bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nocardia paucivorans Endophthalmitis and Cerebral Abscesses in an Immunocompetent Patient
Authors: Thakkar Heeral , Rama Raj Palaniraj , Howard-Jones Annaleise R. , Adler Paul , Menon Vidthiya 
Published: October 2023

Abstract

Nocardia spp are an uncommon cause of central nervous system infections and particularly endophthalmitis. In this case report, we present the first documented case of endogenous Nocardia paucivorans endophthalmitis and subretinal abscesses. We also provide a brief summary of the literature regarding ocular and cerebral nocardiosis. Early diagnosis and management improve outcomes; hence, clinicians should be cognizant of Nocardia infection as a differential diagnosis in cases of cerebral abscess or endophthalmitis, including in the immunocompetent.
Dental Screening and Referral during Prenatal Care
Authors: Spencer Michelle , Idzik Shannon K. 
Published: October 2023

Abstract

Background:
Oral health is an important aspect of overall health and should be maintained during pregnancy. Due to complex physiological changes during pregnancy, the pregnant woman is at risk for developing periodontal disease and dental caries which are associated with poor birth outcomes including preterm births and low birthweight infants. Evidence-based guidelines developed by several professional organizations recommend oral screening be included in the first prenatal visit. The purpose of this quality improvement project was to implement a dental screening tool during prenatal care to identify pregnant patients with oral health needs and provide subsequent referrals to a dentist.

Methods:
The project was implemented over a 14-week period and included an oral health screening using a valid and reliable tool to identify oral health needs. Patients were screened and received a referral for dental care.

Results:

N = 826 pregnant women were screened. Of those screened 36.3% (n = 300) had not had their teeth cleaned in the past 12 months. More than 30% of pregnant patients (n = 316) reported some type of dental problem, 29.5% (n = 244) were screened during the first prenatal visit, and 36.7% (n = 303) were enrolled in Medicaid. At project completion, 74.6% (n = 616) of patients received dental referrals.

Conclusion:
Conducting oral health screenings during the first prenatal visit is important for identifying pregnant women at risk for oral health problems and improving birth outcomes and allows the patient time to visit the dentist prior to birth. Integration of an oral health screening and referral process can be successfully implemented during prenatal care to meet the needs of childbearing women.
Using Machine Learning to Select Breast Implant Volume
Authors: Basile Filipe V. , Oliveira Thais S. 
Published: October 2023

Background:
In breast augmentation surgery, selection of the appropriate breast implant size is a crucial step that can greatly affect patient satisfaction and the outcome of the procedure. However, this decision is often based on the subjective judgment of the surgeon and the patient, which can lead to suboptimal results. The authors aimed to develop a machine-learning approach that can accurately predict the size of breast implants selected for breast augmentation surgery.

Methods:
The authors collected data on patient demographic characteristics, medical history, and surgeon preferences from a sample of 1000 consecutive patients who underwent breast augmentation. This information was used to train and test a supervised machine-learning model to predict the size of breast implant needed.

Results:
The study demonstrated the effectiveness of the algorithm in predicting breast implant size, achieving a Pearson correlation coefficient of 0.9335 (P < 0.001). The model generated accurate predictions in 86% of instances, with a mean absolute error of 27.10 mL. Its effectiveness was confirmed in the reoperation group, in which 36 of 57 patients (63%) would have received a more suitable implant size if the model’s suggestion had been followed, potentially avoiding reoperation.

Conclusions:
The findings show that machine learning can accurately predict the needed size of breast implants in augmentation surgery. By integrating the artificial intelligence model into a decision support system for breast augmentation surgery, essential guidance can be provided to surgeons and patients. This approach not only streamlines the implant selection process but also facilitates enhanced communication and decision-making, ultimately leading to more reliable outcomes and improved patient satisfaction.
Identifying perturbations that boost T-cell infiltration into tumours via counterfactual learning of their spatial proteomic profiles
Authors: Wang Zitong Jerry , Farooq Abdullah S. , Chen Yu-Jen , Bhargava Aman , Xu Alexander M. , Thomson Matt W. 
Published: October 2023

