bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations
Authors: Chen Qingyu , Allot Alexis , Leaman Robert , Islamaj Rezarta , Du Jingcheng , Fang Li , Wang Kai , Xu Shuo , Zhang Yuefu , Bagherzadeh Parsa , Bergler Sabine , Bhatnagar Aakash , Bhavsar Nidhir , Chang Yung-Chun , Lin Sheng-Jie , Tang Wentai , Zhang Hongtong , Tavchioski Ilija , Pollak Senja , Tian Shubo , Zhang Jinfeng , Otmakhova Yulia , Yepes Antonio Jimeno , Dong Hang , Wu Honghan , Dufour Richard , Labrak Yanis , Chatterjee Niladri , Tandon Kushagri , Laleye Fréjus A A , Rakotoson Loïc , Chersoni Emmanuele , Gu Jinghang , Friedrich Annemarie , Pujari Subhash Chandra , Chizhikova Mariia , Sivadasan Naveen , VG Saipradeep , Lu Zhiyong
Published: August 2022

The coronavirus disease 2019 (COVID-19) pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature—at a rate of about 10 000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200 000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g. Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text-mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset—consisting of over 30 000 articles with manually reviewed topics—was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181 and 0.9394 for macro-F1-score, micro-F1-score and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g. 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Database URL https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/
EfGD: the Erianthus fulvus genome database
Authors: Qian Zhenfeng , Li Xuzhen , He Lilian , Gu Shujie , Shen Qingqing , Rao Xibing , Zhang Rongqiong , Di Yining , Xie Linyan , Wang Xianhong , Chen Shuying , Dong Yang , Li Fusheng
Published: August 2022

Erianthus fulvus (TaxID: 154759) is a valuable germplasm resource in sugarcane breeding and research and has excellent agronomic traits, such as drought resistance, cold resistance, barren tolerance and high brix. With a stable chromosome number (2n = 20) and a small genome (0.9 Gb), it is an ideal candidate for research on sugarcane. Next-generation sequencing technology has enabled a growing number of studies to focus on genomics. Due to the large amount of omics data available, a centralized platform is necessary for ensuring the consistency, independence and maintainability of these large-scale datasets through storage, analysis and integration. Here, we present a comprehensive database for the E. fulvus genome, EfGD. By using the new high-quality reference genome and its annotations, the EfGD provides the largest whole-genome sequencing reference dataset for E. fulvus, which archives 27 165 protein-coding genes and 55 564 488 SNPs from 202 newly resequenced genomes. Furthermore, we created a user-friendly graphical interface for visualizing genomic diversity, population structure and evolution and provided other tools on an open platform.

Database URL: https://efgenome.ynau.edu.cn
‘Open’ or ‘Closed’? Participation in English Manorial Presentment Juries, c.1310–c.1600: A Quantitative Approach
Authors: Gibbs Spike
Published: August 2022

Historians of both the medieval and early modern eras have characterised the governing structures of rural communities as being dominated by local elites. However, interpretations are hampered by a lack of clear criteria against which to evaluate whether a village-governance regime was ‘open,’ and characterised by wide participation, or ‘closed’, and characterised by the narrow restriction of office to an elite group, making it difficult to draw comparisons across time and space. This article uses a set of quantitative methodologies to solve this problem. It examines presentment juries in the manorial court, a governing institution which straddles the late medieval and early modern period, in three case-study communities for the period from 1310 to 1600. By applying four measures of participation, the article reveals that post-Black Death juries were characterised by a nuanced system of restriction. They were open in the sense that a large proportion of the male population, drawn from a wide range of families, acted as jurors and there was a continuous turnover in jury panels. However, they were also closed in that a small group of prominent individuals and families served a disproportionately frequent number of times. The results also question an established narrative of increasing monopolisation of village governance by a new ‘middling sort’ over the sixteenth century. Instead, change over time and space reveals a variable set of trends, with no universal linear pattern. The inflexibility of manorial institutions, combined with local demographic regimes and trends in landholding, led to significant differences in political participation between communities.
A novel Candida glabrata doxycycline-inducible system for in vitro/in vivo use
Authors: Schrevens S , Sanglard D
Published: August 2022

Candida glabrata is an important pathogen causing superficial to invasive disease in human. Conditional expression systems are helpful in addressing the function of genes and especially when they can be applied to in vivo studies. Tetracycline-dependent regulation systems have been used in diverse fungi to turn-on (Tet-on) or turn-off (Tet-off) gene expression either in vitro but also in vivo in animal models. Up to now, only a Tet-off expression has been constructed for gene expression in C. glabrata. Here, we report a Tet-on gene expression system which can be used in vitro and in vivo in any C. glabrata genetic background. This system was used in a mice model of systemic infection to demonstrate that the general amino acid permease Gap1 is important for C. glabrata virulence.
Differential hydroxylation efficiency of the two non-heme carotene hydroxylases: DcBCH1, rather than DcBCH2, plays a major role in carrot taproot
Authors: Li Tong , Liu Jie-Xia , Deng Yuan-Jie , Duan Ao-Qi , Liu Hui , Zhuang Fei-Yun , Xiong Ai-Sheng
Published: August 2022

