bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Handout
Authors: Bennett Copp Lauren
Published: September 2024

Patient education is one of the more rewarding aspects of a dermatology visit. However, the time constraints placed upon staff and providers limits the amount of time available to spend on education. Having detailed patient handouts readily available ensures that patients receive all the necessary information, beyond what is discussed during the visit. Patient handouts also serve as a reference for patients to return to once they leave the office and inevitably forget some of the details that were discussed.

Sun protection is one of the most important aspects of skin cancer prevention education. Below is a comprehensive overview of sun protection that addresses many of the questions patients have regarding sunscreen use and sun protection as a whole. The “key takeaways” at the end of the article can easily be converted into a printable patient handout.
Further characteristics of Noonan Syndrome type 13 caused by MAPK1 loss of function variant: Case report and literature review
Authors: Boniel Snir , Rydzanicz Malgorzata , Ploski Rafal , Szczałuba Krzysztof
Published: September 2024

Rationale:

Noonan syndrome type 13 (NS13, OMIM #619087; Orpha #648, NS13) is caused by MAPK1 gene mutations. Individuals generally present with short stature; delayed psychomotor development; attention deficit and hyperactivity; and typical dysmorphism including ptosis, hypertelorism, downslanting palpebral fissures, low-set and posteriorly rotated ears with prominent antitragus, wide nasal bridge, low posterior hairline, dental anomalies, upper lip dysmorphism, and webbed necks. Skin features include multiple pigmented lentigines and café-au-lait spots. Congenital heart defects include atrial septal defect and mitral valve insufficiency. Neurological abnormalities include hypotonia and epileptiform discharges on electroencephalography. We describe a new case of a 6-year-old boy with the clinical presentation characteristic of NS13.

Patient concerns:

He presented with characteristic dysmorphism, behavioral abnormalities, psychomotor and speech development delay, and global hypotonia among other symptoms.

Diagnoses:

A pathogenic heterozygous de novo missense variant in MAPK1 was identified upon genetic testing during the sixth year of his life.

Interventions:

The child is currently under multidisciplinary care.

Outcomes:

This case report sheds light on the rarity and clinical diversity of NS13. In comparison to other NS13 patients from the literature, our patient presented with similar dysmorphic features, joint hypermobility, and neurodevelopmental delay. In contrast, he did not present with short stature, but with downslanting palpebral fissures, epicanthal folds, micrognathia. Our patient carried a MAPK1 missense variant located close to the N-terminal. This variant could contribute to a milder phenotype by causing partial malfunction of the MAPK1 protein.

Lessons:

The identification of a milder form of NS13 highlights the importance of early diagnosis and targeted management. Early recognition may lead to improved patient outcomes and quality of life. It underscores the need for rapid diagnostic tools specific to NS13, emphasizing the importance of continued research.
The Maternal and Child Health Workforce: A Snapshot of Current and Future Needs From Public Health WINS 2021
Authors: Tissue Michelle Menser , Donney Julie Fife , Mullenix Amy , Schaffer Kay , Stampfel Caroline , Ramos Lauren Raskin , Cilenti Dorothy
Published: September 2024

Objective

To summarize and examine data collected from the first-ever Public Health Workforce Interests and Needs Survey Maternal and Child Health (MCH) module.

Design, Setting, and Participants

Responses from MCH governmental public health employees in 47 state health departments and 288 local health departments (LHDs) in the United States.

Main Outcome Measure

Demographic characteristics; 4 measures from the MCH module: the importance of and skill level in 5 MCH competencies in daily work, growth and leadership development opportunities, and additional workforce development needs.

Results

The MCH workforce predominantly self-identified as women (91.2%) and as White, non-Hispanic (55.2%). At least 70% of respondents reported MCH competencies as important in their daily work, but only 44% to 57% reported being proficient in those competencies. The MCH workforce in LHDs were less likely than those in state health departments to report being proficient in MCH competencies (adjusted prevalence rate ratio range: 0.83-0.92) or have growth and leadership development opportunities (adjusted prevalence rate ratio range 0.76-0.90).

Conclusion

The MCH module highlights a need to further prioritize workforce development efforts for governmental public health staff, especially in LHDs. There is an ongoing need to meet public health professionals where they are and to tailor training models and workforce development plans to account for new and ongoing stressors faced by the workforce.
Performance of patient-collected dried blood specimens for HIV-1 viral load testing in South Africa
Authors: Sahu Maitreyi , Schaafsma Torin , Szpiro Adam A. , Van Rooyen Heidi , Asiimwe Stephen , Shahmanesh Maryam , Krows Meighan L. , Sithole Nsika , Van Heerden Alastair , Barnabas Ruanne V.
Published: September 2024

Objective:

Evaluate the clinical utility of patient-collected dried blood spots (DBS) in measuring HIV-1 viral load (VL) for monitoring antiretroviral therapy (ART) compared to provider-collected DBS and blood plasma.

