bluuebunny/crossref_metadata_2025_split huggingface dataset:
A moderate dosage of coffee causes acute retinal capillary perfusion decrease in healthy young individuals
Authors: Zhu Xiaofeng , Zhu Jiong , Wang Yongyi , Chu Zhongdi , Wang Ruikang K. , Xu Yi , Lu Lina , Zou Haidong 
Published: November 2022

AbstractAim:Caffeinated beverages are very popular across populations and cultures, but quantitative evidence of the acute effects of moderate coffee doses on retinal perfusion is sparse and contradicting. Thus, the aim of this randomized, cross-over and parallel-group design study was to investigate whether moderate consumption of coffee alters macular retinal capillary perfusion in young healthy individuals.Methods:Twenty-seven young healthy individuals were recruited for this study. Acute changes in retinal microvasculature were assessed using spectral-domain optical coherence tomography angiography (SD-OCTA) at baseline, 0.5 h, and 2 h after intake of coffee, or water. Meanwhile, cerebral blood flow (CBF) and retina-choroid blood flow were evaluated in a parallel-group design (4 participants each in coffee or water group) using magnetic resonance imaging (MRI) with pseudo-continuous arterial spin labeling sequences.Results:Two hours after coffee intake, blood caffeine concentration increased from 0 to 5.05 ± 1.36 µg/mL. Coffee caused a significant decrease in retinal vessel diameter index (VDI) (19.05 ± 0.24 versus [vs] 19.13 ± 0.26; p < 0.001) and CBF in the frontal lobe (77.47 ± 15.21 mL/100 mL/min vs. 84.13 ± 15.55 mL/100 mL/min; p < 0.05) 2 h after intake. However, it significantly increased retina-choroid blood flow after 0.5 and 2 h (163.18 ± 61.07 mL/100 mL/min vs. 132.68 ± 70.47 mL/100 mL/min, p < 0.001, and 161.21 ± 47.95 vs. 132.68 ± 70.47; p < 0.001, respectively).Conclusion:This is the first study to demonstrate the acute effects of daily dose coffee consumption on retinal capillary perfusion using SD-OCTA combinate with blood flow MRI. The findings imply that although moderate coffee intake caused a significant increase in retina-choroid blood flow, there was a significant acute decrease both in macular retinal capillary perfusion and CBF.
‘A priori’ external contextual factors and relationships with process indicators: a mixed methods study of the pre-implementation phase of ‘Communities in Charge of Alcohol’
Authors: Burns Elizabeth J. , Hargreaves Suzy C. , Ure Cathy , Hare Susan , Coffey Margaret , Hidajat Mira , Audrey Suzanne , de Vocht Frank , Ardern Kate , Cook Penny A. 
Published: November 2022

Abstract
Background
It is widely recognised that complex public health interventions roll out in distinct phases, within which external contextual factors influence implementation. Less is known about relationships with external contextual factors identified a priori in the pre-implementation phase. We investigated which external contextual factors, prior to the implementation of a community-centred approach to reducing alcohol harm called ‘Communities in Charge of Alcohol’ (CICA), were related to one of the process indicators: numbers of Alcohol Health Champions (AHCs) trained.

Methods
A mixed methods design was used in the pre-implementation phase of CICA. We studied ten geographic communities experiencing both high levels of deprivation and alcohol-related harm in the North West of England. Qualitative secondary data were extracted from pre-implementation meeting notes, recorded two to three months before roll-out. Items were coded into 12 content categories using content analysis. To create a baseline ‘infrastructure score’, the number of external contextual factors documented was counted per area to a maximum score of 12. Descriptive data were collected from training registers detailing training numbers in the first 12 months. The relationship between the baseline infrastructure score, external contextual factors, and the number of AHCs trained was assessed using non-parametric univariable statistics.

Results
There was a positive correlation between baseline infrastructure score and total numbers of AHCs trained (Rs = 0.77, p = 0.01). Four external contextual factors were associated with significantly higher numbers of lay people recruited and trained: having a health care provider to coordinate the intervention (p = 0.02); a pool of other volunteers to recruit from (p = 0.02); a contract in place with a commissioned service (p = 0.02), and; formal volunteer arrangements (p = 0.03).