Carotene hydroxylase plays an important role in catalyzing the hydroxylation of carotene to xanthopylls, including two types: non-heme carotene hydroxylase (BCH type) and heme-containing cytochrome P450 hydroxylase (P450 type). Two BCH-encoding genes were annotated in the carrot genome. However, the role of BCHs and whether there are functional interactions between the duplicated BCHs in carrot remains unclear. In this study, two BCH encoding genes, DcBCH1 and DcBCH2, were cloned from carrot. The relative expression level of DcBCH1 was much higher than that of DcBCH2 in carrot taproots with different carotene accumulation levels. Overexpression of DcBCH1 in ‘KRD’ (high carotene accumulated) carrot changed the taproot color from orange to yellow, accompanied by substantial reductions in α-carotene and β-carotene. There was no obvious change in taproot color between transgenic ‘KRD’ carrot overexpressing DcBCH2 and control carrot. Simultaneously, the content of α-carotene in the taproot of DcBCH2-overexpressing carrot decreased, but the content of β-carotene did not change significantly in comparison with control carrot. Using the CRISPR/Cas9 system to knock out DcBCH1 in ‘KRD’ carrot lightened the taproot color from orange to pink-orange; the content of α-carotene in the taproot increased slightly, while the β-carotene content was still significantly decreased, compared with control carrot. In DcBCH1-knockout carrot, the transcript level of DcBCH2 was significantly increased. These results indicated that in carrot taproot, DcBCH1 played the main function of BCH enzyme, which could hydroxylate α-carotene and β-carotene; DcBCH1 and DcBCH2 had functional redundancy, and these two DcBCHs could partially compensate for each other.
Introgression of clubroot resistant gene into
Brassica oleracea
L. from
Brassica rapa
based on homoeologous exchange
Authors: Zhu Mingzhao , Yang Limei , Zhang Yangyong , Zhuang Mu , Ji Jialei , Hou Xilin , Li Zhansheng , Han Fengqing , Fang Zhiyuan , Lv Honghao , Wang Yong
Published: August 2022

Clubroot is a soil-borne disease in cabbage (Brassica oleracea L. var. capitata L.) caused by Plasmodiophora brassicae, which poses a great threat to cabbage production. However, clubroot resistance (CR) genes in Brassica rapa could be introduced into the cabbage via breeding to make it clubroot resistant. In this study, CR genes from B. rapa were introduced into the cabbage genome and the mechanism of gene introgression was explored. Two methods were used to create CR materials: (i) The fertility of CR Ogura CMS cabbage germplasms containing CRa was restored by using an Ogura CMS restorer. After cytoplasmic replacement and microspore culture, CRa-positive microspore individuals were obtained. (ii) Distant hybridization was performed between cabbage and B. rapa, which contained three CR genes (CRa, CRb, and Pb8.1). Finally, BC2 individuals containing all three CR genes were obtained. Inoculation results showed that both CRa-positive microspore individuals and BC2 individuals containing three CR genes were resistant to race 4 of P. brassicae. Sequencing results from CRa-positive microspore individuals with specific molecular markers and genome-wide association study (GWAS) showed penetration at the homologous position of the cabbage genome by a 3.42 Mb CRa containing a fragment from B. rapa; indicating homoeologous exchange (HE) as the theoretical basis for the introgression of CR resistance. The successful introduction of CR into the cabbage genome in the present study can provide useful clues for creating introgression lines within other species of interest.
Glutamine synthetase gene PpGS1.1 negatively regulates the powdery mildew resistance in Kentucky bluegrass
Authors: Sun Xiaoyang , Xie Fuchun , Chen Yajun , Guo Zhixin , Dong Lili , Qin Ligang , Shi Zhenjie , Xiong Liangbing , Yuan Runli , Deng Wenjing , Jiang Yiwei
Published: August 2022

Excessive nitrogen (N) application may induce powdery mildew (PM) in perennial grasses, but the resistance mechanisms to PM remain unclear. This study evaluated the physiological and molecular mechanisms of PM resistance affected by N supplies in Kentucky bluegrass (Poa pratensis L.). Cultivar ‘Bluemoon’ (N tolerant) and ‘Balin’ (N sensitive) were treated with low N (0.5 mM), normal N (15 mM), and high N (30 mM) for 21 d in a greenhouse. With increasing N levels, the disease growth was more severe in ‘Balin’ than in ‘Bluemoon’. RNA-seq and weighted gene coexpression network analysis revealed that the PpGS1.1 gene encoding glutamine synthetase was a potential hub gene for PM resistance after comparisons across cultivars and N treatments. The N metabolism pathway was connected with the plant–pathogen interaction pathway via PpGS1.1. The expression of PpGS1.1 in rice protoplasts indicated that the protein was located in the nucleus and cytoplasm. Overexpression of PpGS1.1 in wild-type Kentucky bluegrass increased carbon and N contents, and the transgenic plants became more susceptible to PM with a lower wax density. The most differentially expressed genes (DEGs) for N metabolism were upregulated and DEGs for fatty acid metabolism pathway were downregulated in the overexpression lines. The results elucidated mechanisms of PM resistance in relation to N metabolism in Kentucky bluegrass.
Clinical decision support malfunctions related to medication routes: a case series
Authors: Wright Adam , Nelson Scott , Rubins David , Schreiber Richard , Sittig Dean F
Published: August 2022