AbstractCancer progression can be slowed down or halted via the activation of either endogenous or engineered T cells and their infiltration of the tumour microenvironment. Here we describe a deep-learning model that uses large-scale spatial proteomic profiles of tumours to generate minimal tumour perturbations that boost T-cell infiltration. The model integrates a counterfactual optimization strategy for the generation of the perturbations with the prediction of T-cell infiltration as a self-supervised machine-learning problem. We applied the model to 368 samples of metastatic melanoma and colorectal cancer assayed using 40-plex imaging mass cytometry, and discovered cohort-dependent combinatorial perturbations (CXCL9, CXCL10, CCL22 and CCL18 for melanoma, and CXCR4, PD-1, PD-L1 and CYR61 for colorectal cancer) that support T-cell infiltration across patient cohorts, as confirmed via in vitro experiments. Leveraging counterfactual-based predictions of spatial omics data may aid the design of cancer therapeutics.
IFIH1loss-of-function predisposes to inflammatory and SARS-CoV-2-related infectious diseases
Authors: Najm Rania , Yavuz Lemis , Jain Ruchi , El Naofal Maha , Ramaswamy Sathishkumar , Abuhammour Walid , Loney Tom , Nowotny Norbert , Alsheikh-Ali Alawi , Abou Tayoun Ahmad , Kandasamy Richard K. 
Published: October 2023

AbstractTheIFIH1gene, encoding melanoma differentiation-associated protein 5 (MDA5), is an indispensable innate immune regulator involved in the early detection of viral infections. Previous studies described MDA5 dysregulation linking it to weakened immunological responses, and increased susceptibility to microbial infections and autoimmune disorders. Monoallelic gain-of-function of theIFIH1gene has been associated with multisystem disorders, namely Aicardi-Goutieres and Singleton-Merten syndromes, while biallelic loss of this gene causes immunodeficiency. In this study, nine patients suffering from different cases of recurrent infections, inflammatory diseases, severe COVID-19, or multisystem inflammatory syndrome in children (MIS-C) were identified with putative loss-of-functionIFIH1variants by whole exome sequencing. All patients revealed signs of lymphopenia and an increase in inflammatory markers, including CRP, amyloid A, ferritin, and IL-6. One patient with a pathogenic homozygous variant c.2807+1G>A was the most severe case showing immunodeficiency and glomerulonephritis. The c.1641+1G>C variant was identified in the heterozygous state in patients suffering from periodic fever, COVID-19, or MIS-C, while the c.2016delA variant was identified in two patients with inflammatory bowel disease or MIS-C. Expression analysis showed that PBMCs of one patient with a c.2016delA variant had a significant decrease inISG15,IFNAandIFNGtranscript levels, compared to normal PBMCs, upon stimulation with poly(I:C), suggesting that MDA5 receptor truncation disrupts the immune response. Our findings accentuate the implication of rare monogenicIFIH1loss-of-function variants in altering the immune response, and severely predisposing patients to inflammatory and infectious diseases, including SARS-CoV-2 related disorders.
Genetic predisposition to altered blood cell homeostasis is associated with glioma risk and survival
Authors: Kachuri Linda , Guerra Geno A. , Wendt George A. , Hansen Helen M. , Molinaro Annette M. , Bracci Paige , McCoy Lucie , Rice Terri , Wiencke John K. , Eckel-Passow Jeanette E. , Jenkins Robert B. , Wrensch Margaret , Francis Stephen S. 
Published: October 2023

ABSTRACTGlioma is a highly fatal brain tumor comprised of molecular subtypes with distinct clinical trajectories. Observational studies have suggested that variability in immune response may play a role in glioma etiology. However, their findings have been inconsistent and susceptible to reverse causation due to treatment effects and the immunosuppressive nature of glioma. We applied genetic variants associated (p<5×10−8) with blood cell traits to a meta-analysis of 3418 glioma cases and 8156 controls. Genetically predicted increase in the platelet to lymphocyte ratio (PLR) was associated with an increased risk of glioma (odds ratio (OR)=1.25, p=0.005), especially in IDH-mutant (IDHmutOR=1.38, p=0.007) and IDHmut1p/19q non-codeleted (IDHmut-noncodelOR=1.53, p=0.004) tumors. However, reduced glioma risk was observed for higher counts of lymphocytes (IDHmut-noncodelOR=0.70, p=0.004) and neutrophils (IDHmutOR=0.69, p=0.019; IDHmut-noncodelOR=0.60, p=0.009), which may reflect genetic predisposition to enhanced immune-surveillance. In contrast to susceptibility, there was no association with survival in IDHmut-noncodel;however, in IDHmut1p/19q co-deleted tumors, we observed higher mortality with increasing genetically predicted counts of lymphocytes (hazard ratio (HR)=1.65, 95% CI: 1.24-2.20), neutrophils (HR=1.49, 1.13-1.97), and eosinophils (HR=1.59, 1.18-2.14). Polygenic scores for blood cell traits were also associated with tumor immune microenvironment features, with heterogeneity by IDH status observed for 17 signatures related to interferon signaling, PD-1 expression, and T-cell/Cytotoxic responses. In summary, we identified novel, immune-mediated susceptibility mechanisms for glioma with potential disease management implications.SIGNIFICANCEThis study suggests that genetic determinants of peripheral blood cell counts influence subtype-specific glioma susceptibility and mortality, with potential effects on the tumor immune microenvironment. These findings may have disease management implications.
A splicing-based multi-tissue joint transcriptome-wide association study identifies susceptibility genes for breast cancer
Authors: Gao Guimin , McClellan Julian , Barbeira Alvaro N. , Fiorica Peter N. , Li James L. , Mu Zepeng , Olopade Olufunmilayo I. , Huo Dezheng , Im Hae Kyung 
Published: October 2023

AbstractSplicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify new susceptibility genes. However, existing splicing-TWASs test association of individual excised introns in breast tissue only and have thus limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 European ancestry women. Splicing level prediction models were trained in GTEx (v8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified 9 additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs and 17 genes in 7 loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our spicing-TWASs with previous gene expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci identified by our splicing-TWASs were not reported in the expression-based TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show significant impact on breast cancer risk, while splicing quantitative trait loci (sQTL) showed strong impact through intron excision events.
Development of a website support intervention for families after sudden cardiac death
Authors: Yeates Laura , Baker Amy , Gardner Karen , Stewart Natalie , Catto Laura , Do Judy , Leslie Felicity , Semsarian Christopher , Gray Belinda , McEwen Alison , Adlard Leesa , Ingles Jodie 
Published: October 2023

ABSTRACTObjectiveTo develop content for the website component of COPE-SCD: an online community supporting families after sudden cardiac death (SCD) and assess its acceptability.MethodsBased on topics from codesign focus groups, website content was drafted, and readability of language assessed. SCD family members were recruited from the Genetic Heart Disease Clinic, Royal Prince Alfred Hospital, Sydney. Demographic and psychological measures were collected at baseline. ‘Think aloud’ interviews were conducted to assess the website with questions mapped to theoretical framework of acceptability.ResultsFourteen webpages were created under six menu options. Topics range from information on SCD, genetic testing, grief and loss and family stories. Average Flesch-Kincaid school grade reading score was 8.75. Six individuals participated in a ‘think aloud’ analysis and interview. Fifty percent were female, and all university educated. Median time since death was three years (range 1-5 years). Participants provided feedback about aesthetics, technical issues, and content. Interview responses were mapped to the theoretical framework of acceptability.ConclusionParticipants found the website a helpful resource, and acceptable when considering the theoretical framework of acceptability.Practice implicationsThis website fills a current gap in the care of families after SCD; more work is needed to assess effectiveness.HIGHLIGHTSSudden cardiac death is a devastating complication of many genetic heart diseases.COPE-SCD is an intervention developed to support families after sudden cardiac death.COPE-SCD includes a website covering a range of topics to help families after sudden cardiac death.Website acceptability was assessed using a theoretical framework of acceptability.
HERC3 E3 ligase provides an ERAD branch eliminating select membrane proteins
Authors: Kamada Yuka , Ohnishi Yuko , Nakashima Chikako , Fujii Aika , Terakawa Mana , Hamano Ikuto , Nakayamada Uta , Katoh Saori , Hirata Noriaki , Tateishi Hazuki , Fukuda Ryosuke , Takahashi Hirotaka , Lukacs Gergely L. , Okiyoneda Tsukasa 
Published: October 2023

AbstractAberrant proteins located in the endoplasmic reticulum (ER) undergo rapid ubiquitination by multiple ubiquitin (Ub) E3 ligases and are retrotranslocated to the cytosol as part of the ER-associated degradation (ERAD). Despite several ERAD branches involving different Ub E3 ligases, each with distinct substrate specificity, the molecular machinery responsible for these ERAD branches in mammalian cells remains not fully understood. In this study, we have discovered a cytosolic Ub ligase called HERC3, which fulfills a distinct role in facilitating the ERAD of select polytopic membrane proteins. Using a series of multiplex knockdown/knockout experiments, we have demonstrated that HERC3 functions independently of the ER-embedded ubiquitin ligases RNF5 and RNF185 (RNF5/185) to facilitate the ubiquitination, retrotranslocation, and ERAD of misfolded CFTR. Furthermore, HERC3 collaborates with RNF5/185 to enhance the association of UBQLN proteins, thereby augmenting the retrotranslocation and ERAD of misfolded CFTR. While RNF5/185 participates in the ERAD process of both misfolded ABCB1 and CFTR, HERC3 specifically promotes the ERAD of CFTR, likely due to its ability to interact with the less hydrophobic membrane-spanning domains of CFTR. HERC3 may detect exposed transmembrane domains on the cytoplasmic surface of the ER, thereby facilitating the recruitment of UBQLN and subsequently accelerating the ERAD of select polytopic membrane proteins.
Cities (r)evolution in the smart era: smart mobility practices as a driving force for tourism flow and the moderating role of airports in cities
Authors: Marchesani Filippo , Masciarelli Francesca , Bikfalvi Andrea 
Published: October 2023

Purpose
The significance of smart mobility practices in shaping cities from a smart perspective has grown in recent years, influencing policies and the choices made by inhabitants. This transformation has led to the emergence of novel services and strategies, creating a new, vibrant and highly personalised urban environment that caters to the needs and preferences of both local residents and visitors. The purpose of this study is to evaluate the influence of smart mobility practices on tourism flows in cities, considering the moderating effect of airport activities on this relationship.

