bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kidney Donor Profile Index and allograft outcomes: interactive effects of estimated post-transplant survival score and ischaemic time
Authors: Prunster Janelle , Wong Germaine , Larkins Nicholas , Wyburn Kate , Francis Ross , Mulley William R , Ooi Esther , Pilmore Helen , Davies Christopher E , Lim Wai H 
Published: October 2022

ABSTRACTBackgroundThe Kidney Donor Profile Index (KDPI) is routinely reported by the donation agencies in Australia. We determined the association between KDPI and short-term allograft loss and assessed if this association was modified by the estimated post-transplant survival (EPTS) score and total ischaemic time.MethodsUsing data from the Australia and New Zealand Dialysis and Transplant Registry, the association between KDPI (in quartiles) and 3-year overall allograft loss was examined using adjusted Cox regression analysis. The interactive effects between KDPI, EPTS score and total ischaemic time on allograft loss were assessed.ResultsOf 4006 deceased donor kidney transplant recipients transplanted between 2010 and 2015, 451 (11%) recipients experienced allograft loss within 3 years post-transplant. Compared with recipients of kidneys with a KDPI of 0–25%, recipients who received donor kidneys with a KDPI &gt;75% experienced a 2-fold increased risk of 3-year allograft loss {adjusted hazard ratio [HR] 2.04 [95% confidence interval (CI) 1.53–2.71]}. The adjusted HRs for kidneys with a KDPI of 26–50% and 51–75% were 1.27 (95% CI 0.94–1.71) and 1.31 (95% CI 0.96–1.77), respectively. There were significant interactions between KDPI and EPTS scores (P-value for interaction &lt;.01) and total ischaemic time (P-value for interaction &lt;.01) such that the associations between higher KDPI quartiles and 3-year allograft loss were strongest in recipients with the lowest EPTS scores and longest total ischaemic time.ConclusionRecipients with higher post-transplant expected survival and transplants with longer total ischaemia who received donor allografts with higher KDPI scores experienced a greater risk of short-term allograft loss compared with those recipients with reduced post-transplant expected survival and with shorter total ischemia.
The ratio of measured and reference effective orifice areas for discriminating prosthetic aortic valve obstruction
Authors: Kim Kyu , Kim Dae-Young , Seo Jiwon , Cho Iksung , Shim Chi Young , Hong Geu-Ru , Ha Jong-Won 
Published: October 2022

Abstract

Aims
We aimed to evaluate the efficacy of the measured effective orifice area (EOA)/reference EOA ratio in discriminating mechanical prosthetic aortic valve (PAV) obstruction.

Methods and results
This is a retrospective study of 193 mechanical PAV patients with an elevated mean transprosthetic pressure gradient (PG) over 20 mmHg or peak velocity over 3 m/s. Of those, 143 patients were objectively proven PAV obstruction with cardiac computed tomography or surgical inspection. The EOA was measured using the continuity equation, and the reference EOA values were obtained from previous guidelines. The measured/reference EOA ratio was significantly lower in the obstruction group (0.63 ± 0.18 vs. 0.86 ± 0.17; P &lt; 0.001). The EOA ratio added incremental value for discriminating obstruction from the conventional parameters recommended in the guidelines. Receiver operating characteristic curve analysis revealed that the measured/reference EOA ratio discriminated PAV obstruction from those without obstruction [area under the curve (AUC), 0.840; 95% confidence interval, 0.783–0.898; P &lt; 0.001]. A cutoff of 0.71 had 73.4% sensitivity and 82.0% specificity. The novel diagnostic algorithm adding the EOA ratio had similar accuracy to previous guideline algorithms, including reference EOA, and conventional Doppler parameters (AUC, 0.763 vs. 0.731; P = 0.309). In patients with a large PAV (≥23 mm), the novel algorithm had higher accuracy than the previous algorithm (AUC, 0.788 vs. 0.642; P = 0.019).

