tasks, as well as in real-world settings characterized by substantial variability. We introduce a novel approach for harnessing DNN verification technology to identify DNN-driven decision rules that exhibit robust generalization to previously unencountered input domains. Our method assesses generalization within an input domain by measuring the level of agreement betweenindependently traineddeep neural networks for inputs in this domain. We also efficiently realize our approach by using off-the-shelf DNN verification engines, and extensively evaluate it on both supervised and unsupervised DNN benchmarks, including a deep reinforcement learning (DRL) system for Internet congestion control—demonstrating the applicability of our approach for real-world settings. Moreover, our research introduces a fresh objective for formal verification, offering the prospect of mitigating the challenges linked to deploying DNN-driven systems in real-world scenarios.
Beyond HIV Shame: Effects of Self-Forgiveness in Improving Mental Health in HIV-Positive Individuals in Poland
Authors: Skalski-Bednarz Sebastian Binyamin , Toussaint Loren L. , Surzykiewicz Janusz 
Published: August 2024

AbstractGuided by the bio-psycho-socio-spiritual approach, this randomized controlled trial assessed the efficacy of a self-forgiveness intervention among 60 HIV-positive individuals in Poland. Participants underwent a 90-min "Restore: The Journey Toward Self-Forgiveness" session, in contrast to a wait-list control group. The intervention significantly enhanced self-forgiveness, spirituality, mental well-being, and heart rate variability in response to a cognitive stressor (i.e., a mental arithmetic challenge). Significant effects were observed in both between-group and within-subject comparisons. These results support the incorporation of self-forgiveness into psychological rehabilitation programs for HIV to improve quality of life and health outcomes.
Uniqueness of tree stand composition and soil microbial communities are related across urban spruce-dominated forests
Authors: Korhonen Aku , Katavisto Oskar , Adamczyk Sylwia , Adamczyk Bartosz , Hamberg Leena 
Published: August 2024

Abstract
Context
Urban forest soils represent significant reservoirs of biodiversity in cities. Retaining this diversity under urban land-use change requires understanding on how species richness, community assembly and uniqueness of species assemblages are related to local forest characteristics and surrounding landscape structure.

Objectives
Our aim was to assess the significance and relative importance of logging history, tree species composition and urbanization in shaping soil microbial communities across urban spruce-dominated forest landscapes. We investigated responses of microbial diversity from three complementary viewpoints: local diversity, community assembly patterns and community uniqueness.

Methods
We collected soil bacterial and fungal metabarcoding data from 73 spruce-dominated forest sites distributed in three urban centers across southern Finland. We related these data to measurements of logging intensity, tree species composition and degree of urbanization.

Results
Logging intensity, tree species composition and urbanization affected site-scale microbial diversity, but the effects varied between microbial groups. Only logging intensity had a significant imprint on microbial assembly, and this effect was restricted to bacteria. Relative uniqueness of microbial assemblages at the landscape-scale was coupled with the uniqueness of tree species composition in all microbial groups, and further affected by tree diversity in saprotrophic fungi and urbanization in ectomycorrhizal fungi.

Conclusions
In the context of urban spruce-dominated forests, locally diverse tree stands are not necessarily the same as those that contribute the most to landscape-scale diversity. Identifying and preserving contrasting tree stand structures, which support distinctive soil microbial assemblages, may be the winning strategy in maintaining a wide range of soil microbial diversity.
The political economy of environmental legislation: evidence from the British Parliament
Authors: Adetutu Morakinyo O. 
Published: August 2024

AbstractThis study investigates how local air quality influences UK Parliament members’ votes on environmental and climate change legislation. Using micro-spatial information at the 1 km-by-1 km grid level, I link local air quality to members of UK parliament (MPs') voting records from 2009 to 2019. I find compelling evidence that MPs representing highly polluted areas are more likely to vote against stringent environmental legislation. I also provide evidence that local political economy considerations constrain pro-environmental voting behaviour: industrialization exacerbates the negative relationship between pollution and pro-environmental voting behaviour by further discouraging MPs representing industrial areas from supporting stringent environmental legislations. These findings underscore the public choice trade-offs between enacting stringent climate change policies and preserving local industry and jobs.
The residential occupation of the Gruta da Aroeira (Almonda, Portugal) cave site: shedding light on hunting and subsistence practices in the Middle Pleistocene of western Eurasia
Authors: Sanz Montserrat , Daura Joan , Rivals Florent , Zilhão João 
Published: August 2024

