bluuebunny/crossref_metadata_2025_split huggingface dataset:
Value and Circumstance
Authors: Macklem Timothy 
Published: December 2024

Abstract
Four values—justice, consent, equality, and collective decision in the form of law—have profoundly shaped the practice of law in the twentieth century and beyond. Value and Circumstance revisits these political and moral ideals, uncovering the relationship between value and the moment. Each of the four key subjects is explored by returning to first principles in a way that invites reflection on the nature and functions of morality itself. The author claims that there is a deep and ongoing connection (and sometimes a dialogue) between the ideal and the everyday. As such, each of those things can be fully understood, appreciated, and pursued only in partnership with the other, even in cases when that partnership is unspoken and unacknowledged. Moreover, the book argues that sound moral comprehension is immanent in experience and engagement. We learn fully what justice calls for by doing justice; learn consent properly through practising consent; learn just when, in what manner, and in what domains to pursue equality through engaging with the prevailing equalities (both secured and unsecured) of our particular times and places; and learn what law should look like only by deciding what law is to be. In this dynamic, the moral world is steadily enlarged by our ordinary engagement with it. We both construct and draw upon the realm of value, to which we are accountable for our flourishing. We cannot live well with reference to the ideal alone.
Afterword: A Philosopher’s Life and its Worth
Authors: Macklem Timothy 
Published: December 2024

Abstract
This chapter offers a brief tribute to the work of Joseph Raz, the purpose of which is to describe a distinctive sense of the value of research, in academic culture and beyond, of which this book seeks to be a manifestation. As I have put it elsewhere, at the end of a life we tend to think in terms of memorable achievements, of how large a mark a person has left upon the world. We tend to be impressed by prominent lives, lived at scale. Yet it is the things that are not noticed that truly shape the world, by quietly remaking its fabric in ways that are seldom recorded and very often aren’t remembered, things pursued steadily and wisely for their own small sake and all the better for that.
Between the Emergency and the Everyday
Authors: Jania Alex 
Published: December 2024

Abstract
This article tells the history of Miyagi Prefecture’s tsunami memorial halls, built following the 1933 Shōwa-Sarniku earthquake and tsunami, to grapple with the challenges of using memorials and collective memory to build resilience to future and recurring threats. The article takes the halls themselves as its main protagonists, following their memorial life cycles from their early conception, to their first lives as tsunami memorial halls, to their varied second lives after being repurposed, and finally to their steady destruction. Using insights from environmental history, memory studies, and critical disaster studies, the piece argues that the rise and fall of the tsunami memorial halls resulted from the incommensurability of human and geological timescales. It shows how the memory of and resilience to long-term seismic threats, which the halls tried to promote, gave way to a focus on everyday concerns at the human scale. These everyday concerns, caused by long-standing socioeconomic struggles and exacerbated in wartime and postwar Japan, led communities to shift the kinds of resilience they pursued with the halls. The article presents the memorial halls as a cautionary tale for those who use memory as a tool of resilience, arguing memorials themselves need to be made resilient to changing social and environmental conditions over deep time scales.
Survey of anatomic and clinical pathology services and infrastructure in Nigeria
Authors: Tucci Jonathan , Jacobs Jeremy W , Ibrahim Zainab U , Yusuf Aminu A , Umar Ali Bala , Milner Danny A , Eichbaum Quentin 
Published: December 2024

Abstract

Objectives
The paucity of data regarding the availability and extent of diagnostic medical services across sub-Saharan Africa hinders appropriate allocation of resources to improve health care in these regions. We assessed anatomic pathology (AP) and clinical pathology (CP) services in Nigeria, one of the most populous and fastest-growing countries in the world.

Methods
Two individual surveys (AP focused and CP focused) were developed by subject matter experts and administered to individuals involved in pathology and laboratory medicine diagnostic services at hospitals and laboratories across Nigeria between June and August 2022 using the American Society for Clinical Pathology email listserv.

