bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identiication of novel ligands for receptors using recombinant peptide libraries
Authors: Cwirla Steven E , Dower William J , Gates Christian M , Wagstrom Christopher R , Schatz Peter J 
Published: November 2023

Abstract
Large libraries containing billions of random peptide sequences have proven to be a rich source of ligands for a wide variety of protein targets. Examples include cytokine and growth factor receptor antagonists and agonists (1-4), protease inhibitors (5, 6), and modulators of ligand gated ion channels (7). In most cases peptide ligands were isolated by screening phage display libraries against an immobilized purified protein. Recent reports indicate that even more com- plex targets such as whole cells and tissues can be used to identify peptides that bind specifically to cell surface antigens (8, 9). High affinity ligands 10-20 amino acids in length have been identified from both linear and cyclic peptide libraries. The majority of these sequences bear no resemblance to known ligands for that particular target protein. Indeed the strength of this technology and other combinatorial approaches is based on the notion that ligands to receptors can be identified without prior knowledge of the nature of the interaction.
Applications of RNA FISH for visualizing gene expression and nuclear architecture
Authors: Tam Rose , Shopland Lindsay S , Johnson Carol V , McNeil John A , Lawrence Jeanne B 
Published: November 2023

Abstract
Fluorescence in situ hybridization is not a singular technique, but a versatile experimental approach that provides ever more precise molecular information directly in the context of cellular structure. This chapter will focus on one major aspect of the molecular cytological approach: the detection of nuclear RNAs, together with their genes or other biochemical components of the cell. Improvements in the development and application of FISH in recent years have demonstrated the value of this approach for studying gene expression as well as processing, transport, and function of various cellular and viral RNAs. Although the basic technique described here is also applicable to detection of cytoplasmic mRNA, our focus will be on methods optimized primarily for high resolution, high sensitivity detection of nuclear transcripts, in precise relation to other nuclear components.
Public Opinion: Myths and Realities
Authors: Ginsberg Benjamin 
Published: November 2023

Abstract
Many of the same Americans who believe in the Easter bunny think that public opinion is a significant force in political life. Perhaps not all would accept James Bryce’s famous assertion that popular support “has been the chief and ultimate power in nearly all nations at all times.”1 Most Americans, however, agree that citizens’ preferences have a good deal of influence over the government and its policies. Nearly 80 percent of those responding to a recent national survey said that the government listened to the people most or at least some of the time. More than 90 percent agreed that elections made the government pay attention to public opinion.2
Hamilton’S Rule
Authors: Hamilton W D 
Published: November 2023

Abstract
If Professor David Glass was cool towards my work at the London School of Economics, Professor Lionel S. Pemose, FRS, at University College was equally so. I believe he definitely saw in me the eugenical spectre I mentioned in the first introduction. Although supervised at the Gaitan Laboratory for 2 years I never had a desk there nor was ever invited to give any presentation to explain my work or my occasional presence to others. I think virtually no one I passed in the corridors or sat with in the library knew my name or what I was doing. Probably this was largely my own fault. I was a student who, if not offered or invited, wouldn’t request, and I think I didn’t ask for desk space either there or at LSE. In fact I had no idea at the time what was normal for graduate students and it is only after seeing arrangements made in other departments both in Britain and the US that my own situation as a graduate has come to seem odd. At the time I hardly knew what a PhD was. I just wanted access to libraries plus some pittance of support; these together would give me freedom to follow my puzzles. Apparently I needed affiliation to colleges to receive my grant and to be a part of London University; two colleges were kindly offering this and that was enough.
Elm And Australian
Authors: Hamilton W D 
Published: November 2023

Abstract
IT would be a gross understatement to say that sexuality was the only evolutionary problem worrying me in the mid-1970s. Generally at any one time I have a half dozen problems, some in the foreground of my mind, some like quiescent volcanoes at the back, some completely laid aside but not forgotten. But in those years one in particular besides sex had become major and was proving to be the special successor to one from the past. More than sex itself, it was proposing very clear-cut and even quantitative questions, similar to those I had had concerning optimal sex ratios under the various groupings and types of control that I had treated in the early 1960s. The new problem was that of dispersal.
In-Hospital Neurologic Complications, Neuromonitoring, and Long-Term Neurologic Outcomes in Patients With Sepsis: A Systematic Review and Meta-Analysis
Authors: Fan Tracey H. , Premraj Lavienraj , Roberts Jacob , Lydston Melissa , Robba Chiara , Hager David , Suarez Jose I. , Battaglini Denise , Cho Sung-Min 
Published: November 2023

OBJECTIVES:
Although delirium is well described in patients with sepsis, there are limited data on other neurologic complications. We aimed to systematically review the prevalence, neuromonitoring tools, and neurocognitive outcomes in sepsis patients with neurologic complications.