Objective

To identify common medication route-related causes of clinical decision support (CDS) malfunctions and best practices for avoiding them.

Materials and Methods

Case series of medication route-related CDS malfunctions from diverse healthcare provider organizations.

Results

Nine cases were identified and described, including both false-positive and false-negative alert scenarios. A common cause was the inclusion of nonsystemically available medication routes in value sets (eg, eye drops, ear drops, or topical preparations) when only systemically available routes were appropriate.

Discussion

These value set errors are common, occur across healthcare provider organizations and electronic health record (EHR) systems, affect many different types of medications, and can impact the accuracy of CDS interventions. New knowledge management tools and processes for auditing existing value sets and supporting the creation of new value sets can mitigate many of these issues. Furthermore, value set issues can adversely affect other aspects of the EHR, such as quality reporting and population health management.

Conclusion

Value set issues related to medication routes are widespread and can lead to CDS malfunctions. Organizations should make appropriate investments in knowledge management tools and strategies, such as those outlined in our recommendations.
Effects of rumen-native microbial feed supplementation on milk yield, composition, and feed efficiency in lactating dairy cows
Authors: Valldecabres Ainhoa , Gilmore Sean P , Embree Jordan J , Zhelev Ivan Z , Gaffney James R , Marotz Clarisse A , Yang Fan , Izzo Andrew S , Embree Mallory M , Lago Alfonso
Published: August 2022

The objective of this study was to evaluate the effects of two rumen-native microbial feed supplements (MFS) on milk production, milk composition, and feed efficiency. A total of 90 multiparous cows between 40 and 60 d in milk were enrolled in a randomized block design study. Within each block (baseline milk yield), cows were randomly assigned to: control (no microbial feed supplementation), MFS1 (0.33 g/kg total mixed ration [TMR] of an MFS containing a minimum of Clostridium beijerinckii at 2 × 106 CFU/g and Pichia kudriavzevii at 2 × 107 CFU/g), or MFS2 (0.33 g/kg TMR of a MFS containing a minimum of C. beijerinckii at 2 × 106 CFU/g, P. kudriavzevii at 2 × 107 CFU/g, Ruminococcus bovis at 2 × 107 CFU/g, and Butyrivibrio fibrisolvens at 2 × 107 CFU/g). Cows were housed in a single group and fed the study diets ad libitum for 270 d. Individual milk yield was recorded using electronic milk meters, and milk fat and protein were measured using optical in-line analyzers at each of two daily milkings. Treatment and treatment by time effects were assessed through multiple linear regression analyses. Treatment effects were observed for milk and energy-corrected milk (ECM) yields, milk fat and protein yields and concentrations, dry matter intake (DMI), and feed efficiency; those effects were conditional to time for milk yield, DMI, and feed efficiency. Overall, milk, ECM, fat, and protein yields were higher for MFS2 compared with control cows (+3.0, 3.7, 0.12, and 0.12 kg/d, respectively). Compared with MFS1, milk yield was higher and protein yield tended to be higher for MFS2 cows (+2.9 and 0.09 kg/d, respectively). In contrast, MFS1 cows produced 0.17 and 0.08 units of percentage per day more fat and protein than MFS2 cows, and 0.07 units of percentage per day more protein than control cows. Dry matter intake and feed efficiency were higher for MFS2 cows compared with MFS1 cows (+1.3 kg/d and 0.06, respectively), and feed efficiency was higher for MFS2 cows compared with control cows (+0.04). Where observed, treatment by time effects suggest that the effects of MFS2 were more evident as time progressed after supplementation was initiated. No effects of microbial supplementation were observed on body weight, body condition score, somatic cell count, or clinical mastitis case incidence. In conclusion, the supplementation of MFS2 effectively improved economically important outcomes such as milk yield, solids, and feed efficiency.
iNaturalist is useful at enhancing biodiversity studies as evident from southern African freshwater crabs (Decapoda: Brachyura: Potamonautidae)
Authors: Daniels Savel R , Barnes Aaron , Peer Nasreen , Egan Vincent T , Taylor Ricky , Taylor Robert W , van der Colff Dewidine
Published: August 2022