Conclusion
The ratio of measured/reference EOA adds incremental value over conventional Doppler parameters and might be helpful for distinguishing PAV obstruction.
Long-Term and Intergenerational Effects of Education: Evidence from School Construction in Indonesia
Authors: Akresh Richard , Halim Daniel , Kleemans Marieke 
Published: October 2022

AbstractWe study long-term and intergenerational effects of the 1970s Indonesian school construction program. Exploiting variation across birth cohorts and districts in the number of schools built suggests that 43 years later men are more likely to work formally, outside agriculture, and migrate, and that men and women have better marriage market outcomes. Households with exposed women have higher living standards and pay more taxes. The mother's program exposure leads to increased schooling for her children, with larger effects in secondary and tertiary education. Cost-benefit analyses indicate that school construction leads to higher tax revenues and improved living standards, offsetting construction costs within 18–54 years.
RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif
Authors: Amodeo Maria E , Mitchell Shane P C , Pavan Vincent , Kuehner Jason N 
Published: October 2022

Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10–15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1–Nab3–Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3′-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
Health-care worker retention in post-conflict settings: a systematic literature review
Authors: Lin Tracy Kuo , Werner Kalin , Kak Mohini , Herbst Christopher H 
Published: October 2022

AbstractConflicts affect health-care systems not only during but also well beyond periods of violence and immediate crises by draining resources, destroying infrastructure and perpetrating human resource shortages. Improving health-care worker (HCW) retention is critical to limiting the strain placed on health systems already facing infrastructure and financial challenges. We reviewed the evidence on the retention of HCWs in fragile, conflict-affected and post-conflict settings and evaluated strategies and their likely success in improving retention and reducing attrition. We conducted a systematic review of studies, following PRISMA guidelines. Included studies (1) described a context that is post-conflict, conflict-affected or was transformed by war or a crisis; (2) examined the retention of HCWs; (3) were available in English, Spanish or French and (4) were published between 1 January 2000 and 25 April 2021. We identified 410 articles, of which 25 studies, representing 17 countries, met the inclusion criteria. Most of the studies (22 out of 25) used observational study designs and qualitative methods to conduct research. Three studies were literature reviews. This review observed four main themes: migration intention, return migration, work experiences and conditions of service and deployment policies. Using these themes, we identify a consolidated list of six push and pull factors contributing to HCW attrition in fragile, conflict-affected and post-conflict settings. The findings suggest that adopting policies that focus on improving financial incentives, providing professional development opportunities, establishing flexibility and identifying staff with strong community links may ameliorate workforce attrition.
Viridiplantae Body Plans Viewed Through the Lens of the Fossil Record and Molecular Biology
Authors: Niklas Karl J , Tiffney Bruce H 
Published: October 2022

Abstract
A review of the fossil record coupled with insights gained from molecular and developmental biology reveal a series of body plan transformations that gave rise to the first land plants. Across diverse algal clades, including the green algae and their descendants, the plant body plan underwent a unicellular $\to $ colonial $\to $ simple multicellular → complex multicellular transformation series. The colonization of land involved increasing body size and associated cell specialization, including cells capable of hydraulic transport. The evolution of the life-cycle that characterizes all known land plant species involved a divergence in body plan phenotypes between the haploid and diploid generations, one adapted to facilitate sexual reproduction (a free-water dependent gametophyte) and another adapted to the dissemination of spores (a more water-independent sporophyte). The amplification of this phenotypic divergence, combined with indeterminate growth in body size, resulted in a desiccation-adapted branched sporophyte with a cuticularized epidermis, stomates, and vascular tissues. Throughout the evolution of the land plants, the body plans of the sporophyte generation involved “axiation,” i.e., the acquisition of a cylindrical geometry and subsequent organographic specializations.
Do International Dispute Bodies Overreach? Reassessing World Trade Organization Dispute Ruling
Authors: Kucik Jeffrey , Puig Sergio 
Published: October 2022