DATA SOURCES:
MEDLINE and six other databases (Embase, Web of Science, Cochrane CENTRAL, and ClinicalTrials.gov) were searched through January 2023.

STUDY SELECTION:
Studies of adult patients with sepsis reported neurologic complications, use of neuromonitoring tools, neuropathology, and cognitive outcomes.

DATA EXTRACTION:
Two independent reviewers extracted the data. Random-effect meta-analyses were used to pool data.

DATA SYNTHESIS:
Seventy-four studies (n = 146,855) were included. Neurologic complications were reported in 38 studies (n = 142,193) including septic encephalopathy (36%, 95% CI, 27–46%; I2 = 99%), ischemic stroke (5%, 95% CI, 2.1–11.5; I2 = 99%), intracranial hemorrhage (2%, 95% CI, 1.0–4.4%; I2 = 96%), seizures (1%, 95% CI, 0.2–7%; I2 = 96%), posterior reversible encephalopathy syndrome (9%), and hypoxic-ischemic brain injury (7%). In the meta-regression analysis, pulmonary infection, sepsis induced by a gram-positive organism, higher sequential organ failure assessment score, acute physiology and chronic health evaluation II score at admission, and longer ICU length of stay were associated with higher risk of developing septic encephalopathy. Three studies (n = 159) reported postmortem neuropathological findings, acute brain injury was noted in 47% of patients. Twenty-six studies (n = 1,358) reported the use of neuromonitoring tools, electroencephalogram was the most used tool for seizure detection. Transcranial Doppler and near infrared spectroscopy were used for monitoring cerebral hemodynamic changes to detect early ischemia. Six studies reported cognitive outcomes (n = 415) up to 12 months postdischarge and cognitive impairment (≥ one domain) was reported in 30%.

CONCLUSIONS:
In-hospital neurologic complications are common in patients with sepsis. However, the mechanism and timing of those sepsis-associated complications are poorly understood and there are limited data on standardized neuromonitoring in this population.
Inframammary versus Periareolar Incision: A Comparison of Early Complications in Nipple-sparing Mastectomy
Authors: Cavalcante Francisco P. , Lima Ticiane O. , Alcantara Ryane , Cardoso Amanda , Ulisses Flora , Novita Guilherme , Zerwes Felipe , Millen Eduardo 
Published: November 2023

Background:
Nipple-sparing mastectomy (NSM), either used therapeutically or prophylactically, may yield more complications than conventional mastectomy. The incision may affect aesthetic outcome and complication rates, with periareolar incisions being associated with nipple–areolar complex (NAC) necrosis.

Methods:
Early complications were compared between NSM performed in 2015–2022 using inframammary fold (IMF) or periareolar incisions.

Results:
Overall, 180 procedures in 152 patients (bilateral NSM = 28) were included (IMF = 104; periareolar = 76). Mean age (47 versus 43.9 years; P < 0.038), mastectomy weight (312.7 versus 246.8 grams; P < 0.001), implant volume (447.5 versus 409.0 mL; P = 0.002), and use of tissue expanders (68.4% versus 50.0%; P = 0.013) were all greater with periareolar incisions. Prepectoral reconstruction was more common with IMF (18.3% versus 3.9%; P = 0.004). Forty-three complications (23.9%) were recorded (periareolar n = 27, 35%; IMF n = 16, 15.3%; P = 0.0002). NAC necrosis accounted for 17 complications (22.4%) in the periareolar group versus nine (8.5%) in the IMF group (P = 0.002). Necrosis was predominantly moderate (n = 6, 8.3% versus n = 1, 1.0%, respectively) (P = 0.014). Unadjusted odds ratios (OR) for complications [3.05; 95% confidence interval (CI): 1.27–7.26] and necrosis (3.04; 95% CI: 1.27–7.27) were higher in the periareolar group. In the multivariate analysis, necrosis was associated with periareolar incisions [adjusted odds ratio (aOR): 2.92; 95% CI: 1.14–7.44]. Prepectoral reconstruction was associated with IMF incisions (aOR: 25.51; 95% CI: 3.53–184.23; P = 0.001) and with body mass index of more than 25–30 (aOR: 37.09; 95% CI: 5.95–231.10; P < 0.001). Therapeutic mastectomies (aOR: 68.56; 95% CI: 2.50–188.36; P = 0.012) and tissue expanders (aOR: 18.36; 95% CI: 1.89–178.44; P = 0.026) were associated with seromas.