The value of the citizen science platform iNaturalist was explored using photographic observations of southern African freshwater crabs (Potamonautidae Bott, 1970, among two genera Potamonautes sensu stricto MacLeay, 1838 and MartimonautesCumberlidge & Daniels, 2022) in combination with specimen data deposited in the South African Museum (Iziko Museums of Cape Town, South Africa). Species identification of photographic observations were assessed, and the identification of taxa corrected where necessary. From these records, the habitat type and distribution of the species were noted. The area of occupancy (AOO) and the extent of occurrence (EOO) were calculated where range extensions for species were observed. The results demonstrate that riverine/mountain stream freshwater crabs are over-represented in their frequency but species occurring in swamps/forests were under-represented. Using iNaturalist spatial data for South Africa we can identify several unsampled gaps in the country which included the Free State and North West, Gauteng and the Northern Cape, followed by Limpopo, Mpumalanga, and the Eastern Cape provinces. The Western Cape and KwaZulu-Natal had the highest number of freshwater crab records on iNaturalist. The remaining southern African countries, Angola, Botswana, Eswatini, Lesotho, Malawi, Mozambique, Namibia, and Zimbabwe, have few iNaturalist records. Range extensions were observed in four South African species based on iNaturalist records (P. clarusGouws, Stewart & Coke, 2000, P. flavusjoDaniels, Phiri, & Bayliss, 2014, P. isimangaliso Peer & Gouws, 2015, and P. mariepskoppieDaniels, Barnes, Marais & Gouws, 2021) with increases in AOO and EOO. We also observed a new undescribed freshwater crab on iNaturalist and corroborated this observation by sequencing these specimens for the cytochrome oxidase one subunit (COI) locus. Photographic quality is critical for taxonomic inference. Citizen science ­platforms such as iNaturalist can be invaluable for the discovery and documentation of biodiversity and provide new spatial data for species distributions that in turn can aid conservation tools.
Neonatal Herpes Simplex Virus: Cutaneous Recurrence Is Common on Stopping Prophylactic Suppression Therapy
Authors: Waheed Sabrina , Nuttall Luke , Fidler Katy , Dudley Julia , Bamford Alasdair , Lyall Hermione
Published: August 2022

Neonatal herpes simplex virus (HSV) infection is a potentially devastating disease. Data on the recurrence of disease while on suppressive therapy are limited. We reviewed cases of neonatal HSV. Prematurity was associated with more recurrence. No systemic or CNS recurrence occurred, but there were frequent recurrences of skin lesions.
Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes
Authors: Lalli Matthew , Yen Allen , Thopte Urvashi , Dong Fengping , Moudgil Arnav , Chen Xuhua , Milbrandt Jeffrey , Dougherty Joseph D , Mitra Robi D
Published: August 2022

Calling cards technology using self-reporting transposons enables the identification of DNA–protein interactions through RNA sequencing. Although immensely powerful, current implementations of calling cards in bulk experiments on populations of cells are technically cumbersome and require many replicates to identify independent insertions into the same genomic locus. Here, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells by introducing a DNA barcode into the calling card itself. An additional barcode incorporated during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recover in vitro binding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2 and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. Lastly, we demonstrated barcoded calling cards can record binding in vivo in the mouse brain. In sum, RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is an efficient and powerful method to infer gene regulatory networks in a population of cells.
T cell receptor dynamic and transcriptional determinants of T cell expansion in glioma-infiltrating T cells
Authors: Lu Kevin Hai-Ning , Michel Julius , Kilian Michael , Aslan Katrin , Qi Hao , Kehl Niklas , Jung Stefanie , Sanghvi Khwab , Lindner Katharina , Zhang Xin-Wen , Green Edward W , Poschke Isabel , Ratliff Miriam , Bunse Theresa , Sahm Felix , von Deimling Andreas , Wick Wolfgang , Platten Michael , Bunse Lukas
Published: August 2022

Background

Glioblastoma (GBM) is characterized by low numbers of glioma-infiltrating lymphocytes (GIL) with a dysfunctional phenotype. Whether this dysfunctional phenotype is fixed or can be reversed upon ex vivo culturing is poorly understood. The aim of this study was to assess T cell receptor (TCR)-dynamics and -specificities as well as determinants of in vitro GIL expansion by sequencing-based technologies and functional assays to explore the use of GIL for cell therapy.

Methods

By means of flow cytometry, T cell functionality in GIL cultures was assessed from 9 GBM patients. TCR beta sequencing (TCRB-seq) was used for TCR repertoire profiling before and after in vitro expansion. Microarrays or RNA sequencing (RNA-seq) were performed from 6 micro-dissected GBM tissues and healthy brain RNA to assess the individual expression of GBM-associated antigens (GAA). GIL reactivity against in silico predicted tumor-associated antigens (TAA) and patient-individual GAA was assessed by ELISpot assay. Combined ex vivo single cell (sc)TCR-/RNA-seq and post-expansion TCRB-seq were used to evaluate transcriptional signatures that determine GIL expansion.