Design/methodology/approach
Using a generalised method of moments estimation and focusing on 20 Italian cities over an eight-year period, the authors highlight the current relationship between smart mobility practices and tourism flows. Moreover, the authors demonstrate that the yearly advancement of airports positively moderates this relationship.

Findings
The findings indicate a significant relationship between smart mobility practices in modern cities and tourism inflows because they influence the development of tourism services and emerging trends such as smart tourism and smart destinations. Furthermore, airport activities as a proxy for city openness play a crucial role in this link. The study shows that airports have an incremental impact on tourism and on the relationship between tourism and sustainable practices.

Research limitations/implications
The limitations of this quantitative approach include the focus on a single country, the challenge of measuring the development of smart mobility practices due to a lack of standardised variables and the need for future research to expand the sample to different countries in relation to tourism inflows.

Practical implications
This study has practical implications for policymakers and governance in their task of effectively coordinating internal smart mobility practices and managing incoming tourism flows.

Social implications
This study has social implications, highlighting the need for policymakers and governance to address the societal impacts of smart mobility practices and tourism inflows, ensuring inclusive and sustainable outcomes for local communities.

Originality/value
This study contributes to the existing literature as one of the first attempts to examine the interplay between smart mobility practices in smart cities and tourism flows. Furthermore, it emphasises the role of airports in this relationship, highlighting how the interaction between these variables benefits both stakeholders.
PIILO: an open-source system for personally identifiable information labeling and obfuscation
Authors: Holmes Langdon , Crossley Scott , Sikka Harshvardhan , Morris Wesley 
Published: October 2023

Purpose
This study aims to report on an automatic deidentification system for labeling and obfuscating personally identifiable information (PII) in student-generated text.

Design/methodology/approach
The authors evaluate the performance of their deidentification system on two data sets of student-generated text. Each data set was human-annotated for PII. The authors evaluate using two approaches: per-token PII classification accuracy and a simulated reidentification attack design. In the reidentification attack, two reviewers attempted to recover student identities from the data after PII was obfuscated by the authors’ system. In both cases, results are reported in terms of recall and precision.

Findings
The authors’ deidentification system recalled 84% of student name tokens in their first data set (96% of full names). On the second data set, it achieved a recall of 74% for student name tokens (91% of full names) and 75% for all direct identifiers. After the second data set was obfuscated by the authors’ system, two reviewers attempted to recover the identities of students from the obfuscated data. They performed below chance, indicating that the obfuscated data presents a low identity disclosure risk.

Research limitations/implications
The two data sets used in this study are not representative of all forms of student-generated text, so further work is needed to evaluate performance on more data.

Practical implications
This paper presents an open-source and automatic deidentification system appropriate for student-generated text with technical explanations and evaluations of performance.

Originality/value
Previous study on text deidentification has shown success in the medical domain. This paper develops on these approaches and applies them to text in the educational domain.
“Trust us,” they said. Mapping the contours of trustworthiness in learning analytics
Authors: Slade Sharon , Prinsloo Paul , Khalil Mohammad 
Published: October 2023

Purpose
The purpose of this paper is to explore and establish the contours of trust in learning analytics and to establish steps that institutions might take to address the “trust deficit” in learning analytics.

Design/methodology/approach
“Trust” has always been part and parcel of learning analytics research and practice, but concerns around privacy, bias, the increasing reach of learning analytics, the “black box” of artificial intelligence and the commercialization of teaching and learning suggest that we should not take stakeholder trust for granted. While there have been attempts to explore and map students’ and staff perceptions of trust, there is no agreement on the contours of trust. Thirty-one experts in learning analytics research participated in a qualitative Delphi study.

Findings
This study achieved agreement on a working definition of trust in learning analytics, and on factors that impact on trusting data, trusting institutional understandings of student success and the design and implementation of learning analytics. In addition, it identifies those factors that might increase levels of trust in learning analytics for students, faculty and broader.

Research limitations/implications
The study is based on expert opinions as such there is a limitation of how much it is of a true consensus.

Originality/value
Trust cannot be assumed is taken for granted. This study is original because it establishes a number of concerns around the trustworthiness of learning analytics in respect of how data and student learning journeys are understood, and how institutions can address the “trust deficit” in learning analytics.