Conclusions:
Both incisions are viable options; however, the risk of NAC necrosis increased with the periareolar approach. Further research is required.
The Implications of Virtual Learning on Plastic Surgery Education: A National Survey of Plastic Surgery Residents and Fellows
Authors: Arora Jagmeet S. , Pham Jason T. , Alaniz Leonardo , Khoshab Nima , Tang Cathy J. 
Published: November 2023

Background:
Graduate medical education during the COVID-19 pandemic has seen the shift to a “virtual learning” format in many aspects of training. The purpose of this study was to describe the perceived strengths and weaknesses of virtual learning compared with a conventional, in-person format.

Methods:
A 45-question survey was sent to independent and integrated plastic surgery residents and postresidency fellows nationally. The survey collected basic demographic information and evaluated three general categories of virtual learning in comparison to an in-person format: (1) time, (2) learning proficiency, and (3) collaboration.

Results:
In total, 108 surveys were submitted from 48 different training programs. Participants reported that virtual learning was more efficient (mean: 3.9), conducive to more free time (mean: 3.9), and a more comfortable medium for expressing opinions (mean: 3.5) and asking questions (mean: 3.6) compared with an in-person format. When stratified between training levels, the PGY 1–3 group reported more difficulties in exam preparedness (P = 0.05), motivation to study (P = 0.01) and less time-saving benefits (P = 0.05) with a virtual format than the PGY 4+ group. Lastly, respondents who had higher self-reported levels of multitasking were found to have lower mean Likert scale scores on all questions related to “time,” “learning proficiency,” and “collaboration” (P < 0.01).

Conclusions:
A virtual and in-person hybrid approach toward plastic surgery education may be beneficial for encouraging flexibility. Our results demonstrate impairment with collaboration and learning proficiency with a virtual format, especially with increased multitasking, but increased comfort with expressing opinions and asking questions.
Transmitted Drug Resistance and HIV Diversity Among Adolescents Newly Diagnosed With HIV in Spain
Authors: Epalza Cristina , Valadés-Alcaraz Ana , González-Alba José María , Beltrán-Pavez Carolina , Gutiérrez-López Miguel , Rubio-Garrido Marina , Fortuny Clàudia , Frick Marie Antoinette , Muñoz Medina Leopoldo , Moreno Santiago , Sanz José , Rojo Pablo , Navarro María Luisa , Holguín África ,   on behalf of the Cohort of the Spanish HIV/AIDS Pediatric (CoRISpe) and Adult (CoRIS) Networks
Published: November 2023

Background:
Virologic characterization of newly HIV-diagnosed adolescents could help to improve their specific needs. The objective was to describe the transmitted drug resistance mutations (TDR) and its transmission by clusters in this population in Spain.

Methods:
TDR to retrotranscriptase and protease inhibitors included in the WHO TDR list 2009 implemented in the Calibrated Population Resistance tool v8.0 (Stanford) were studied in HIV pol sequences from all HIV-diagnosed adolescents (12–19-year-old) enrolled during 2004–2019 period in the Spanish pediatric and adult (CoRISpe-CoRIS) cohorts. The found TDR were compared with the provided by the Stanford algorithm v9.0 2021. HIV-1 variants and transmission clusters were also studied.

Results:
Among 410 HIV-1 adolescents diagnosed, 141 (34.4%) had available ART-naive sequences. They were mostly male (81.6%), Spanish (55.3%) and with behavioral risk (92.2%), mainly male-to-male sexual contact (63.1%). TDR prevalence was significantly higher by Stanford versus WHO list (18.4% vs. 7.1%; P = 0.004). The most prevalent TDR by the WHO list was K103N (3.6%) and by Stanford E138A (6.6%), both at retrotranscriptase. E138A, related to rilpivirine/etravirine resistance, was absent in the WHO list. One in 4 adolescents carried HIV-1 non-B variants. We described 5 transmission clusters, and 2 carried TDR mutations.