Conclusions
Data suggest that there were four key components that significantly influenced establishing an Alcohol Health Champion programme in areas experiencing both high levels of deprivation and alcohol-related harm. There is added value of capturing external contextual factors a priori and then testing relationships with process indicators to inform the effective roll-out of complex interventions. Future research could explore a wider range of process indicators and outcomes, incorporating methods to rate individual factors to derive a mean score.

Trial registration
ISRCTN81942890, date of registration 12/09/2017.
Localization of the ilioischial line on axial computed tomography images for preoperative planning of total hip arthroplasty
Authors: Kato Michitaka , Warashina Hideki , Kataoka Akito , Ando Takanori , Mitamura Shingo 
Published: November 2022

Abstract
Background
If the bony region indicating the ilioischial line is established on the preoperative axial computed tomography (CT) image, the distance between the simulated cup and the ilioischial line can be measured on this image so that the surgeon can use these data to define a more accurate preoperative two-dimensional (2D) template of total hip arthroplasty (THA). This study aimed to verify the hypothesis that on the CT axial image, the cortical bone area, indicated by the superimposition of a line (line α) with a perspective projection angle to the ilioischial line on radiography and tangent to the medial acetabular wall, is the cortical bone that represents the ilioischial line on radiography.

Methods
Study 1: If the two measured distances (distance A’ and distance B) are sufficiently equal, then the hypothesis can be supported. Distance A’ was calculated by multiplying the distance A, between the ilioischial line and the medial margin of the metal cup after THA measured at the level of the hip joint center on the pelvic radiograph, by 0.91 to correct for radiographic magnification. Distance B was defined as the distance between the medial margin of the metal cup and line α on the axial CT image at the level of the hip joint center. These two distances were measured for all 51 hip joints included in the study.
Study 2: The difference between distance A and distance A# (distance A on the 2D template) was compared between the group containing 59 primary THAs in which distance B′ was measured (distance B in the simulation) and the control group containing 59 primary THAs.

Results
Study 1: The average distance for A’ was 4.5 ± 2 mm, and the average distance for B was 4.7 ± 2.1 mm. The difference between distances A and B was 0.2 ± 0.2 mm.
Study 2: The mean difference between distance A and distance A# for the measurement and control groups was 1.8 ± 1.3 mm and 3.7 ± 2.4 mm, respectively (P < 0.001).

Conclusions
The ilioischial line is located in the bony region where line α intersects the medial acetabular wall with a maximum overlap on axial CT images.
First-year medical students’ perceptions of a self-regulated learning-informed intervention: an exploratory study
Authors: Boyd Taylor , Besche Henrike , Goldhammer Richard , Alblooshi Afaf , Coleman Bradley I. 
Published: November 2022

Abstract
Background
Students with developed self-regulated learning (SRL) skills demonstrate an ability to set individualized educational goals, select optimal learning strategies for reaching these goals, and reflect on overall progress. The primary aims of this study were to investigate first-year medical students’ perceived utility of a self-regulated learning-informed intervention and to assess the impact of its implementation on students’ intended use of SRL throughout medical school.

Methods
A two-part educational intervention focused on SRL skill development was carried out at Harvard Medical School during the start of the 2021 academic year. For the first component of the intervention, 169 first-year medical students engaged in an interactive class session structured around SRL concept videos, a brief lecture, small group discussions and individual reflection. Students completed pre- and post-intervention surveys which inquired about learners’ current and anticipated application of SRL skills. During the second component of the intervention, 15 first-year medical students participated in a set of one-on-one academic SRL coaching sessions. All coaching participants completed follow-up semi-structured interviews.

Results
A statistically significant increase was observed between students’ use of skills in all domains of self-regulated learning prior to the intervention and their anticipated use of these skills following the intervention. Prior to the intervention, 60.1% (n = 92) of students reported utilizing evidence-based learning strategies, compared to 92.8% (n = 142) of students (p < 0.001) who anticipated applying this SRL skills at the completion of the classroom session. Six core themes emerged from qualitative analysis of the post-intervention survey including learning plan development, accountability and progress tracking, goals for growth, engagement through active learning, routine reflection, and adapting to the curriculum.