AbstractThe Gruta da Aroeira (Torres Novas, Portugal), with evidence of human occupancy dating back ∼ 400,000 years, is one of very few Middle Pleistocene cave sites to provide a fossil hominin cranium in association with Acheulean bifaces and the by-products of fire usage. Zooarchaeological, taphonomic and tooth-wear analyses suggest that the accumulation of the faunal remains and their modification are anthropogenic. Large game constituted the basis of subsistence, with equids and cervids being preferentially targeted. Woodland and open landscapes formed the ecosystems supporting the populations of the mammals that were preyed upon by the inhabitants of the site. Most of the animal carcasses were carried to, and fully butchered at the site, which was used as a residential base camp. The features of the Aroeira faunal assemblage foreshadow the subsistence strategies developed by the hunter-gatherers of the Middle and the Upper Palaeolithic and testify to their very ancient roots.
Policy makers as experts and teachers in need of reform: a critique of ‘evidence-based’ reforms of initial teacher education in Australia
Authors: Deuchar Andrew 
Published: August 2024

AbstractIn 2023 the Australian government mandated reforms to initial teacher education (ITE) courses across Australia. The key rationale of the Strong Beginnings Report is to better prepare teachers for the classroom and help stem the flow of teachers leaving the profession. This article suggests that the Strong Beginnings Report mobilises forms of evidence that privilege bureaucratic intervention over teachers’ insight and capacity. Using Bacchi’s ‘What’s the problem represented to be?’ approach to policy analysis, I argue that the Report selectively draws on evidence to position teachers as underprepared for the classroom and in need of reform. It does this by (i) suggesting that one of the main reasons teachers leave the profession is because they have inadequate skills, (ii) downplaying the broader social, economic and political context in which teacher attrition occurs, and (iii) deprofessionalising teaching by casting it as a technical process. Building on works that critique the impacts of standardisation, regulation and oversight in educational reform, I contend that the proposed reforms will do little to improve ITE or address teacher attrition. More than this, they will work to further discredit teachers and undermine the value of public education.
Pachychoroid disease: review and update
Authors: Cheung Chui Ming Gemmy , Dansingani Kunal K. , Koizumi Hideki , Lai Timothy Y. Y. , Sivaprasad Sobha , Boon Camiel J. F. , Van Dijk Elon H. C. , Chhablani Jay , Lee Won Ki , Freund K. Bailey 
Published: August 2024

AbstractThe pachychoroid disease spectrum is a phenotype characterized by alterations in choroidal vasculature which result in outer retinal and choriocapillaris damage and visual loss. The presence of pachyvessels is one of the key features of the pachychoroid phenotype. Recent imaging studies suggest that pachyvessels may form because of choroidal venous congestion in one or more quadrants. The formation of intervortex anastomosis may function as a compensatory mechanism to dissipate the increased venous pressure, while outflow obstruction has been hypothesized to occur at the site of the vortex vein exiting the sclera. This review aims to summarize recent imaging findings and discuss evolution in the understanding of pathogenesis of the pachychoroid disease spectrum. We have summarized notable treatment trials in central serous chorioretinopathy and polypoidal choroidal vasculopathy and included an update of the current diagnostic and management strategies of the entities that are part of the pachychoroid disease spectrum.
ODUSSEAS: Upgraded version with new reference scale and parameter determinations for 82 planet-host M dwarf stars in SWEET-Cat
Authors: Antoniadis-Karnavas A. , Sousa S. G. , Delgado-Mena E. , Santos N. C. , Andreasen D. T. 
Published: August 2024

Aims. Obtaining accurate derivations of stellar atmospheric parameters is crucial in the fields of stellar and exoplanet characterization. We present the upgraded version of our computational tool ODUSSEAS with a new reference scale applied to derive Teff and [Fe/H] values for M dwarfs.
Methods. The new reference dataset of ODUSSEAS consists of Teff values based on interferometry, and [Fe/H] values derived by applying updated values for the parallaxes. These reference parameters are related to the pseudo-equivalent widths (EWs) of more than 4000 stellar absorption lines. The machine learning Python “scikit learn” package creates models to determine the stellar parameters for subsequent analysis.
Results. We determined Teff and [Fe/H] values for 82 planet-host stars in SWEET-Cat. We demonstrate that our new version of ODUSSEAS is capable of determining the parameters with a greater accuracy than the original by comparing our results to other methods in literature. We also compared our parameters for the same stars by measuring their spectra obtained from several instruments, showing the consistency of our determinations with standard deviation of 30 K and 0.03 dex. Finally, we examined the correlation among planetary mass and stellar metallicity, confirming prior evidence indicating that massive planets mainly form around metal-rich stars in the case of M dwarfs as well.