Conclusions:
Our data suggest a high TDR prevalence in adolescents with a new HIV diagnosis in Spain, similar to adults, 2 active TDR transmission clusters, and the need for the WHO TDR list update. These findings could have implications for the options of the recently available rilpivirine-related long-acting treatment and in first-line regimen election.
Comparison of posterior capsule rupture rates during phacoemulsification using 3D heads-up visualization system and traditional microscopes
Authors: Jeon Hyun Sun , Kim Min Hwan , Joo Kwangsic , Park Sang Jun , Lee Eun Ji , Hyon Joon Young , Kim Tae-Woo , Park Kyu Hyung , Woo Se Joon 
Published: November 2023

Purpose:
To compare the posterior capsule rupture (PCR) rates of cataract surgery using a traditional ophthalmic surgical microscope (OSM) and a 3D heads-up visualization system (HUVS).

Setting:
Single tertiary referral center.

Design:
Retrospective study.

Methods:
This study included 10 101 eyes that underwent phacoemulsification cataract surgery. Surgeries were performed using either 3D HUVS (1964 eyes, performed by 2 surgeons, HUVS group) or traditional OSM (8137 eyes, performed by 6 surgeons, OSM group) from February 2018 to June 2022. Data were collected based on the diagnosis-related group system, and the rate of PCR requiring vitrectomy and the surgical time were evaluated.

Results:
The PCR rates were not significantly different between the OSM (n = 63; 0.7%) and HUVS (n = 19; 0.9%, P = .392) groups. The mean surgical time was significantly longer in the HUVS group (14.7 ± 10.6 minutes) than in the OSM group (12.9 ± 9.9 minutes, P < .001). In the 3D HUVS group, there were no PCR cases among the initial 100 patients. In both groups, no significant difference was observed in the PCR rates over time. Although the difference was not statistically significant, the PCR rate decreased over time in the HUVS group.

Conclusions:
The results indicate that 3D HUVS-based cataract surgery performed by experienced cataract surgeons had a PCR rate similar to that of traditional OSM-based surgery during the 4-year study period. Although the surgical time was slightly longer with 3D HUVS, cataract surgery using 3D HUVS can be performed safely by experienced surgeons.
Current approaches to overcome recurrent focal segmental glomerulosclerosis after kidney transplantation
Authors: Ahmad Syeda Behjat , Peleg Yonatan , Ahn Wooin 
Published: November 2023

Purpose of review
Recurrent focal segmental glomerulosclerosis (FSGS) presents with nephrotic syndrome shortly after kidney transplantation. This review will overview the role of circulating permeability factors in disease pathogenesis and treatment options for recurrent FSGS.

Recent findings
Novel circulating permeability factors have been identified in serum samples. Current research is focused on detection of permeability factors as a marker of treatment response. Furthermore, novel monoclonal antibodies are being utilized to further induce remission.

Summary
Posttransplant recurrent FSGS can have a deleterious effect on allograft. Early detection of disease recurrence with prompt treatment is optimal for clinical remission. Plasmapheresis with anti-B cell therapy is considered the mainstay of treatment. Newer B cell therapies and detection of circulating factors in serum may help in providing targeted treatment in a subset of patients.
Uncovering the Risks of Anticancer Therapy Through Incident Report Analysis Using a Newly Developed Medical Oncology Incident Taxonomy
Authors: Jacobson Joseph O. , Zerillo Jessica A. , Doolin James , Stuver Sherri O. , Revette Anna , Mulvey Therese 
Published: November 2023

Background
Incident reporting systems were developed to identify possible and actual harm in healthcare facilities. They have the potential to capture important safety trends and to enable improvements that can mitigate the risk of future patient harm and suffering. We recently developed and validated a taxonomy specific for medical oncology designed to enhance the identification, tracking, and trending of incidents that may lead to patient harm. The current project was designed to test the ability of such a taxonomy to be applied across different organizations delivering medical oncology care and to identify specific risks that could result in future harm.

Methods
We analyzed 309 randomly selected medical oncology–related incident reports from 3 different cancer centers that had been posted between January 2019 and December 2020. Each report was assigned up to 2 incident categories. We used a 2-step process to reconcile reviewer discrepancies. In a secondary analysis, each of the incidents was reviewed and recoded to identify events which may result in major or catastrophic harm.