Conclusions
Both classroom-based learning sessions and one-on-one academic coaching programs are feasible approaches for encouraging the use of self-regulated learning techniques in the preclinical setting.
Senior surgeons as role models in the operating theatre: a thematic analysis through the lens of aristotelian ethics
Authors: Leung-Tack Mirana , Khanna Divya , Jones June , Elledge Ross O. C. 
Published: November 2022

Abstract
Background
Surgeons are commonly evaluated by surgical skills and outcomes rather than their character traits. We sought to examine role model behaviours of senior surgeons through the lens of Aristotelian (virtue) ethics.

Methods
Semi-structured focus group interviews were undertaken of anaesthetic trainees at a large university hospital NHS Foundation Trust and transcripts were subjected to thematic analysis to yield themes and subthemes. Participation of the trainees was entirely voluntary and focus groups were conducted using Zoom™.

Results
The overarching themes identified were ‘Teamwork makes the dream work’, ‘Captain of the ship’ and ‘Strong foundations’.

Conclusion
We hope to take lessons learnt in conjunction with our previous work to help refocus surgical training towards a process of character reformation, rather than simply imparting technical skills to trainees.
Involvement in the tumor-infiltrating CD8+ T cell expression by the initial disease of remnant gastric cancer
Authors: Kakiuchi Yoshihiko , Kikuchi Satoru , Kuroda Shinji , Kagawa Shunsuke , Fujiwara Toshiyoshi 
Published: November 2022

Abstract
Background
Remnant gastric cancer (RGC) has been increasing for various reasons such as a longer life span, medical progress, and others. It generally has a poor prognosis, and its mechanism of occurrence is unknown. The purpose of this study was to evaluate the clinicopathological features of and clarify the oncological features of RGC.

Methods
Between January 2002 and January 2017, 39 patients with RGC following distal gastrectomy underwent curative surgical resection at the Okayama University Hospital; their medical records and immunohistochemically stained extracted specimens were used for retrospective analysis.

Results
On univariate analysis, initial gastric disease, pathological lymph node metastasis, and pathological stage were the significant factors associated with poor overall survival (p=0.014, 0.0061, and 0.016, respectively). Multivariate analysis of these 3 factors showed that only initial gastric disease caused by malignant disease was an independent factor associated with a poor prognosis (p=0.014, hazard ratio: 4.2, 95% confidence interval: 1.3–13.0). In addition, tumor-infiltrating CD8+ T cells expression was higher in the benign disease group than in the malignant group (p=0.046).

Conclusions
Initial gastrectomy caused by malignant disease was an independent poor prognostic factor of RGC, and as one of the causes, lower level of tumor-infiltrating CD8+ T cells in RGC may involve in.
T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
Authors: Almeida da Paz Michelle , Taher Leila 
Published: November 2022

Abstract
Background
Despite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome’s regulatory landscape, many challenges remain. In particular, because of their repetitive nature, the sequencing reads derived from transposable elements (TEs) pose a real bioinformatics challenge, to the point that standard analysis pipelines typically ignore reads whose genomic origin cannot be unambiguously ascertained.

Results
We show that discarding ambiguously mapping reads may lead to a systematic underestimation of the number of reads associated with young TE families/subfamilies. We also provide evidence suggesting that the strategy of randomly permuting the location of the read mappings (or the TEs) that is often used to compute the background for enrichment calculations at TE families/subfamilies can result in both false positive and negative enrichments. To address these problems, we present the Transposable Element Enrichment Estimator (T3E), a tool that makes use of ChIP-seq data to characterise the epigenetic profile of associated TE families/subfamilies. T3E weights the number of read mappings assigned to the individual TE copies of a family/subfamily by the overall number of genomic loci to which the corresponding reads map, and this is done at the single nucleotide level. In addition, T3E computes ChIP-seq enrichment relative to a background estimated based on the distribution of the read mappings in the input control DNA.
We demonstrated the capabilities of T3E on 23 different ChIP-seq libraries. T3E identified enrichments that were consistent with previous studies. Furthermore, T3E detected context-specific enrichments that are likely to pinpoint unexplored TE families/subfamilies with individual TE copies that have been frequently exapted as cis-regulatory elements during the evolution of mammalian regulatory networks.