Results
A total of 75 responses (29 AP and 46 CP) were received from 48 unique laboratories. Twenty-four sites provided AP services and 35 provided CP services. Eleven respondents performed both AP and CP services. Among AP services, basic surgical and cytopathology capabilities were available at most sites; however, the availability of automated technologies (eg, automated sample processing and staining) was more variable. Advanced diagnostic techniques, (eg, immunohistochemistry, human papillomavirus testing, molecular diagnostics) were rarely performed. The most frequently available CP services included hematology, microbiology, and chemistry. Microbiology services appeared to be among the most robust laboratory medicine services, particularly parasitology and bacteriology testing. Similar to AP services, more advanced diagnostic assays, such as flow cytometry, cytogenetics, and molecular testing, were largely unavailable.

Conclusions
These findings augment earlier studies and identify gaps that should be prioritized from a policy perspective to improve medical services and the overall health care infrastructure in Nigeria.
On Legal Expertise
Authors: Jiménez Felipe 
Published: December 2024

Abstract
Legal experts can reliably ascertain which legal norms are valid, and therefore which legal propositions are true. Legal experts are in this position because they have a grasp of the deep cognitive structure of law: the habits, commitments, and values that characterize the practice of legal argument in a specific jurisdiction. Legal expertise, thus understood, determines the content of the law, which is therefore not reducible to an aggregation of authoritative legal texts. Because social facts about legal experts’ values and commitments can determine the content of the law, references to moral considerations and principles of justice as valid legal reasons, in legal argument, are not a problem for (at least some forms of) legal positivism. Legal expertise thus shows that non-positivists might be right about (as they would put it) the irreducibility of legal content to communicative content without being right about the claims that moral facts determine the content of the law or that the validity of legal norms turns on moral considerations. Legal expertise also plays an important causal role in legal decision-making and is not, as some of the literature on judicial decision-making might suggest, epiphenomenal. From a moral perspective, while the existence of a class of legal experts is not necessarily valuable, it does have certain benefits, particularly in conditions of moral disagreement.
Overcoming COVID-19 vaccine hesitancy: An investigation of the Foreign Language Effect
Authors: Schmid Monika S , Roehr-Brackin Karen 
Published: December 2024

Abstract
Vaccine hesitancy remains one of the greatest challenges for global health. Previous research has shown that the recruitment of rational processes is increased in hypothetical decision-making scenarios when the underpinning information is presented in a foreign language. We investigate whether vaccine campaigns could benefit from this Foreign Language Effect (FLE) in order to overcome vaccine hesitancy. We conceptually replicated a recent study on COVID-19 vaccine campaigns (Freeman et al. 2021) to assess whether information can more successfully reduce vaccine hesitancy when presented in a foreign language as well as how other factors, such as language proficiency, impact the FLE. Based on a survey of 436 participants, we conclude that there may be the potential to lower vaccine hesitancy among individuals with English as a foreign language by presenting information in English, rather than in their native language. Conversely, participants who are native speakers of English and negatively predisposed against the COVID-19 vaccine react more negatively to information they read in a foreign language compared to their native language.
Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy
Authors: Xu Long , Yang Qiang , Dong Weihe , Li Xiaokun , Wang Kuanquan , Dong Suyu , Zhang Xianyu , Yang Tiansong , Luo Gongning , Liao Xingyu , Gao Xin , Wang Guohua 
Published: December 2024

Abstract
Accurate prediction of binding between human leukocyte antigen (HLA) class I molecules and antigenic peptide segments is a challenging task and a key bottleneck in personalized immunotherapy for cancer. Although existing prediction tools have demonstrated significant results using established datasets, most can only predict the binding affinity of antigenic peptides to HLA and do not enable the immunogenic interpretation of new antigenic epitopes. This limitation results from the training data for the computational models relying heavily on a large amount of peptide-HLA (pHLA) eluting ligand data, in which most of the candidate epitopes lack immunogenicity. Here, we propose an adaptive immunogenicity prediction model, named MHLAPre, which is trained on the large-scale MS-derived HLA I eluted ligandome (mostly presented by epitopes) that are immunogenic. Allele-specific and pan-allelic prediction models are also provided for endogenous peptide presentation. Using a meta-learning strategy, MHLAPre rapidly assessed HLA class I peptide affinities across the whole pHLA pairs and accurately identified tumor-associated endogenous antigens. During the process of adaptive immune response of T-cells, pHLA-specific binding in the antigen presentation is only a pre-task for CD8+ T-cell recognition. The key factor in activating the immune response is the interaction between pHLA complexes and T-cell receptors (TCRs). Therefore, we performed transfer learning on the pHLA model using the pHLA-TCR dataset. In pHLA binding task, MHLAPre demonstrated significant improvement in identifying neoepitope immunogenicity compared with five state-of-the-art models, proving its effectiveness and robustness. After transfer learning of the pHLA-TCR data, MHLAPre also exhibited relatively superior performance in revealing the mechanism of immunotherapy. MHLAPre is a powerful tool to identify neoepitopes that can interact with TCR and induce immune responses. We believe that the proposed method will greatly contribute to clinical immunotherapy, such as anti-tumor immunity, tumor-specific T-cell engineering, and personalized tumor vaccine.
CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs
Authors: Ferrari Ivan , De Grossi Federica , Lai Giancarlo , Oliveto Stefania , Deroma Giorgia , Biffo Stefano , Manfrini Nicola 
Published: December 2024

