bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

AbstractThis 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractThe 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

AbstractDuring 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.