bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncharacterized and lineage-specific accessory genes within the
Proteus mirabilis
pan-genome landscape
Authors: Potter Robert F. , Zhang Kailun , Reimler Ben , Marino Jamie , Muenks Carol E. , Alvarado Kelly , Wallace Meghan A. , Westblade Lars F. , McElvania Erin , Yarbrough Melanie L. , Hunstad David A. , Dantas Gautam , Burnham Carey-Ann D. 
Published: June 2023

ABSTRACT

Proteus mirabilis
is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria,
P. mirabilis
may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of
P. mirabilis
genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060
Proteus
genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related
P. mirabilis
genomes, and pan-genome annotation to identify genes of interest not present in the model
P. mirabilis
strain HI4320. Within our cohort,
Proteus
is composed of 10 named species and 5 uncharacterized genomospecies.
P. mirabilis
can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The
P. mirabilis
pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain
P. mirabilis
HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome.

IMPORTANCE

Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on
P. mirabilis
, but similar to other Gram-negative bacteria,
P. mirabilis
has a mosaic genome with a linkage between phylogenetic position and accessory genome content.
P. mirabilis
encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.
Return to driving following surgery to the upper limb: a scoping review protocol
Authors: Rankin Carly Renee , Smith Simon 
Published: June 2023

IntroductionUpper limb surgery is a common burden on the active and ageing population, often resulting in a transient state of functional impairment. Many activities of daily living can be affected, including ability to drive. Currently there are no guidelines regarding safe return to driving following upper limb surgery. This scoping review aims to systematically review the current literature on the topic of driving following surgery to the upper limb.Methods and analysisInformed by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses—Scoping Review extension guidelines, this protocol details the scoping review’s methodological and analytical approaches. The review will consider all primary and secondary source articles that examine return to driving following surgery to the upper limb, including the impact of orthoses on functional ability to drive. All studies will be included regardless of methodology and text and opinion pieces will also be considered. Studies conducted in any geographical location or setting will be included in the review. Systematic searches of scientific databases such as OVID (MEDLINE, EMBASE and Cochrane), NCBI (PubMed), Scopus, PsycINFO, EBSCOhost (CINAHL), Web of Science, Google Scholar and ProQuest will be conducted. In addition, relevant organisational websites, dissertations, theses from university repositories and grey literature will be included. Further articles will be identified by searching references of relevant studies. Studies conducted in English in any year will be included. Two independent reviewers will screen identified literature sources based on predetermined inclusion/exclusion criteria. Discrepancies will be resolved through discussion, therefore, negating the need for a third reviewer. Article data will be presented in tabular or graphical format along with a narrative summary.Ethics and disseminationEthics approval is not required. Findings will be disseminated through professional networks, peer-reviewed publications and conference presentations.
Acupuncture for gait disturbance of patients with subacute and chronic stroke: a systematic review and meta-analysis protocol
Authors: Sun Zheng , Lin Yi-ren , Lu Meng-jiang , Huang Kai-yu , Sun Ke , Zhang Jian-bin 
Published: June 2023

IntroductionHemiparetic gait is one of the most common sequelae of a stroke. Acupuncture has shown potential in correcting hemiplegic gait patterns and improving motor function recovery after stroke. However, controversial findings and a lack of supportive evidence on the effectiveness of acupuncture for post-stroke hemiplegia. The intelligent gait analysis system provides a new perspective for the study of hemiparetic gait. This systematic review aims to collect relevant studies and critically evaluate the efficacy and safety of acupuncture in alleviating gait disturbance of post-stroke hemiplegia based on quantified gait parameters.Methods and analysisA comprehensive search of PubMed, Embase, Cochrane stroke group trials register, Cochrane Central Register of Controlled Trials, CINAHL, AMED, three Chinese databases (Chinese Biomedical Literatures database (CBM), National Knowledge Infrastructure (CNKI), and Wan fang Digital Periodicals), four trails registries (The WHO International Clinical Trials Registry Platform, The Chinese Clinical Trial Registry, The US National Institutes of Health Ongoing Trials Register, and The Australian New Zealand Clinical Trials Registry) will be conducted to identify randomised controlled trials of acupuncture for gait disturbance in post-stroke patients. No restrictions on language or publication status. The primary outcomes are gait temporospatial parameters (eg, step length, stride length, step width, step frequency (cadence), walking speed, etc), and gait kinematic parameters (eg, hip peak flex/extend angle, knee peak flex/extend angle, ankle peak dorsi/plantar-flexion angle, etc). We will assess bias using the approach recommended by the Cochrane Handbook for Systematic Reviews of Interventions. A meta-analysis will be conducted to synthesise the evidence for each outcome measure. The χ2test and I2statistic will be used for assessing heterogeneity between studies.Ethics and disseminationNo ethical approval is needed because no primary data is collected. Scientific conferences or peer-reviewed journals will publish the findings.PROSPERO registration numberCRD42022384348.
Automated catheter segmentation and tip detection in cerebral angiography with topology-aware geometric deep learning
Authors: Ghosh Rahul , Wong Kelvin , Zhang Yi Jonathan , Britz Gavin W , Wong Stephen T C 
Published: June 2023