Results

Human GIL regains cellular fitness upon in vitro expansion. Profound TCR dynamics were observed during in vitro expansion and only in one of six GIL cultures, reactivity against GAA was observed. Paired ex vivo scTCR/RNA-seq and TCRB-seq revealed predictive transcriptional signatures that determine GIL expansion.

Conclusions

Profound TCR repertoire dynamics occur during GIL expansion. Ex vivo transcriptional T cell states determine expansion capacity in gliomas. Our observation has important implications for the use of GIL for cell therapy including genetic manipulation to maintain both antigen specificity and expansion capacity.
Archiving Praxis
Authors: Stoler Ann Laura
Published: August 2022

This chapter mentions the Palestinian Museum that has garnered international attention as its signature exhibits were conceived by the well-known Palestinian curator, Jack Persekian. It talks about the other archival venture, the Birzeit University Digital Archive or Awraq, which was initiated by a historian that had been teaching at Birzeit University for a long time. It also highlights how both the Palestinian Museum and Awraq fragmented the Palestinian archival field within and beyond the borders of occupied Palestine. The chapter delves into the c of Palestinians and Palestine, which is considered deeply political, emphatically anticolonial, and bold in its methods of requisition. It explores the term archiving, which offers an imaginative rethinking of political praxis instead of expending energy on countering authoritative inscriptions of state and institutional command.
The de Lagunas’ Dogmatism and Evolution
Authors: Katzav Joel
Published: August 2022

Willard V. Quine’s 1951 article, “Two Dogmas of Empiricism” (Two Dogmas) was taken to be revolutionary because it rejects the analytic-synthetic distinction and the thesis that empirical statements are confirmed individually rather than holistically. The present chapter, however, argues that the overcoming of modern philosophy already included the overcoming of these theses by Hegelians, pragmatists, and two critics of Hegelianism and pragmatism, Grace and Theodore de Laguna. From this perspective, “Two Dogmas” offers a Hegelian epistemology that was already superseded in 1910. The perspective is largely based on the de Lagunas’ 1910 book Dogmatism and Evolution: Studies in Modern Philosophy. The de Lagunas’ book also helps to make clear that the real revolution “Two Dogmas” participated in was the marginalization of their work and that of other speculative philosophers. Grace de Laguna surely recognized much of this when she stood opposite Quine as he first presented “Two Dogmas.”
The Specters of Black Self-Governance
Authors: Graubart Karen B.
Published: August 2022

Black self-governance was present in Seville but absent in Lima. In Seville, the alcalde de los negros likely functioned as a kind of ombudsman or mayordomo of a confraternity, resolving small disputes and organizing festival behavior. In the New World, such an office was abandoned on a general level, particularly as Atlantic slavery grew exponentially in the seventeenth century. But Spanish leaders did embrace the Black republic in certain forms: to force free Black men and women to work in mining, or to entice cimarrones (runaway slaves) to form free towns, pay tribute, and police future runaways. In Lima, Black confraternities became voluntary spaces of limited self-governance and mutual aid. But Lima’s authorities often regretted the lack of Black leaders with incentives to extract wealth and labor from the city’s large Black population.
What Babies Know
Authors: Spelke Elizabeth S.
Published: August 2022

What do infants know, and how does the knowledge that they begin with prepare them for learning about the particular physical, cultural, and social world in which they live? Answers to this question shed light not only on infants but on children and adults in all cultures, because the core knowledge possessed by infants never goes away. Instead, it underlies the unspoken, commonsense knowledge of people of all ages, in all societies. By studying babies, researchers gain insights into infants themselves, into older children’s prodigious capacities for learning, and into some of the unconscious assumptions that guide our thoughts and actions as adults. To share these insights, the author distills the findings from research in developmental, comparative, and cognitive psychology, with excursions into studies of animal cognition in psychology and in systems and cognitive neuroscience, and studies in the computational cognitive sciences. Weaving across these disciplines, she paints a picture of what young infants know, and what they quickly come to learn, about objects, places, number, geometry, and people’s actions, social engagements, and mental states.
Beyond Core Knowledge
Authors: Spelke Elizabeth S.
Published: August 2022

Human children are arguably the most capable learners on earth: In a few short years, they learn their native language, the actions, customs, and relationships among the people in their social world, the spatial layout of their environment, and the forms and functions of myriad objects. Children learn these things even in cultures in which people rarely speak to them until they can speak competently themselves. Their learning far outpaces that of their household pets, who inhabit the same environment. Since core knowledge is shared by infants and animals alike, these observations suggest that some uniquely human talent or penchant carries children beyond core knowledge. Here the author hypothesizes that a new learning process emerges at the end of the first year, as infants use their growing knowledge of language to gain new insights into their own and others’ mental states. Infants come to view people as social agents whose mental states are both phenomenal and intentional, and who engage with one another so as to share their actions and their experiences of things and events. By sharing with other people, construed as social agents, children may gain a uniquely human capacity for fast and flexible learning.
The Varieties of Spiritual Experience
Authors: Yaden David B. , Newberg Andrew
Published: August 2022