AbstractCompliance with World Trade Organization dispute rulings declined in recent years. Governments frequently accuse the Appellate Body (AB) of exceeding its mandate by relying on precedent despite having no such authority. Is this criticism fair? We use new data on over 5,000 applications of legal precedent in AB rulings to test competing hypotheses. The “legal coherence hypothesis” says that legal systems adhere to precedent because they have strong incentives to appear consistent in their rulings over time. Alternatively, the “adaptation hypothesis” says that legal systems respond to political resistance, such as noncompliance, by subtly modifying precedent. The results lend greater support to the “adaptation hypothesis.” The AB is much more likely to drift from previous rulings when those decisions failed to induce compliance. The results speak to common criticisms about the intransigence of international legal systems and the ways in which international case law evolves.
Short Communication: effect of sodium butyrate, monensin, and butyric acid on the viability of Eimeria bovis sporozoites and their degree of damage to a bovine epithelial cell line
Authors: Klobucher Katrina N , Badger Rachel , Foxall Thomas , Erickson Peter S 
Published: October 2022

Abstract
This study aimed to determine the viability of sporozoites from Eimeria bovis when exposed to sodium butyrate (SB), monensin (MON), or butyric acid (BA), and to determine the effects of SB on sporozoite invasion of cells in comparison to MON as measured by the damage to a bovine epithelial cell line. To determine viability, isolated sporozoites were suspended in one of four treatments: control (CON) of cell culture medium alone, SB = 0.028 mg/mL suspended in control medium, MON = 0.01 mg/mL suspended in CON, and BA = 0.18 mg/mL suspended in CON. The number of live sporozoites was less for the MON and BA treatments compared to the CON and SB treatments. The number of dead sporozoites was similar regardless of treatment. There was a trend for treatment to affect the percent sporozoite viability. Control, SB and BA treatments were similar, while MON compared to control and SB had decreased percent viability. Results for MON, when compared to BA, were similar for percent viability. Lactate dehydrogenase (LDH) release was used to determine cellular damage to Madin Darby Bovine Kidney (MDBK) cells when exposed to E. bovis sporozoites in vitro. Cells were exposed to similar numbers of sporozoites and treated with: CON, SB = 0.028 mg/mL in control medium, MON = 0.01 mg/mL in control medium. Control LDH result (with sporozoites) was greater than both the SB and MON treatments while the LDH for SB and Mon and cells not exposed to sporozoites were similar. SB and MON were both shown to decrease cellular damage to MDBK cells as determined by decreased LDH release. SB has the potential to act as an anticoccidial alternative to MON.
Somatic inactivation of breast cancer predisposition genes in tumors associated with pathogenic germline variants
Authors: Lim Belle W X , Li Na , Mahale Sakshi , McInerny Simone , Zethoven Magnus , Rowley Simone M , Huynh Joanne , Wang Theresa , Lee Jue Er Amanda , Friedman Mia , Devereux Lisa , Scott Rodney J , Sloan Erica K , James Paul A , Campbell Ian G 
Published: October 2022