Background
Visual perception of catheters and guidewires on x-ray fluoroscopy is essential for neurointervention. Endovascular robots with teleoperation capabilities are being developed, but they cannot ‘see’ intravascular devices, which precludes artificial intelligence (AI) augmentation that could improve precision and autonomy. Deep learning has not been explored for neurointervention and prior works in cardiovascular scenarios are inadequate as they only segment device tips, while neurointervention requires segmentation of the entire structure due to coaxial devices. Therefore, this study develops an automatic and accurate image-based catheter segmentation method in cerebral angiography using deep learning.

Methods
Catheters and guidewires were manually annotated on 3831 fluoroscopy frames collected prospectively from 40 patients undergoing cerebral angiography. We proposed a topology-aware geometric deep learning method (TAG-DL) and compared it with the state-of-the-art deep learning segmentation models, UNet, nnUNet and TransUNet. All models were trained on frontal view sequences and tested on both frontal and lateral view sequences from unseen patients. Results were assessed with centerline Dice score and tip-distance error.

Results
The TAG-DL and nnUNet models outperformed TransUNet and UNet. The best performing model was nnUNet, achieving a mean centerline-Dice score of 0.98 ±0.01 and a median tip-distance error of 0.43 (IQR 0.88) mm. Incorporating digital subtraction masks, with or without contrast, significantly improved performance on unseen patients, further enabling exceptional performance on lateral view fluoroscopy despite not being trained on this view.

Conclusions
These results are the first step towards AI augmentation for robotic neurointervention that could amplify the reach, productivity, and safety of a limited neurointerventional workforce.
Optimising messages and images for e-cigarette warnings
Authors: Lazard Allison J , Ebrahimi Kalan Mohammad , Nicolla Sydney , Hall Marissa G , Ribisl Kurt M , Sheldon Jennifer Mendel , Whitesell Callie , Queen Tara L , Brewer Noel T 
Published: June 2023

Background
The US Food and Drug Administration (FDA) requires electronic cigarettes (e-cigarettes) to have a single addiction warning, but many other health harms are associated with vaping and warnings grow stale over time. We aimed to develop new warning messages and images to discourage e-cigarette use.

Methods

Participants were 1629 US adults who vaped or smoked. We randomised each participant to evaluate 7 of 28 messages on newly developed
warning themes
(metals exposure, DNA mutation, cardiovascular problems, chemical exposure, lung damage, impaired immunity, addiction), and the current FDA-required warning (total of 8 messages). Then, participants evaluated images of hazards (eg, metal), internal harms (eg, organ damage) or people experiencing harms.

Results
Regarding intended effects, new warning themes all discouraged vaping more than the current FDA-required warning (all p<0.001), led to greater negative affect (all p<0.001) and led to more anticipated social interactions (all p<0.001). The most discouraging warnings were about toxic metals exposure. Regarding unintended effects, the new themes led to more stigma against people who vape (6 of 7 themes, p<0.001) and led to a greater likelihood of thinking vaping is more harmful than smoking (all 7 themes, p<0.001), although unintended effects were smaller than intended effects. Images of harms (internal or people experiencing) discouraged vaping more than images of hazards (all p<0.001).

Discussion
Vaping warning policies should communicate a broader range of hazards and harms, beyond addiction, to potentially increase awareness of health harms. Images of internal harm or people experiencing harms may be particularly effective at discouraging vaping.
Startups in Algeria - Towards the promotion of the economic development movement as an alternative to wealth creation without depending on economic rents
Authors: Souiki Horiya 
Published: June 2023

The Algerian legislator sought to establish a legal framework for emerging enterprises whose managers aim to create and market new technologies with the intention of promoting the economic development and encouraging investment and innovation in the field of information and communication technology. For this, he first started by embodying a committee specialized in granting the label of an emerging enterprise or Startup, with the introduction of provisions that simplify the requirements and conditions for establishing a simple Joint-Stock Company with the label of a Startup. For the first time ever, the legislator added a number of amendments to the Labor Law and the Basic Law of Public Function in order to give the employee the possibility to invest in the private sector and establish his own enterprise. In addition, regarding the university student, the legislator gave him a chance to prepare a new form of graduation dissertation project about the creation of startup. In this case, this student can therefore benefit from financial support and funding. This would certainly make the university student a creator of new job positions, which will surely help to reduce the unemployment rate.
The present study aims to carry out an analytical interpretation of the different recent legal texts in order to frame them within the Algerian law.
Materia Medica in a Multilingual Context: Avicenna’s Canon of Medicine and Its Latin Translation of Book II
Authors: Veit Raphaela 
Published: June 2023