Spiritual experiences have occurred in people around the world and throughout history, up to and including the present day. The founders of every major religion described them, philosophers since the ancient Greeks have pondered them, and according to recent Gallup polls, about 30% of people in the United States and the United Kingdom still report them. A century ago, in The Varieties of Religious Experience, philosopher and psychologist William James famously analyzed accounts of these experiences and raised questions for future scientific study. What triggers these events? How are the brain and body affected? How do these brief moments have such lasting effects? Now, modern science has some answers. This book, The Varieties of Spiritual Experience: Twenty-First Century Research and Perspectives explores scientific breakthroughs on spiritual experiences from the fields of psychology and neuroscience. Readers are invited into laboratories around the world to learn about the methods scientists use to study these elusive yet profound inner events. Survey questions included throughout the book allow readers to discover how scientists would classify various experiences. The book also features examples of spiritual experiences drawn from a diverse set of personal accounts. For many people, spiritual experiences rank alongside marriage and childbirth as among life’s most meaningful moments—this book builds on William James’s theoretical foundation and provides the basis for a scientifically informed contemporary understanding of these profound and mysterious experiences.
The Kingdom of Babylon and the Kingdom of the Sealand
Authors: Boivin Odette
Published: August 2022

The Old Babylonian kingdom of Babylon emerged in the fragmented political landscape of the early second millennium, as one among other states under Amorite rulership, reaching its short-lived zenith in the eighteenth century bc with Hammurabi’s sweeping conquests. At the time, it controlled most of the Mesopotamian plain, the Diyala valley, and northeastern Syria. Its kings elevated Babylon to the status of royal capital, laying the ideological and political foundations of the later metropolis that entered the Bible and Greek sources. This chapter presents a survey of the political and social history of the kingdom, explores its ideological underpinnings, and discusses aspects of its intellectual history. During the three centuries of its existence, the kingdom was part of a complex and unstable web of shifting vassalage and alliances. The rulers of Babylon implemented a palace-centric tributary economy, in which entrepreneurs played an important role. Scribal activity blossomed, and several of the main literary works constituting the corpus of cuneiform literature were composed in that period. The kingdom disintegrated gradually, beginning with the loss of southern Babylonia, where the kingdom of the Sealand arose in the latter part of the eighteenth century bc. From then on, the history of Babylonia is a history of two kingdoms, Babylon in the north and the Sealand in the south. This chapter discusses also how the Sealand rulers maintained power over their dominion after the collapse of Babylon in ca. 1595 bc, before falling prey to the new Kassite dynasty of Babylon.
Middle Kingdom Egypt and the Eastern Mediterranean
Authors: Marcus Ezra S.
Published: August 2022

During the Middle Kingdom, Egypt had a complex relationship with the region of the Eastern Mediterranean and its peoples, ranging from belligerency to cooperation. The former is reflected in military forays by land and sea into the Levant, while the latter is 21.1 exemplified by royal trade expeditions to the Levant and Sinai; tribute extraction, as recorded in text and art, lay between these extremes. These activities resulted in much-needed material imports originating from the Mediterranean coast (e.g., coniferous longwoods) and even farther afield, which enriched and strengthened the Egyptian crown and the elite. At the same time, over the course of the period in question, “Asiatic” immigrants arrived in Egypt, either by force or by their own volition, and throughout the Nile valley found increasingly more important roles in society and the economy; their acculturation is documented in both texts and depictions. This chapter reconsiders the nature of this relationship based on the most up-to-date data. In particular, the analysis eschews previous explanations that were predicated on the assumption of a unique relationship between Egypt and the northern Levantine port of Byblos. Instead, the evidence suggests the existence of a much more complex web of relationships, based both on maritime and land contacts, with a range of places along the Eastern Mediterranean littoral zone. These relationships were ultimately the basis for the large-scale immigration of “Asiatics” to the Nile delta, whose prominence rose as the Middle Kingdom declined.
Socializing Justice
Authors: Sabbagh Clara
Published: August 2022

This book offers a comprehensive view of the numerous and robust roles of justice in three education spheres: public and globalized schools, non-formal education, and the family. It develops a heuristic framework for taking account of issues related to distributive justice in the everyday lives of children and young people and to the pillars of justice in various socialization spheres. It makes a compelling case that not only schools, but also non-formal education and the family are primary socialization agents that help align new citizens’ conduct with competing yet coexisting justice ideals in democratic societies. The book shows how children’s and young people’s educational justice experiences affect their beliefs and behavior. Moreover, it examines the justice perspectives of other educational agents—the actual purveyors of distributive justice—such as policymakers, teachers, and parents. Children and young people are conceptualized not merely as subjects experiencing justice or injustice (i.e., as recipients or observers), but also as objects of social justice, targeted by different education agents in an effort to establish and sustain justice in democratic societies. This inquiry into justice research interfaces other, more established disciplines, such as education, sociology of education, social psychology, and political philosophy, and relies on the quantitative and ethnographic methodological traditions in these fields. Such an interdisciplinary framework has made it possible to identify controversies within justice theory regarding the distributive roles of education and to illustrate how the forms of justice underlying educational spheres are universal yet sensitive to sociocultural variation.
A Multifaceted Justice Perspective on Education Spheres
Authors: Sabbagh Clara
Published: August 2022