Conclusions
T3E is a novel open-source computational tool (available for use at: https://github.com/michelleapaz/T3E) that overcomes some of the pitfalls associated with the analysis of ChIP-seq data arising from the repetitive mammalian genome and provides a framework to shed light on the epigenetics of entire TE families/subfamilies.
Next-generation proteomics of serum extracellular vesicles combined with single-cell RNA sequencing identifies MACROH2A1 associated with refractory COVID-19
Authors: Kawasaki Takahiro , Takeda Yoshito , Edahiro Ryuya , Shirai Yuya , Nogami-Itoh Mari , Matsuki Takanori , Kida Hiroshi , Enomoto Takatoshi , Hara Reina , Noda Yoshimi , Adachi Yuichi , Niitsu Takayuki , Amiya Saori , Yamaguchi Yuta , Murakami Teruaki , Kato Yasuhiro , Morita Takayoshi , Yoshimura Hanako , Yamamoto Makoto , Nakatsubo Daisuke , Miyake Kotaro , Shiroyama Takayuki , Hirata Haruhiko , Adachi Jun , Okada Yukinori , Kumanogoh Atsushi 
Published: November 2022

Abstract
Background
The coronavirus disease 2019 (COVID-19) pandemic is widespread; however, accurate predictors of refractory cases have not yet been established. Circulating extracellular vesicles, involved in many pathological processes, are ideal resources for biomarker exploration.

Methods
To identify potential serum biomarkers and examine the proteins associated with the pathogenesis of refractory COVID-19, we conducted high-coverage proteomics on serum extracellular vesicles collected from 12 patients with COVID-19 at different disease severity levels and 4 healthy controls. Furthermore, single-cell RNA sequencing of peripheral blood mononuclear cells collected from 10 patients with COVID-19 and 5 healthy controls was performed.

Results
Among the 3046 extracellular vesicle proteins that were identified, expression of MACROH2A1 was significantly elevated in refractory cases compared to non-refractory cases; moreover, its expression was increased according to disease severity. In single-cell RNA sequencing of peripheral blood mononuclear cells, the expression of MACROH2A1 was localized to monocytes and elevated in critical cases. Consistently, single-nucleus RNA sequencing of lung tissues revealed that MACROH2A1 was highly expressed in monocytes and macrophages and was significantly elevated in fatal COVID-19. Moreover, molecular network analysis showed that pathways such as “estrogen signaling pathway,” “p160 steroid receptor coactivator (SRC) signaling pathway,” and “transcriptional regulation by STAT” were enriched in the transcriptome of monocytes in the peripheral blood mononuclear cells and lungs, and they were also commonly enriched in extracellular vesicle proteomics.

Conclusions
Our findings highlight that MACROH2A1 in extracellular vesicles is a potential biomarker of refractory COVID-19 and may reflect the pathogenesis of COVID-19 in monocytes.
Fast-forward modeling of borehole nuclear magnetic resonance measurements acquired in deviated wells and spatially heterogeneous formations
Authors: Albusairi Mohammad , Torres-Verdín Carlos 
Published: November 2022

High-angle and horizontal (HAHz) wells are routinely drilled to enhance reservoir exposure and increase fluid productivity. The interpretation of nuclear magnetic resonance (NMR) measurements entails major technical challenges in horizontal layers penetrated by HAHz wells or through dipping formation layers penetrated by a vertical well. Three-dimensional geometric effects, coupled with spatially and petrophysically heterogeneous rocks, may bias petrophysical estimates obtained from borehole NMR measurements using methods designed for vertical wells and horizontal layers. Reliable interpretation requires an accurate and rapid forward-modeling method that integrates NMR physics and tool/instrument specifications, borehole, and 3D formation geometric properties. The latter is possible with the recent development of a forward-modeling algorithm that accurately and efficiently simulates NMR measurements based on 3D spatial sensitivity functions (SSFs). We implement and quantify this forward-modeling approximation across dipping formations penetrated by deviated wells in the presence of mud-filtrate invasion. We validate and verify the fast approximation against a 3D multiphysics model using challenging synthetic cases, in highly apparent dip wells with the varying radial front of the mud-filtrate invasion. Our work compares the effect of radial length of investigation from the three distinct NMR acquisition shells to better understand borehole NMR measurements acquired in 3D complex geometries. On average, the fast approximation via SSFs reproduces NMR measurements in 3 s of central processing unit time with maximum root-mean-square errors below 1% and can therefore be used for real-time calculations and interpretations. Modeling results indicate that thinly bedded formations and their petrophysical properties can be resolved with relatively low measurement resolution in HAHz wells and dipping formations.
Finding the Center:Mrs Dalloway's Bureaucrats and State Centralization
Authors: Hentea Marius 
Published: November 2022