Abstract
Conventional approaches to predict protein involvement in cancer often rely on defining either aberrant mutations at the single-gene level or correlating/anti-correlating transcript levels with patient survival. These approaches are typically conducted independently and focus on one protein at a time, overlooking nucleotide substitutions outside of coding regions or mutational co-occurrences in genes within the same interaction network. Here, we present CancerHubs, a method that integrates unbiased mutational data, clinical outcome predictions and interactomics to define novel cancer-related protein hubs. Through this approach, we identified TGOLN2 as a putative novel broad cancer tumour suppressor and EFTUD2 as a putative novel multiple myeloma oncogene.
Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method
Authors: Xi Duo , Zhang Minjianan , Shang Muheng , Du Lei , Han Junwei ,   Alzheimer’s Disease Neuroimaging Initiative
Published: December 2024

Abstract

Motivation
Alzheimer’s disease (AD) typically progresses gradually for ages rather than suddenly. Thus, staging AD progression in different phases could aid in accurate diagnosis and treatment. In addition, identifying genetic variations that influence AD is critical to understanding the pathogenesis. However, staging the disease progression and identifying genetic variations is usually handled separately.

Results
To address this limitation, we propose a novel sparse multi-stage multi-task mixed-effects collaborative longitudinal regression method (MSColoR). Our method jointly models long disease progression as a multi-stage procedure and identifies genetic risk factors underpinning this complex trajectory. Specifically, MSColoR models multi-stage disease progression using longitudinal neuroimaging-derived phenotypes and associates the fitted disease trajectories with genetic variations at each stage. Furthermore, we collaboratively leverage summary statistics from large genome-wide association studies to improve the powers. Finally, an efficient optimization algorithm is introduced to solve MSColoR. We evaluate our method using both synthetic and real longitudinal neuroimaging and genetic data. Both results demonstrate that MSColoR can reduce modeling errors while identifying more accurate and significant genetic variations compared to other longitudinal methods. Consequently, MSColoR holds great potential as a computational technique for longitudinal brain imaging genetics and AD studies.

Availability and implementation
The code is publicly available at https://github.com/dulei323/MSColoR.
European Society of Endocrinology Curriculum and Training Recommendation in Endocrinology
Authors: Luger Anton , Durkan Maeve , Christ-Crain Mirjam , Marques Pedro 
Published: December 2024

Abstract
The European Society of Endocrinology (ESE) and the Union Européenne des Médecins Spécialistes (U.E.M.S.) Section and Board of Endocrinology have produced a Curriculum and Training Recommendation in Endocrinology to provide updated recommendations concerning the content and structure of postgraduate training. Cornerstones of the Curriculum are the integrity of Endocrinology not to be divided into subspecialties such as diabetology or thyroidology, recommendation of 6 years full-time training comprising 1–3 years (preferably 2–3 years) of General Internal Medicine followed by 3–5 years of specialist training in Endocrinology across 13 core areas. In addition to knowledge and experience in the many fields of Endocrinology, the Curriculum includes specific attitudes, communication skills, training to work in and lead multidisciplinary teams, resource management, quality assurance, human-error management, and critical incidents reporting as well as the commitment to life-long learning expected from a trainee and from an Endocrinologist. The Curriculum also includes requirements for training centres, for assessment of training and for competencies of trainers. The aim of the ESE Curriculum and Training Recommendation in Endocrinology is to harmonise postgraduate training and help provide the best medical care for patients with endocrine diseases across Europe.
The C. elegans LON-1 protein requires its CAP domain for function in regulating body size and BMP signaling
Authors: Serrano Maria Victoria , Cottier Stéphanie , Wang Lianzijun , Moreira-Antepara Sergio , Nzessi Anthony , Liu Zhiyu , Williams Byron , Lee Myeongwoo , Schneiter Roger , Liu Jun 
Published: December 2024