Abstract
For centuries, Avicenna’s Canon of Medicine was a crucial text used in medical studies across the Islamicate area as well as in Latin Europe. It was first translated from Arabic into Latin by Gerard of Cremona (d. 1187) and his students in Toledo. This article focuses on the second book of the Canon which is dedicated to the description of simple drugs. It is in this part of the Canon that we find many references not only to borrowings from Ancient Greek but also from Eastern material. A careful comparison of the Arabic text and the Latin translation demonstrates that the Latin translation was often imprecise, and while it eliminated some but not all obvious Muslim religious references, it did not try to adapt the material to the Latin readership in other ways.
Food in the Frankish Levant: a Case Study of Cultural Borrowing
Authors: Bronstein Judith 
Published: June 2023

Abstract
The Crusader movement called for the liberation of the Holy Land and the expulsion of non-Christians. Yet in reality, the Frankish states of Edessa, Antioch, Tripoli and Jerusalem, established as the result of the Crusades, were to become heterogeneous societies, with a plurality of ethnic and religious groups ruled by a Latin Frankish elite. In recent decades, historians, art historians and archaeologists have turned much attention to the study of influences and cultural borrowing in artistic, architectural, religious, military, governmental, administrative and intellectual activities that resulted from almost two centuries of co-existence of the Latins with the local population in the Levant: Eastern Christians, Muslims, and Jews. This article strives to contribute to this ongoing discussion by analyzing some aspects of everyday life in the Frankish Levant, focusing mainly on foodstuffs and food habits. The study of preservation of culinary traditions, consumption of new food products, as well as technological and administrative changes related to food production, are valuable tools in understanding coexistence and cultural borrowing in the Frankish Levant.
Cringing at Benevolence
Authors: McCrary Charles 
Published: June 2023

Abstract
Engaging with Logan’s third chapter, on the American Seamen’s Friends Society, this piece reflects on what it means to cringe in the context of a benevolent or charitable relationship. People cringe when they are made painfully aware of the gap between their self-conception (and/or their ideal self) and the way others perceive them. Logan shows us, in her study of the ASFS, the cringeworthy nature of antebellum benevolent societies: they learned about the objects of their benevolence (in this case, sailors), performed rituals alongside them, and attempted to befriend them, and yet they did not ultimately want to be them or be like them but, rather, to change them.
Awkward History, Awkward Theory
Authors: MacCormack Ian 
Published: June 2023

Abstract
Based on a contribution to a panel discussion on Dana Logan’s Awkward Rituals, this essay addresses the first chapter of the book, in which Logan discusses the rites of Freemasons in the early American republic. It considers the particular significance of Masonic ritual practice with respect to Logan’s arguments about patterns of change in pre- and post-Revolutionary America; and reflects on the general theoretical import of this notion of ritual awkwardness, embodied by the Freemasons, considered as a form of purposive activity. It raises questions about the broader applicability in comparative religious studies of Logan’s insights, both for studying history and for thinking about ritual.
Response to Symposium on Awkward Rituals
Authors: Logan Dana 
Published: June 2023

Abstract
In this response to the symposium on Awkward Rituals, Logan responds to questions such as “do her subjects know that they are awkward?” “are awkward rituals effective?” “is this a theoretical or a historical intervention?” and “what is the role of American exceptionalism in this argument?” In response to these questions the author looks towards a future of ritual studies in which we might take seriously the limits of a scholars’ temporal and geographical boundaries while also building new genealogies of ritual as a category of analysis and practice grounded in historical exchanges.
Theorizing Awkwardness, with Style, in the Study of Religion: A Forum on Dana W. Logan’s Awkward Rituals (2022)
Authors: Hazard Sonia 
Published: June 2023

Abstract
The 2022 meeting of the American Academy of Religion in Denver featured a book panel on Dana W. Logan’s Awkward Rituals: Sensations of Governance in Protestant America (University of Chicago Press, 2022). This essay introduces a forum based on the panel, featuring four scholars representing diverse subfields in religious studies: Ian MacCormack, Charles McCrary, Constance Furey, and Marko Geslani. It argues that Awkward Rituals, though embedded in ritual studies and the historiography of American religion, is a generative theoretical text for many areas of inquiry in the wider study of religion: the disjunctures and incoherences in religions; the practical applications of a mind/body dualism; the uses of the personal experiences of the scholar; and the endurance of comparison as a method.
The ‘House of Song’, the *‘House of Clay’, Arm. gerezman, and Caucaso-Albanica
Authors: Schwartz Martin 
Published: June 2023

