bluuebunny/crossref_metadata_2025_split huggingface dataset:
American Literary History in Pieces
Authors: Sinche Bryan 
Published: February 2024

Abstract
Daniel Diez Couch’s American Fragments offers a scholarly analysis of the fragment, a mainstay of American print culture in the early national period. In American Fragments, Couch argues that fragments were central to both American aesthetics and American political culture. Insisting that the fragment was an inclusive and progressive form that invited readers to consider the relationship between a part and the whole, Couch shows how fragments helped Americans understand themselves and their place in a democratic republic. Couch’s book is deeply researched, and it provides insightful readings of well-known texts like Hannah Fosters’s The Coquette, Charles Brockden Brown’s Edgar Huntly, and Washington Irving’s Sketch Book while also introducing readers to a host of poems and other shorter writings that appeared in newspapers, periodicals, and gift books throughout the early nineteenth century. The original research in American Fragments is engaging, and it is also emblematic of a new wave of scholarship enabled by the widespread digitization of books and newspapers in that it introduces so many new texts that are difficult to connect to existing timelines and canons. In this respect, Couch’s book also reveals the limitations of the monograph as a tool for revisioning our collective scholarly project.[R]ight now, the scholarship pushing us to reimagine our literary past is running ahead of the forms in which it might be published.
History in Oblivion
Authors: Yu Timothy 
Published: February 2024

Abstract
The new editions of Theresa Hak Kyung Cha’s Dictée and Exilée and Temps Morts from UC Press provide an opportunity for reflection on the texts’ histories. First published in 1982, just before Cha’s tragic murder, Dictée languished in obscurity until being rediscovered by Asian American critics in the 1990s. In the last few years, Dictée has gained increasing mainstream recognition, but that recognition has often been accompanied by criticism of academic scholars, who, despite their efforts in championing Cha’s work, are now viewed as gatekeepers who have avoided grappling with the facts of Cha’s life and death. Evidence that Cha’s life and work can be brought together emerges from the work of poets influenced by her, including Myung Mi Kim and Divya Victor, while the work collected in Exilée usefully places Cha’s writing in the larger context of her work as an artist. The best scholarly readings of Cha’s work, far from denying Cha’s embodiment, close the gap between word and body, following Cha’s own call to explore history “to the very flesh and bone, to the core.”[I]t is undoubtedly gratifying to see this new discovery of Cha by mainstream readers. But it’s a shame that literary scholars, who for 30 years have been her primary champions . . . are now being portrayed as gatekeepers.
Toward a Taxonomy of the Unpublished
Authors: Fagg John 
Published: February 2024

Abstract
Unpublished texts come in many forms: rejected submissions, lost manuscripts, unfinished, sometimes fabled, books. Our present moment, in which archival practices have made unpublished material widely accessible and the internet has frayed the binary un/published distinction, offers a perspective from which to view the unpublished within US literary history. Attending to the various circumstances in which writing went unpublished draws out the contingencies and inequities of publication and the transgressive allure of writing that, in one way or another, was not supposed to be read. F. Scott’s Fitzgerald’s lost short stories gain value from at first being rejected; Claude McKay’s novel was lost to the structural racism that thwarted the careers of mid–twentieth-century Black writers; and Eileen Myles’ various lost poems and notebooks suggest, perhaps, a casualization of attitudes toward getting work published. An awareness of the unpublished structures and illuminates our engagement with published writing.It is now possible to see the rigid un/published binary in its historical moment. . . . From this vantage, writers and practices that broke from that binary stand out, as do the time-bound value systems that reinforced it.
The Impact of Adverse Childhood Experiences on Symptom and Performance Validity Tests Among a Multiracial Sample Presenting for ADHD Evaluation
Authors: Gonzalez Christopher , Finley John-Christopher A , Khalid Elmma , Basurto Karen S , VanLandingham Hannah B , Frick Lauren A , Brooks Julia M , Ellison Rachael L , Ulrich Devin M , Soble Jason R , Resch Zachary J 
Published: February 2024

Abstract

Objective
Adverse childhood experiences (ACEs) are commonly reported in individuals presenting for attention-deficit hyperactivity disorder (ADHD) evaluation. Performance validity tests (PVTs) and symptom validity tests (SVTs) are essential to ADHD evaluations in young adults, but extant research suggests that those who report ACEs may be inaccurately classified as invalid on these measures. The current study aimed to assess the degree to which ACE exposure differentiated PVT and SVT performance and ADHD symptom reporting in a multi-racial sample of adults presenting for ADHD evaluation.