Abstract
The CAP (cysteine-rich secretory proteins, antigen-5, and pathogenesis-related) proteins are widely expressed and have been implicated to play diverse roles ranging from mammalian reproduction to plant immune response. Increasing evidence supports a role of CAP proteins in lipid binding. The Caenorhabditis elegans CAP protein LON-1 is known to regulate body size and bone morphogenetic protein (BMP) signaling. LON-1 is a secreted protein with a conserved CAP domain and a C-terminal unstructured domain with no homology to other proteins. In this study, we report that the C-terminal domain of LON-1 is dispensable for its function. Instead, key conserved residues located in the CAP domain are critical for LON-1 function in vivo. We further showed that LON-1 is capable of binding sterol, but not fatty acid, in vitro, and that certain key residues implicated in LON-1 function in vivo are also important for LON-1 sterol binding in vitro. These findings suggest a role of LON-1 in regulating body size and BMP signaling via sterol binding.
Proteolytic regulation of mitochondrial magnesium channel by m-AAA protease and prohibitin complex
Authors: Joshi Alaumy , Stanfield Rachel A , Spletter Andrew T , Gohil Vishal M 
Published: December 2024

Abstract
Mitochondrial membrane phospholipid cardiolipin is essential for the stability of several inner mitochondrial membrane protein complexes. We recently showed that the abundance of mitochondrial magnesium channel MRS2 is reduced in models of Barth syndrome, an X-linked genetic disorder caused by a remodeling defect in cardiolipin. However, the mechanism underlying the reduced abundance of MRS2 in cardiolipin-depleted mitochondria remained unknown. In this study, we utilized yeast mutants of mitochondrial proteases to identify an evolutionarily conserved m-AAA protease, Yta10/Yta12, responsible for degrading Mrs2. The activity of m-AAA protease is regulated by the inner mitochondrial membrane scaffolding complex prohibitin, and consistent with this role, we find that Mrs2 turnover is increased in yeast prohibitin mutants. Importantly, we find that deleting Yta10 in cardiolipin-deficient yeast cells restores the steady-state levels of Mrs2 to the wild-type cells, and the knockdown of AFG3L2, a mammalian homolog of Yta12, increases the abundance of MRS2 in a murine muscle cell line. Thus, our work has identified the m-AAA protease/prohibitin complex as an evolutionarily conserved regulator of Mrs2 that can be targeted to restore Mrs2 abundance in cardiolipin-depleted cells.
Metaxin-2 tunes mitochondrial transportation and neuronal function in Drosophila
Authors: Zhang Ting , Li Ling , Fan Xiaoyu , Shou Xinyi , Ruan Yina , Xie Xiaojun 
Published: December 2024