Chapter 2 maps out and discusses the diverse forms of justice, as conceptualized largely in organizational contexts, and details the academic debate over this issue. Organizational justice frameworks distinguish three primary forms of justice that govern resource distribution. Distributive justice, which is the spotlight of this inquiry, relates to distribution preference regarding the principles and rules that regulate resource distribution (e.g., equality, need, and contribution) and the subjective sense of injustice evoked by a perceived gap between the distribution principles viewed as just and those actually implemented. Procedural justice concerns the justice of the procedures through which resources are distributed; in other words, the focus is on processes rather than outcomes of resource distribution. Finally, interactional justice involves the justice of interactions on a personal level attendant on the distribution of resources and the implementation of procedures.
Teacher–Student Relations
Authors: Sabbagh Clara
Published: August 2022

Chapter 7 discusses students’ perceptions of teacher–student relations in light of the distributive, procedural, and interactional aspects of organizational justice. Teachers distribute a wide range of relational resources: they allot attention, help students as needed, react to non-routine events (distractions, class fights), give either encouragement or disapproval, and show respect and affection. In the understanding of students, teachers should distribute these relational resources according to a principle of equality; in practice, however, they often deviate from this rule and treat students unequally. This gap between expectations and actual distribution evokes in students a sense of relational injustice that, in turn, affects a wide range of their attitudes and behaviors, such as social trust, endorsement of the teacher’s legitimacy, learning motivation, and rule compliance. The chapter provides two opposing perspectives regarding relational justice at the organizational level: emotional work and caring, and retributive/restorative justice.
The World Culture Perspective
Authors: Sabbagh Clara
Published: August 2022

Chapter 8 examines the effect of globalization on schooling and its distributive roles through the world culture lens. According to this perspective, one aspect of globalized schooling is manifested in access to education, where the focus in the discourse on justice has shifted from social rights to human rights. Moreover, grading practices have become predicated on a global ethos of meritocracy, which is realized through international tests like the Program for International Student Assessment and Trends in International Mathematics and Science Study. Finally, globalized schooling has extended the scope of school curriculum, covering topics related to diversity and progressive issues, such as student-centeredness and environmental concerns. The chapter contends that these changes, as understood in the world culture perspective, are grounded in justice tenets underlying Western liberalism. Moreover, it discusses the shortcomings of this perspective in addressing local, culturally specific factors, leading to the emergence of hybrid educational cultures.
Justice in Parent–Child Relations
Authors: Sabbagh Clara
Published: August 2022

Chapter 13 contends that distributive justice plays a salient role in regulating parent–child relationships. For instance, parental distribution practices include love and respect, housework chores, and pocket money. Family life in democracies is governed by Western egalitarian justice, but daily family practices often deviate from this ideal. Thus, parental differential treatment is common, though not necessarily perceived as unjust. The chapter explains that, in light of comparisons drawn within the family and the understanding of equitable social exchange, inequality in parent–child relations is often seen as legitimate. At the same time, it stresses that children’s sense of injustice concerning parenting practices has harmful implications for their subjective well-being and for the quality of sibling relationships. Finally, the chapter discusses the feminist critique maintaining that the family is a significant agent of gender inequality within its unit and in the broader society.
Epilogue
Authors: Sabbagh Clara
Published: August 2022

This book argues that issues related to justice, particularly distributive justice, are paramount in diversified education experiences that are part of children’s and young people’s daily lives. It distinguishes three education spheres of justice: schools, non-formal education, and the family. Through this plurality, young generations experience and internalize what scholars term the “pillars” that sustain their future roles as citizens in democratic societies. Schools encompass the inherently competitive economic domain, non-formal education, and the political domain, while the family incorporates ascriptive domains, such as gender. The three education spheres outlined here share a Western egalitarian ethos yet in practice inequality is widespread. Depending on whether children and young people perceive the distribution of resources as just or unjust, their attitudes and behavior are affected either positively or negatively. In default of a consensus about distributive justice in education, most chapters elaborate different perspectives through which educational justice can be understood and discussed.
Naturalized Epistemology, Morality, and the Real World
Authors: Antony Louise
Published: August 2022