AbstractAlthough the rise of the bureaucratic state was one of the most startling transformations of early twentieth-century British society, novelists raised on a diet of laissez-faire liberalism tended to shy away from direct representations of bureaucracy (with some prominent exceptions, such as the Circumlocution Office in Charles Dickens's Little Dorrit or Anthony Trollope's Three Clerks). Although squarely set within the “governing-class spirit” of Westminster and populated with a bevy of civil servants, Virginia Woolf's Mrs Dalloway tends to be read as maintaining a strict public-private division with a marked preference for the richness and beauty of private life. This article argues that Woolf, no stranger to the civil service through her family and personal networks, had a more strained and ambivalent response to bureaucracy as an idea and government form. A close reading of the structural importance of Hugh Whitbread's character, a minor figure who is often read as an empty, flat Dickensian caricature of the gentleman, shows a more ambivalent response to how bureaucracy and its forms impacted the wider concerns raised about governmentality in Woolf's novel.
The End of the City and the Coming of the Urban: Georges Perec's An Attempt at Exhausting a Place in Paris
Authors: Soule Jacob 
Published: November 2022

Abstract
Georges Perec's short experimental novella An Attempt at Exhausting a Place in Paris documents, with inert fascination, everything that passes through the busy Parisian square of Place Saint-Sulpice over the course of several days, from pedestrians to the continuous stream of buses and taxis. Why, this article asks, does Perec present this magisterial and oft-storied city in centrifugal terms as a place through which things only pass on their way to somewhere else? Once characterized as a rich tapestry of architecture and possible encounters, Paris in 1975 is, from the perspective of this novelist, transformed beyond recognition by the infrastructure of circulation. No longer the imagined center of a productive economy that draws people and objects into its orbit in order to assign them places as characters in the vast amphitheater of class relations—as in the classic city novels of Balzac or Eugène Sue—Perec's experiment shows the social space of the city in the process of becoming only one site among others in the postwar project of urbanization. On this basis, Perec's novella marks the 1970s as an important transition point in the history of the city novel: the old city, once a site of social possibility and conflict, seems to be in its final stage of exhaustion by the centrifugal forces of urbanization. As the process of urbanization becomes legible through its disfigurations of the traditional city novel, the novel forecasts what happens when the spatial development of global capitalism eclipses national culture and its arrangement of people and things.
Loss of WNT4 in the gubernaculum causes unilateral cryptorchidism and fertility defects
Authors: Seth Abhishek , Bournat Juan C. , Medina-Martinez Olga , Rivera Armando , Moore Joshua , Flores Hunter , Rosenfeld Jill A. , Hu Liya , Jorgez Carolina J. 
Published: November 2022

ABSTRACT
Undescended testis (UDT) affects 6% of male births. Despite surgical correction, some men with unilateral UDT may experience infertility with the contralateral descended testis (CDT) showing no A-dark spermatogonia. To improve our understanding of the etiology of infertility in UDT, we generated a novel murine model of left unilateral UDT. Gubernaculum-specific Wnt4 knockout (KO) mice (Wnt4-cKO) were generated using retinoic acid receptor β2-cre mice and were found to have a smaller left-unilateral UDT. Wnt4-cKO mice with abdominal UDT had an increase in serum follicle-stimulating hormone and luteinizing hormone and an absence of germ cells in the undescended testicle. Wnt4-cKO mice with inguinal UDT had normal hormonal profiles, and 50% of these mice had no sperm in the left epididymis. Wnt4-cKO mice had fertility defects and produced 52% fewer litters and 78% fewer pups than control mice. Wnt4-cKO testes demonstrated increased expression of estrogen receptor α and SOX9, upregulation of female gonadal genes, and a decrease in male gonadal genes in both CDT and UDT. Several WNT4 variants were identified in boys with UDT. The presence of UDT and fertility defects in Wnt4-cKO mice highlights the crucial role of WNT4 in testicular development.