Abstract
Metaxins are a family of evolutionarily conserved proteins that reside on the mitochondria outer membrane (MOM) and participate in the protein import into the mitochondria. Metaxin-2 (Mtx2), a member of this family, has been identified as a key component in the machinery for mitochondrial transport in both C. elegans and human neurons. To deepen our understanding of Mtx2's role in neurons, we examined the homologous genes CG5662 and CG8004 in Drosophila. The CG5662 is a non-essential gene while CG8004 null mutants die at late pupal stages. The CG8004 protein is widely expressed throughout the Drosophila nervous system and is targeted to mitochondria. However, neuronal CG8004 is dispensable for animal survival and is partially required for mitochondrial distribution in certain neuropil regions. Conditional knockout of CG8004 in adult gustatory receptor neurons (GRNs) impairs mitochondrial trafficking along GRN axons and diminishes the mitochondrial quantities in axon terminals. The absence of CG8004 also leads to mitochondrial fragmentation within GRN axons, a phenomenon that may be linked to mitochondrial transport through its genetic interaction with the fusion proteins Marf and Opa1. While the removal of neuronal CG8004 is not lethal during the developmental stage, it does have consequences for the lifespan and healthspan of adult Drosophila. At last, double knockout (KO) of CG5662 and CG8004 shows similar phenotypes as the CG8004 single KO, suggesting that CG5662 does not compensate for the loss of CG8004. In summary, our findings suggest that CG8004 plays a conserved and context-dependent role in axonal mitochondrial transport, as well it is important for sustaining neuronal function. Therefore, we refer to CG8004 as the Drosophila Metaxin-2 (dMtx2).
Mining the cucumber core collection: Phenotypic and genetic characterization of morphological diversity for fruit quality characteristics
Authors: Lin Ying-Chen , Weng Yiqun , Fei Zhangjun , Grumet Rebecca 
Published: December 2024

Abstract
Commercial value of cucumber is primarily driven by fruit quality. However, breeding goals frequently focus on production constraints caused by biotic and abiotic stresses. As sources of resistances are often present in unadapted germplasm, we sought to provide morphological and genetic information characterizing the diversity of fruit quality traits present in the CucCAP cucumber core collection. These 388 accessions representing &gt;96% of the genetic diversity for cucumber present in the U.S. National Plant Germplasm System harbor important sources of resistances and extensive morphological diversity. Data were collected for skin color, length/diameter ratio (L/D), tapering, curvature, and spine density for young fruits [5-7 days post-pollination (dpp)], and length, diameter, L/D, skin color, netting, seed cavity size, flesh thickness, hollowness, and flesh color for mature fruits (30-40 dpp. Significant associations of SNPs with each trait were identified from genome-wide association studies (GWAS). In several cases, QTL for highly correlated traits were closely clustered. Principal component analysis, driven primarily by the highly correlated traits of fruit length, young and mature L/D ratios, and curvature showed a clear divergence of East Asian accessions. Significant SNPs contributing to the longest fruits, including development-stage specific QTL, were distributed across multiple chromosomes, indicating broad genomic effects of selection. Many of the SNPs identified for the various morphological traits were in close vicinity to previously identified fruit trait QTL and candidate genes, while several novel genes potentially important for these traits were also identified.
Estimation of the Harvey Bradshaw Index from the Patient Reported Outcome-2 in Crohn’s Disease
Authors: Khanna Reena , Son Surim , Zou Guangyong , Roshanov Pavel S 
Published: December 2024

Abstract

Background
Many registrational trials in Crohn’s disease assess treatment efficacy with the 2-item Patient-Reported Outcome (PRO2), while the Harvey–Bradshaw Index (HBI) is prominent in pragmatic trials and clinical practice. The translation between PRO2 and HBI has not been established.

Methods
Data from a Phase 3 trial of vedolizumab in Crohn’s disease were used to determine the Pearson correlation between PRO2 and HBI. Linear regression was used to fit equations that estimate between indices; 95% prediction intervals were determined for HBI scores corresponding to PRO2 thresholds for disease activity. Internal validation of the conversion equations was performed using the bootstrap methods.

Results
PRO2 and HBI were highly correlated at baseline (r = 0.75 95% confidence interval (CI) 0.73-0.78; P &lt; .001), induction (r = 0.87; 95% CI, 0.85-0.88; P &lt; .001), and maintenance (r = 0.88; 95% CI, 0.85-0.90; P &lt; .001). PRO2 and HBI change scores were moderately correlated (r = 0.72; 95% CI 0.69-0.75; P &lt; .001) in induction and more strongly correlated during maintenance (r = 0.81; 95% CI 0.78- 0.84; P &lt; .001). Regression equations for conversion of PRO2 to HBI from all cohorts (induction, maintenance, randomized, open-label) support an approximate conversion where HBI = 0.5 PRO2. As expected from the imperfect correlation between scores, the prediction intervals were generally wide. No evidence of overfitting was seen in bootstrap internal validation.

Conclusions
PRO2 and HBI correlate strongly and conversion between them is possible. These findings facilitate the practical application of trial results and clinical guidelines.