Results
Three hundred four incidents met criteria for inclusion. Three hundred incidents (98.7%) were successfully coded. Sixty-seven percent of incidents were encompassed by the following 4 of 21 categories: prescriber ordering (22%), nursing care (15%), pharmacy (14%), and relational/communication issues (15%). Of 297 evaluable incidents, 47% did not reach the patient, 44.7% reached the patient without harm, 7.7% caused minor injury, and 0.7% caused severe injury or death. Submission rates by physicians varied between the 3 sites accounting for 1.7%, 10.7%, and 16.1% of reports. Secondary analysis identified 9 distinct scenarios that may result in major or catastrophic patient harm.

Conclusions
A medical oncology–specific incident reporting taxonomy has the potential to increase our understanding of inherent risks and may lead to process improvements that improve patient safety.
WhatIsMyGene: Back to the Basics of Gene Enrichment
Authors: Hodge Kenneth , Saethang Thammakorn 
Published: November 2023

WIMG AbstractSince its inception over 20 years ago, gene enrichment has been largely associated with curated gene lists (e.g. GO) that are constructed to represent various biological concepts; the cell cycle, cancer drivers, protein-protein interactions, etc. Researchers expect that a comparison of their own lab-generated lists with curated lists should produce insight. Despite the abundance of such curated lists, we here show that they rarely outperform comparisons against existing individual lab-generated datasets when measured using standard statistical tests of study/study overlap. This demonstration is enabled by the WhatIsMyGene database, which we believe to be the single largest compendium of transcriptomic and micro-RNA perturbation data. The database also houses voluminous proteomic, cell type clustering, lncRNA, epitranscriptomic (etc.) data. In the case of enrichment tools that do incorporate specific lab studies in underlying databases, WIMG generally outperforms in the simple task of reflecting back to the user known aspects of the input set (cell type, the type of perturbation, species, etc.), enhancing confidence that unknown aspects of the input may also be revealed in the output. A limited number of GO lists are included in the database. However, these lists are assigned backgrounds, meaning that GO lists that are replete with abundant entities do not inordinately percolate to the highest ranking positions in output. We delineate a number of other features that should make WIMG indispensable in answering essential questions such as “What processes are embodied in my gene list?” and “What does my gene do?”
Automated segmentation by deep learning of neuritic plaques and neurofibrillary tangles in brain sections of Alzheimer’s Disease Patients
Authors: Ingrassia Lea , Boluda Susana , Jimenez Gabriel , Kar Anuradha , Racoceanu Daniel , Delatour Benoît , Stimmer Lev 
Published: November 2023

AbstractAlzheimer’s Disease (AD) is a neurodegenerative disorder with complex neuropathological features, such as phosphorylated tau (p-tau) positive neurofibrillary tangles (NFTs) and neuritic plaques (NPs). The quantitative evaluation of p-tau pathology is a key element for the diagnosis of AD and other tauopathies. Assessment of tauopathies relies on semi-quantitative analysis and does not consider lesions heterogeneity (e.g., load and density of NFTs vs NPs).In this study, we developed a deep learning-based workflow for automated annotation and segmentation of NPs and NFTs from AT8-immunostained whole slide images (WSIs) of AD brain sections. Fifteen WSIs of frontal cortex from four biobanks with different tissue quality, staining intensity and scanning formats were used for the present study. We first applied an artificial intelligence (AI-)-driven iterative procedure to improve the generation of pathologist validated training datasets for NPs and NFTs. This procedure increased the annotation quality by more than 50%, especially for NPs when present in high density. Using this procedure, we obtained an expert validated annotation database with 5013 NPs and 5143 NFTs. As a second step, we trained two U-Net convolutional neural networks (CNNs) for accurate detection and segmentation of NPs or NFTs. The workflow achieved a high accuracy and consistency, with a mean Dice similarity coefficient of 0.81 for NPs and 0.77 for NFTs. The workflow also showed good generalization performance across different patients with different staining and tissue quality. Our study demonstrates that artificial intelligence can be used to correct and enhance annotation quality especially for complex objects, even when intermingled and present in high density, in brain tissue. Furthermore, the expert validated databases allowed to generate highly accurate models for segmenting discrete brain lesions using a commercial software. Our annotation database will be publicly available to facilitate human digital pathology applied to AD.