This essay addresses the charge that naturalized epistemology abandons normative goals, and shows how a naturalized approach yields insight into the epistemic norm of objectivity. It then argues for applying the naturalized approach to moral epistemology. Attention to the actual conditions under which beings seek to act rightly not only permits the endorsement of moral norms, but provides normative guidance for knowing and acting within the constraints that define the human epistemic and moral condition. A naturalized approach to moral epistemology is possible—naturalizing does not entail the elimination of normativity—and, moreover, salutary. Taking seriously the actual moral judgments human beings make, we learn a great deal about the limits of a priori moral theorizing. Taking seriously the conditions set by our particular embodiment on the exercise of our moral faculties and the expression of our moral principles, we can achieve a reconciliation between a norm of moral objectivity and a recognition of the moral value of affective partiality.
How to use this book
Authors: Dev Harveer , Metcalfe David
Published: August 2022

This chapter discusses how best to use this book to prepare for the SJT, including an overview of the practice topics, as well as a discussion on the assessment methods of the SJT—there are no ‘right’ or ‘wrong’ SJT answers.
Commitment to professionalism
Authors: Dev Harveer , Metcalfe David
Published: August 2022

This chapter presents SJT questions on commitment to professionalism. It will test your probity by exploring responses to scenarios that might require you to challenge unacceptable behaviour, maintain confidentiality, and, as always, prioritize patient safety. You need to demonstrate a commitment to achieving your various clinical responsibilities, as well as a desire for continued learning and a commitment to helping the development of others. These scenarios test your honesty towards patients and colleagues, and a willingness to admit mistakes.
The generativist non-dominance of the field in the 1970s and 1980s
Authors: Newmeyer Frederick J.
Published: August 2022

While most commentators have agreed that the work of Chomsky and his TGG cothinkers profoundly shook up the field in the fifties and sixties, ironically, generative grammarians continued to be a minority tendency in American linguistics into the seventies and eighties. They occupied fewer than half of the LSA offices, published fewer than half of the articles appearing in Language, and received only small share of allocated grants. Many factors combine to explain this perhaps surprising state of affairs: the diverse nature of the field, the rise of specialist journals, the lack of need for grant-funded research, and Chomsky’s own negative attitude towards the LSA.
Plenitude and Recombination
Authors: Wilson Alastair
Published: August 2022

In On the Plurality of Worlds, David Lewis imposes a condition on realist theories of modality which he calls ‘plenitude’. Lewis apparently assigns this condition considerable importance, and uses it to motivate his Humean principle of recombination, but he never says exactly what plenitude amounts to. This chapter first sets aside some obvious ways of reconstructing the plenitude criterion which do not fit with the textual evidence. An objection to modal realism due to John Divers and Joseph Melia is diagnosed as equivocating between an overly demanding plenitude constraint and a weaker constraint which fails to establish their conclusion. An alternative deflationary interpretation of the plenitude condition has it following from an application of standard theoretical virtues to a modal realist’s total theory; Lewis’s correspondence provides new evidence in support of this interpretation. The deflationary plenitude criterion also has broader application, beyond Lewisian modal realism.
Carnap’s Second Aufbau and David Lewis’s Aufbau
Authors: Chalmers David J.
Published: August 2022

There is a deep continuity between central projects of Rudolf Carnap and David Lewis: Carnap’s logical construction of the world in Der logische Aufbau der Welt and Lewis’s program of vindicating Humean supervenience through conceptual analysis. Carnap promised but never wrote a second volume of his Aufbau, using a physical basis in place of the phenomenal basis he had used in the first Aufbau. Even using tools available to him at the time, Carnap’s physicalist construction would have been a viable philosophical project; but Lewis’s program delivers a more sophisticated construction in the same spirit. A Carnap-Lewis Aufbau thus constitutes a philosophically viable blueprint for the world.
Lewis: Metaphysics First
Authors: Jackson Frank
Published: August 2022

What kind of world do we inhabit? David Lewis was a believer in what is commonly known as the block universe answer to this question. We inhabit a huge four-dimensional aggregation in the mereological sense, and we inhabit it by being a (tiny) part of it. One way to make good sense of Lewisian views about language, belief, the necessary a posteriori, the de se, Twin Earth, and conceptual analysis is by seeing them as deriving from this view in metaphysics. Much of the discussion is set inside a possible worlds framework, but not one that distinguishes metaphysically possible worlds from conceptually or epistemically possible worlds.
Naturalness, Arbitrariness, and Serious Ontology
Authors: Fisher A.R.J.
Published: August 2022

David Lewis is typically interpreted as a class nominalist. One consequence of class nominalism, which he embraced, is that the reduction of ordered pairs, triples, etc. to unordered sets of sets is conventional. The reaction by his Australian counterparts D.M. Armstrong and Peter Forrest was that Lewis was not being ontologically serious. This chapter evaluates this debate over serious ontology. It is argued that in one sense Lewis is ontologically serious, but that his additional commitment to structuralism about classes should push him to adopt a trope-theoretic account of naturalness, which opens up another way to respond to the charge of not doing serious ontology. This conclusion is supported by certain remarks he makes in his correspondence, thus revealing how his thinking about properties appears to have evolved from property-egalitarianism to a sparse theory of tropes.