Method
This study included 170 adults referred for outpatient neuropsychological ADHD evaluation who completed the ACE Checklist and a neurocognitive battery that included multiple PVTs and SVTs. Analysis of variance was used to examine differences in PVT and SVT performance among those with high (≥4) and low (≤3) reported ACEs.

Results
Main effects of the ACE group were observed, such that high ACE group reporting demonstrated higher scores on SVTs assessing ADHD symptom over-reporting and infrequent psychiatric and somatic symptoms on the Minnesota Multiphasic Personality Inventory-2-Restructured Form. Conversely, no significant differences emerged in total PVT failures across ACE groups.

Conclusions
Those with high ACE exposure were more likely to have higher scores on SVTs assessing over-reporting and infrequent responses. In contrast, ACE exposure did not affect PVT performance. Thus, ACE exposure should be considered specifically when evaluating SVT performance in the context of ADHD evaluations, and more work is needed to understand factors that contribute to different patterns of symptom reporting as a function of ACE exposure.
Microbiologic Profile of Nipple Swab Culture and its Association With Postoperative Complications in Prosthetic Breast Reconstruction
Authors: Moon Yi-Jun , Chung Jae-Ho , Lee Hyung-Chul , Jung Seung-Pil , Yoon Eul-Sik 
Published: February 2024

Abstract

Background
In breast surgeries, a lactiferous duct leading to lactic glands of breast parenchyma allows direct contamination by normal bacterial flora of the nipple-areola complex. Complete blockage of nipple flora from the intraoperative field is almost impossible.

Objectives
We aimed to analyze the microbiological profile of nipple flora of breast cancer patients who underwent an implant-based immediate breast reconstruction after a total mastectomy, and to evaluate the association of nipple bacterial flora with postoperative complications.

Methods
A retrospective chart review was performed of patients who underwent an implant-based immediate breast reconstruction after a total mastectomy. A nipple swab culture was performed preoperatively. Patient demographics, surgical characteristics, and complications were compared between positive and negative nipple swab culture groups. Microbiological profile data including antibacterial resistance were collected.

Results
Among 128 breasts, 60 cases (46.9%) had positive preoperative nipple swab culture results. Staphylococcus epidermidis accounted for 41.4% of microorganisms isolated. A multivariate logistic regression analysis of postoperative complications revealed that the presence of nipple bacterial flora was a risk factor for capsular contracture. Seven cases of postoperative infection were analyzed. In 2 cases (40% of pathogen-proven infection), the causative pathogen matched the patient's nipple bacterial flora, which was methicillin-resistant S. epidermidis in both cases.

Conclusions
Nipple bacterial flora was associated with an increased risk of capsular contracture. Preoperative analysis of nipple bacterial flora can be an informative source for treating clinically diagnosed postoperative infections. More studies are needed to determine the effectiveness of active antibiotic decolonization of the nipple.

Level of Evidence: 3
Artificial Intelligence–Generated Social Media Content Creation and Management Strategies for Plastic Surgeons
Authors: Abi-Rafeh Jad , Cattelan Leila , Xu Hong Hao , Bassiri-Tehrani Brian , Kazan Roy , Nahai Foad 
Published: February 2024

Abstract

Background
Social media platforms have come to represent integral components of the professional marketing and advertising strategy for plastic surgeons. Effective and consistent content development, however, remains technically demanding and time consuming, prompting most to employ, at non-negligible costs, social media marketing specialists for content planning and development.

Objectives
In the present study, we aimed to investigate the ability of presently available artificial intelligence (AI) models to assist plastic surgeons in their social media content development and sharing plans.

Methods
An AI large language model was prompted on the study's objectives through a series of standardized user interactions. Social media platforms of interest, on which the AI model was prompted, included Instagram, TikTok, and X (formerly Twitter).