AbstractBackgroundBreast cancers (BCs) that arise in individuals heterozygous for a germline pathogenic variant in a susceptibility gene, such as BRCA1 and BRCA2, PALB2, and RAD51C, have been shown to exhibit biallelic loss in the respective genes and be associated with triple-negative breast cancer (TNBC) and distinctive somatic mutational signatures. Tumor sequencing thus presents an orthogonal approach to assess the role of candidate genes in BC development.MethodsExome sequencing was performed on paired normal-breast tumor DNA from 124 carriers of germline loss-of-function (LoF) or missense variant carriers in 15 known and candidate BC predisposition genes identified in the BEACCON case-control study. Biallelic inactivation and association with tumor genome features including mutational signatures and homologous recombination deficiency (HRD) score were investigated.ResultsBARD1-carrying TNBC (4 of 5) displayed biallelic loss and associated high HRD scores and mutational signature 3, as did a RAD51D-carrying TNBC and ovarian cancer. Biallelic loss was less frequent in BRIP1 BCs (4 of 13) and had low HRD scores. In contrast to other established BC genes, BCs from carriers of CHEK2 LoF (6 of 17) or missense (2 of 20) variant had low rates of biallelic loss. Exploratory analysis of BC from carriers of LoF variants in candidate genes such as BLM, FANCM, PARP2, and RAD50 found little evidence of biallelic inactivation.ConclusionsBARD1 and RAD51D behave as classic BRCA-like predisposition genes with biallelic inactivation, but this was not observed for any of the candidate genes. However, as demonstrated for CHEK2, the absence of biallelic inactivation does not provide definitive evidence against the gene’s involvement in BC predisposition.
What’s Old and New in Tuberculosis Vaccines for Children
Authors: Cranmer Lisa M , Cotton Mark F , Day Cheryl L , Nemes Elisa 
Published: October 2022

Abstract
Tuberculosis (TB) is a leading cause of global child mortality. Until the turn of the 21st century, Mycobacterium bovis bacille Calmette-Guerin (BCG) was the only vaccine to prevent TB. The pediatric TB vaccine pipeline has advanced in the past decade to include the evaluation of novel whole cell vaccines to replace infant BCG and investigation of subunit and whole cell vaccines to boost TB immunity during adolescence. We describe the history of BCG, current TB vaccine candidates in clinical trials, and the challenges and opportunities for future TB vaccine research in children. Children are a critical target population for TB vaccines, and expansion of the pediatric TB vaccine pipeline is urgently needed to end the TB pandemic.
Simultaneous operation of empyema and secondary thoracic deformity
Authors: Wang Wenlin , Long Weiguang , Liu Yang , Cai Bin , Luo Juan 
Published: October 2022

Abstract
Empyema often leads to secondary thoracic deformity, but it has not been treated before. In order to eliminate the harm of this deformity, we adopted simultaneous surgery to treat empyema and secondary deformity. In this article, we introduce the operation of a 35-year-old male patient with empyema and secondary thoracic deformity. We first cleared the lesions in the thoracic cavity, and then used MatrixRIB to correct the thoracic deformity, and achieved satisfactory results.
Surgical treatment of an overgrown asphyxiating thoracic dystrophy patient
Authors: Wang Wenlin , Long Weiguang , Liu Yang , Cai Bin , Luo Juan 
Published: October 2022

Abstract
Asphyxiating thoracic dystrophy may affect the development of multiple organs of the body, so these kinds of patients are usually short and thin. We met a 16-year-old female patient whose development exceeded the normal level. Although she was only 16 years old, her height was 167 cm and her weight was 71 Kg. Such development is extremely rare for this kind of patient, and there is no similar report in the previous literature. Comparatively, her thorax was narrow and small, and the ratio of thorax to trunk was uncoordinated, which made her situation particularly serious. We adopted Wenlin procedure combined with Wang procedure for correction. Since these two procedures were ideal orthopaedic operations, and could correct the depression effectively, we finally achieved satisfactory results.
LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA–target regulations in human diseases
Authors: Zhao Hongying , Yin Xiangzhe , Xu Haotian , Liu Kailai , Liu Wangyang , Wang Lixia , Zhang Caiyu , Bo Lin , Lan Xicheng , Lin Shihua , Feng Ke , Ning Shangwei , Zhang Yunpeng , Wang Li 
Published: October 2022