Abstract
This paper begins with an examination of the phrase /garah dmāna-/, the most common designation for Paradise in the Gathas, for which the traditional translation ‘House of Song’ is upheld. Its dualistic opposite /drujah dmāna-/ ‘House of Wrongness’ for Hell leads to the question of why for Paradise one doesn’t have the expected opposite *‘House of Rightness’ instead of ‘House of Song’. The answer proceeds from the etymologically unrelated Armenian gerezman ‘grave, tomb’, whose origin has been hitherto unknown, despite attempts toward its etymology. In view of the Indo-European phrase for the grave (i.e., burial mound) as ‘the House of Clay’, it is then suggested that the Arm. word is from a Median phrase, which is reconstructed as *gṛda- *zmani- ‘*clay (*zmani-) house (*gṛda-)’. The phonic similarity of this phrase to /garah dmāna-/ (/garah/ ‘song’s’ and /dmāna-/ ‘house’), with referential contrast is then seen as the chief motivation for Zarathushtra’s use of /garah dmāna-/ for ‘Paradise’. Then there ensues a discussion of the archeological-historical contexts for the latter development. Next, a phonologically systematic account is offered for Arm. gerezman becoming “Caucasian Albanian” garazman ‘grave, tomb’, in accord with hitherto unnoted aspects of “Caucasian Albanian” historical vocalism. The modern Udi derivative of garazman, i.e. gärämzä, is also accounted for. The loanwords in “Caucasian Albanian” are then divided into two main strata, first the Armenian (Iranian loans and indigenous Arm. words), including some forms from Armenian antedating Armenian literacy, and second a stratum of words, which are here called “Parthic”, of a vintage par with Manichean Parthian. These “Parthic” words, with their religious references, point to an Iranian group which (after the Armenian phase of loanwords) influenced the development of Christianity among the “Caucasian Albanians”, suggesting the existence of a “Christian Parthian”.
Visuo-Tactile Congruence Leads to Stronger Illusion Than Visuo-Proprioceptive Congruence: a Quantitative and Qualitative Approach to Explore the Rubber Hand Illusion
Authors: Bartoletti Roxane L. , Denis-Noël Ambre , Boulvert Séraphin , Lopez Marie , Faure Sylvane , Corveleyn Xavier 
Published: June 2023

Abstract
The Rubber Hand Illusion (RHI) arises through multisensory congruence and informative cues from the most relevant sensory channels. Some studies have explored the RHI phenomenon on the fingers, but none of them modulated the congruence of visuo-tactile and visuo-proprioceptive information by changing the posture of the fingers. This study hypothesizes that RHI induction is possible despite a partial visuo-proprioceptive or visuo-tactile incongruence. With quantitative and qualitative measures, we observed that gradual induction of the sense of body ownership depends on the congruence of multisensory information, with an emphasis on visuo-tactile information rather than visuo-proprioceptive signals. Based on the overall measures, the RHI observed went from stronger to weaker with full congruence; visuo-proprioceptive incongruence and visuo-tactile congruence; visuo-proprioceptive congruence and visuo-tactile incongruence; full incongruence. Our results confirm that congruent visual and tactile mapping is important, though not mandatory, to induce a strong sense of ownership. By changing index finger and thumb postures rather than the rotation of the whole hand, our study investigates the contribution of visuo-proprioception and postural congruence in the field of RHI research. The results are in favor of a probabilistic multisensory integration theory and do not resonate with rules and constraints found in internal body models. The RHI could be illustrated as a continuum: the more multisensory information is congruent, the stronger the RHI.
Strengthening Capacity in Ocean Governance
Authors: Young Margaret A. 
Published: June 2023

Abstract
Ocean governance presents special challenges for States in understanding and carrying out their obligations. The United Nations Convention on the Law of the Sea is supported by secretariats that provide capacity building, training and technical assistance. Yet ocean governance is fragmented, and there are many multilateral and regional institutions that have competences in fisheries, climate change, trade, shipping and other aspects of ocean affairs. Challenges in inter-regime coordination arise, both practically and theoretically. This article describes collaborative training initiatives in ocean governance in the Asia-Pacific, to which UN agencies, the World Bank and academic partners contribute. It seeks to account for these activities according to the precepts of regime interaction and the duty to cooperate in international law, and demonstrates the importance of an inclusive approach to learning and capacity-building in ocean governance.