Results
A 1-year, entirely AI-generated social media plan, comprising a total of 1091 posts for the 3 aforementioned social media platforms, is presented. Themes of the AI-generated content proposed for each platform were classified in 6 categories, including patient-related, practice-related, educational, “uplifting,” interactive, and promotional posts. Overall, 91 publicly recognized holidays and observant and awareness days were incorporated into the content calendars. The AI model demonstrated an ability to differentiate between the distinct formats of each of the 3 social media platforms investigated, generating unique ideas for each, and providing detailed content development and posting instructions, scripts, and post captions, leveraging features specific to each platform.

Conclusions
By providing detailed and actionable social media content creation and posting plans to plastic surgeons, presently available AI models can be readily leveraged to assist in and significantly alleviate the burden associated with social media account management, content generation, and potentially patient conversion.
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs
Authors: Charron Philippe , Kang Mingsong 
Published: February 2024

Abstract

Motivation
Genomic variations comprise a spectrum of alterations, ranging from single nucleotide polymorphisms (SNPs) to large-scale structural variants (SVs), which play crucial roles in bacterial evolution and species diversification. Accurately identifying SNPs and SVs is beneficial for subsequent evolutionary and epidemiological studies. This study presents VariantDetective (VD), a novel, user-friendly, and all-in-one pipeline combining SNP and SV calling to generate consensus genomic variants using multiple tools.

Results
The VD pipeline accepts various file types as input to initiate SNP and/or SV calling, and benchmarking results demonstrate VD's robustness and high accuracy across multiple tested datasets when compared to existing variant calling approaches.

Availability and implementation
The source code, test data, and relevant information for VD are freely accessible at https://github.com/OLF-Bioinformatics/VariantDetective under the MIT License.
T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition
Authors: Guan Xiaoyu , Shao Wei , Zhang Daoqiang 
Published: February 2024

Abstract

Motivation
Nanopore sequencing is a new macromolecular recognition and perception technology that enables high-throughput sequencing of DNA, RNA, even protein molecules. The sequences generated by nanopore sequencing span a large time frame, and the labor and time costs incurred by traditional analysis methods are substantial. Recently, research on nanopore data analysis using machine learning algorithms has gained unceasing momentum, but there is often a significant gap between traditional and deep learning methods in terms of classification results. To analyze nanopore data using deep learning technologies, measures such as sequence completion and sequence transformation can be employed. However, these technologies do not preserve the local features of the sequences. To address this issue, we propose a sequence-to-image (S2I) module that transforms sequences of unequal length into images. Additionally, we propose the Transformer-based T-S2Inet model to capture the important information and improve the classification accuracy.

Results
Quantitative and qualitative analysis shows that the experimental results have an improvement of around 2% in accuracy compared to previous methods. The proposed method is adaptable to other nanopore platforms, such as the Oxford nanopore. It is worth noting that the proposed method not only aims to achieve the most advanced performance, but also provides a general idea for the analysis of nanopore sequences of unequal length.

Availability and implementation
The main program is available at https://github.com/guanxiaoyu11/S2Inet.
Randomized phase II selection design with order constrained strata
Authors: Chen Yi , Yu Menggang 
Published: February 2024

ABSTRACT
The exploratory nature of phase II trials makes it quite common to include heterogeneous patient subgroups with different prognoses in the same trial. Incorporating such patient heterogeneity or stratification into statistical calculation for sample size can improve efficiency and reduce sample sizes in single-arm phase II trials with binary outcomes. However, such consideration is lacking in randomized phase II trials. In this paper, we propose methods that can utilize some natural order constraints that may exist in stratified population to gain statistical efficiency for randomized phase II designs. For thoroughness and simplicity, we focus on the randomized phase II selection designs in this paper, although our method can be easily generalized to the randomized phase II screening designs. We consider both binary and time-to-event outcomes in our development. Compared with methods that do not use order constraints, our method is shown to improve the probabilities of correct selection or reduce sample size in our simulation and real examples.
Quantifying the HIV reservoir with dilution assays and deep viral sequencing
Authors: Lotspeich Sarah C , Richardson Brian D , Baldoni Pedro L , Enders Kimberly P , Hudgens Michael G 
Published: February 2024