Abstract
An updated LncTarD 2.0 database provides a comprehensive resource on key lncRNA–target regulations, their influenced functions and lncRNA-mediated regulatory mechanisms in human diseases. LncTarD 2.0 is freely available at (http://bio-bigdata.hrbmu.edu.cn/LncTarD or https://lnctard.bio-database.com/). LncTarD 2.0 was updated with several new features, including (i) an increased number of disease-associated lncRNA entries, where the current release provides 8360 key lncRNA–target regulations, with 419 disease subtypes and 1355 lncRNAs; (ii) predicted 3312 out of 8360 lncRNA–target regulations as potential diagnostic or therapeutic biomarkers in circulating tumor cells (CTCs); (iii) addition of 536 new, experimentally supported lncRNA–target regulations that modulate properties of cancer stem cells; (iv) addition of an experimentally supported clinical application section of 2894 lncRNA–target regulations for potential clinical application. Importantly, LncTarD 2.0 provides RNA-seq/microarray and single-cell web tools for customizable analysis and visualization of lncRNA–target regulations in diseases. RNA-seq/microarray web tool was used to mining lncRNA–target regulations in both disease tissue samples and CTCs blood samples. The single-cell web tools provide single-cell lncRNA–target annotation from the perspectives of pan-cancer analysis and cancer-specific analysis at the single-cell level. LncTarD 2.0 will be a useful resource and mining tool for the investigation of the functions and mechanisms of lncRNA deregulation in human disease.
Markedness and Unmarkedness in Identities and Social Interaction
Authors: Brekhus Wayne H. 
Published: October 2022

Abstract
This chapter explores how the semiotic processes of cultural markedness and unmarkedness influence perception, drive social attention, and shape identities and interactional constructions of meaning. Markedness and unmarkedness are advanced as central sensitizing concepts for an expansive symbolic interactionism focused on power and complex inequalities. Symbolic interactionism (SI), like many longstanding theoretical traditions, developed in a historical context where sociologists gave greater epistemological weight to the ideas of scholars who represented unmarked, privileged social standpoints (e.g., white, Anglo-European/colonizer, male) rather than to those who represented marked positions of marginality. This has unnecessarily narrowed SI’s analytic foci and limited our full potential to address issues of structural inequality related to the most significant social problems of the twenty-first century. We can correct this problem by broadening our guiding canonical concerns to focus on the interactional and discursive dynamics of markedness and unmarkedness in the construction of meaning and the production of social power and knowledge. Scholars taking on the challenge of developing a critical symbolic interactionism focused on how social inequalities are produced and reproduced in everyday life are highlighted as exemplars for advancing SI research that analytically emphasizes the complex interplay of the marked and the unmarked.
Fire and the Transformation of Landscapes
Authors: Rowe Cassandra , Stevenson Janelle , Connor Simon , Adeleye Matthew 
Published: October 2022

Abstract
Australia is a fire-prone continent, and its long-term history of burning is the product of millennia of interactions between climatic and cultural fire. Australia is also highly diverse, both in terms of landscape composition and fire regimes, as well as ecosystem responses to fire-regime changes. This article presents a compilation of research on Holocene fire histories across major climatic and biogeographic zones of Australia into New Guinea. It then brings together research on pollen-based vegetation change and fire history for key sites within each zone. The result is a series of ecosystem ‘fire moments’ that explore fire’s role as an environmental transformer, an artefact of climate, vegetation, and culture. This article seeks to promote collaborative research in the examination of fire and its effects in time and space, ultimately seeking fine-resolution transdisciplinary studies that encompass a range of knowledge systems in partnership research and as a means to address future methodological challenges.
The Meaning of Ditches
Authors: Ballard Chris 
Published: October 2022

Abstract
When is a ditch not—or not simply—a ditch? This article explores the idea of the ditch or drain, drawing on ethnographic, archaeological, and agronomic accounts of field systems in the New Guinea Highlands. The ways in which Huli speakers use ditches to manage their landscapes, subsistence regimes, social relationships, histories, and cosmologies demonstrate the links between field systems composed of ditches and other kinds of networks. Huli understandings of the potency of water and other fluids govern their approaches to wetland drainage and provide a daily, habitual model for the challenges of management in the maintenance of fertility on a cosmological scale. The failure and abandonment of Huli drainage projects needs to be understood within this cosmological frame of struggle and inevitable decline.