ABSTRACT
People living with HIV on antiretroviral therapy often have undetectable virus levels by standard assays, but “latent” HIV still persists in viral reservoirs. Eliminating these reservoirs is the goal of HIV cure research. The quantitative viral outgrowth assay (QVOA) is commonly used to estimate the reservoir size, that is, the infectious units per million (IUPM) of HIV-persistent resting CD4+ T cells. A new variation of the QVOA, the ultra deep sequencing assay of the outgrowth virus (UDSA), was recently developed that further quantifies the number of viral lineages within a subset of infected wells. Performing the UDSA on a subset of wells provides additional information that can improve IUPM estimation. This paper considers statistical inference about the IUPM from combined dilution assay (QVOA) and deep viral sequencing (UDSA) data, even when some deep sequencing data are missing. Methods are proposed to accommodate assays with wells sequenced at multiple dilution levels and with imperfect sensitivity and specificity, and a novel bias-corrected estimator is included for small samples. The proposed methods are evaluated in a simulation study, applied to data from the University of North Carolina HIV Cure Center, and implemented in the open-source R package SLDeepAssay.
Cancer type and histology influence cutaneous immunotherapy toxicities: a multi-institutional cohort study
Authors: Wan Guihong , Khattab Sara , Leung Bonnie W , Zhang Shijia , Nguyen Nga , Tran Matthew , Lin Chuck , Chang Crystal , Alexander Nora , Jairath Ruple , Phillipps Jordan , Tang Kimberly , Rajeh Ahmad , Zubiri Leyre , Chen Steven T , Demehri Shadmehr , Yu Kun-Hsing , Gusev Alexander , Kwatra Shawn G , LeBoeuf Nicole R , Reynolds Kerry L , Semenov Yevgeniy R 
Published: February 2024

Abstract

Background
Cutaneous immune-related adverse events (cirAEs) are the most common toxicities to occur in the setting of immune checkpoint inhibitor (ICI) therapy. Identifying patients who are at increased risk of developing cirAEs may improve quality of life and outcomes.

Objectives
To investigate the influence of cancer type and histology on the development of cirAEs in the setting of ICI therapy and survival outcomes.

Methods
This retrospective cohort study included patients recruited between 1 December 2011 and 30 October 2020. They received ICI from 2011 to 2020 with follow-up of outcomes through October 2021. We identified 3668 recipients of ICI therapy who were seen at Massachusetts General Brigham and Dana-Farber. Of these, 669 developed cirAEs. Records that were incomplete or categories of insufficient sample size were excluded from the study cohort. Multivariate Cox proportional hazards models were used to investigate the impact of cancer organ system and histology on cirAE development, after adjusting for demographics, Charlson Comorbidity Index, ICI type, cancer stage at ICI initiation, and year of ICI initiation. Time-varying Cox proportional hazards modelling was used to examine the impact of cirAE development on mortality.

Results
Compared with other nonepithelial cancers (neuroendocrine, leukaemia, lymphoma, myeloma, sarcoma and central nervous system malignancies), cutaneous squamous cell carcinoma [cSCC; hazard ratio (HR) 3.57, P &lt; 0.001], melanoma (HR 2.09, P &lt; 0.001), head and neck adenocarcinoma (HR 2.13, P = 0.009), genitourinary transitional cell carcinoma (HR 2.15, P &lt; 0.001) and genitourinary adenocarcinoma (HR 1.53, P = 0.037) were at significantly higher risk of cirAEs in multivariate analyses. The increased risk of cirAEs translated into an adjusted survival benefit for melanoma (HR 0.37, P &lt; 0.001) and cSCC (HR 0.51, P = 0.011).

Conclusions
The highest rate of cirAEs and subsequent survival benefits were observed in cutaneous malignancies treated with ICI therapies. This study improves our understanding of patients who are at highest risk of developing cirAEs and would, therefore, benefit from appropriate counselling and closer monitoring by their oncologists and dermatologists throughout their ICI therapy. Limitations include its retrospective nature and cohort from one geography.
Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features
Authors: Iruzubieta Pablo , Damborenea Alberto , Ioghen Mihaela , Bajew Simon , Fernandez-Torrón Roberto , Töpf Ana , Herrero-Reiriz Álvaro , Epure Diana , Vill Katharina , Hernández-Laín Aurelio , Manterola María , Azkargorta Mikel , Pikatza-Menoio Oihane , Pérez-Fernandez Laura , García-Puga Mikel , Gaina Gisela , Bastian Alexandra , Streata Ioana , Walter Maggie C , Müller-Felber Wolfgang , Thiele Simone , Moragón Saioa , Bastida-Lertxundi Nerea , López-Cortajarena Aitziber , Elortza Felix , Gereñu Gorka , Alonso-Martin Sonia , Straub Volker , de Sancho David , Teleanu Raluca , López de Munain Adolfo , Blázquez Lorea 
Published: February 2024

Abstract
Alterations in RNA-splicing are a molecular hallmark of several neurological diseases, including muscular dystrophies, where mutations in genes involved in RNA metabolism or characterized by alterations in RNA splicing have been described. Here, we present five patients from two unrelated families with a limb-girdle muscular dystrophy (LGMD) phenotype carrying a biallelic variant in SNUPN gene.
Snurportin-1, the protein encoded by SNUPN, plays an important role in the nuclear transport of small nuclear ribonucleoproteins (snRNPs), essential components of the spliceosome. We combine deep phenotyping, including clinical features, histopathology and muscle MRI, with functional studies in patient-derived cells and muscle biopsies to demonstrate that variants in SNUPN are the cause of a new type of LGMD according to current definition. Moreover, an in vivo model in Drosophila melanogaster further supports the relevance of Snurportin-1 in muscle.
SNUPN patients show a similar phenotype characterized by proximal weakness starting in childhood, restrictive respiratory dysfunction and prominent contractures, although inter-individual variability in terms of severity even in individuals from the same family was found. Muscle biopsy showed myofibrillar-like features consisting of myotilin deposits and Z-disc disorganization. MRI showed predominant impairment of paravertebral, vasti, sartorius, gracilis, peroneal and medial gastrocnemius muscles. Conservation and structural analyses of Snurportin-1 p.Ile309Ser variant suggest an effect in nuclear-cytosol snRNP trafficking. In patient-derived fibroblasts and muscle, cytoplasmic accumulation of snRNP components is observed, while total expression of Snurportin-1 and snRNPs remains unchanged, which demonstrates a functional impact of SNUPN variant in snRNP metabolism. Furthermore, RNA-splicing analysis in patients’ muscle showed widespread splicing deregulation, in particular in genes relevant for muscle development and splicing factors that participate in the early steps of spliceosome assembly.
In conclusion, we report that SNUPN variants are a new cause of limb girdle muscular dystrophy with specific clinical, histopathological and imaging features, supporting SNUPN as a new gene to be included in genetic testing of myopathies. These results further support the relevance of splicing-related proteins in muscle disorders.
Distinct functional subnetworks of cognitive domains in older adults with minor cognitive deficits
Authors: Drenth Nadieh , van Dijk Suzanne E , Foster-Dingley Jessica C , Bertens Anne Suzanne , Rius Ottenheim Nathaly , van der Mast Roos C , Rombouts Serge A R B , van Rooden Sanneke , van der Grond Jeroen 
Published: February 2024

Abstract
Although past research has established a relationship between functional connectivity and cognitive function, less is known about which cognitive domains are associated with which specific functional networks. This study investigated associations between functional connectivity and global cognitive function and performance in the domains of memory, executive function and psychomotor speed in 166 older adults aged 75–91 years (mean = 80.3 ± 3.8) with minor cognitive deficits (Mini-Mental State Examination scores between 21 and 27). Functional connectivity was assessed within 10 standard large-scale resting-state networks and on a finer spatial resolution between 300 nodes in a functional connectivity matrix. No domain-specific associations with mean functional connectivity within large-scale resting-state networks were found. Node-level analysis revealed that associations between functional connectivity and cognitive performance differed across cognitive functions in strength, location and direction. Specific subnetworks of functional connections were found for each cognitive domain in which higher connectivity between some nodes but lower connectivity between other nodes were related to better cognitive performance. Our findings add to a growing body of literature showing differential sensitivity of functional connections to specific cognitive functions and may be a valuable resource for hypothesis generation of future studies aiming to investigate specific cognitive dysfunction with resting-state functional connectivity in people with beginning cognitive deficits.