Design:

In a randomized trial of community-based delivery of ART in South Africa, we assessed performance of: DBS specimens compared to plasma, and participant-collected vs. staff-collected DBS specimens, to measure HIV-1 VL.

Methods:

The bioMérieux NucliSENS EasyQ HIV-1 v2.0 assay was used for VL measurement. From October 2017 to November 2019, we collected 996 pairs of plasma/DBS specimens from 760 participants and 315 pairs of staff-/participant-collected DBS cards from 261 participants. We assessed DBS test sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) using the WHO failure threshold of 1000 copies/ml. Log-transformed VL was compared using concordance correlation coefficients (CCC) and mean differences from linear mixed models.

Results:

In a population with 13% detectable VL, DBS VL compared with plasma VL had 91% [95% confidence interval (CI): 86–95] sensitivity, 99% (98–100) specificity, 94% (90–98) PPV, and 99% (98–99) NPV. We observed high agreement between staff-collected DBS VL and plasma VL (CCC: 0.94), and between participant-collected DBS VL and plasma VL (CCC: 0.92). We did not observe a statistically significant difference between participant- and staff-collected DBS VL and correlation was very high (CCC: 0.97).

Conclusions:

VL results from participant-collected DBS are clinically comparable with those collected by clinical staff and using blood plasma. Self-collected DBS has potential for use for ART monitoring outside the clinic.
Health-Related Quality of Life in Young Adults With Perinatal HIV After Transfer to Adult Health Care in the Netherlands
Authors: Weijsenfeld Annouschka , van der Knaap Linda , Sattoe Jane , van Staa AnneLoes , Vermont Clementien , Nellen Jeannine F. J. B. , Pajkrt Dasja
Published: September 2024

Introduction:

Health-related quality of life (HRQoL) in adult people with HIV is lower than that of the general population. Previously, no differences were detected in HRQoL of Dutch children with perinatal HIV (PHIV) compared with norm groups. In this study, we compared HRQoL of PHIV young adults (PHIV-YA, aged 18–30 years) with 2 norm groups, the healthy Dutch YA population and YA with various chronic conditions.

Methods:

Participants received questionnaires on HRQoL, adherence, and demographics. Additional social and health care-related variables were collected from patients' medical files. We explored correlations between HRQoL and demographic characteristics. Effect sizes (ES, Hedges 'g with confidence intervals) were calculated to quantify the difference between PHIV-YA and norm groups.

Results:

Of 81 participants, 53 filled out the questionnaires. Compared with the healthy Dutch YA population, PHIV-YA aged 18–30 years had significantly lower HRQoL scores in the school/work subscale. PHIV-YA aged 26–30 years had significantly lower total, physical and psychosocial HRQoL scores as well. Participants in the older age category had lower HRQoL scores throughout all subcategories as compared with the younger age group. For PHIV-YA aged 18–25 years, lower scores on the school/work subscale were correlated with substance use and being born outside the Netherlands.

Conclusions:

PHIV-YA had low HRQoL scores in school/work functioning compared with the healthy Dutch YA population. The circumstances driving these outcomes are likely to be multidimensional, including HIV infection, social background, and challenges in growing up with a chronic condition.
Content Analysis of the Top 25 Most Cited Articles of the Journal of Craniofacial Surgery With ChatGPT-4o
Authors: Durna Yusuf Muhammed , Teki̇n Mustafa Said , Duymaz Yaşar Kemal , Teki̇n Ahmet Mahmut , Bahşi İlhan
Published: September 2024

Objective:

Since 1990, the Journal of Craniofacial Surgery has been an important resource for clinicians and basic scientists. The journal addresses clinical practice, surgical innovations, and educational issues. This study aims to evaluate the contribution of these articles to clinical practice innovations and surgical procedures by analyzing the content of the 25 most cited articles published in the journal. It also aims to demonstrate the potential of artificial intelligence tools in academic content analysis.

Methods:

All articles published in the Journal of Craniofacial Surgery on June 13, 2024, were searched using the Web of Science Database, and the 25 most cited articles were identified. The full texts of these articles were saved in PDF format and metadata were saved as plain text files. Content analysis of these 25 articles was performed using ChatGPT-4o.

Results:

As a result of the analysis, some articles stood out in terms of clinical importance. It also appeared that ChatGPT could be used to compare multiple articles.

Conclusion:

In this study, the authors analyzed the content of the 25 most cited articles published in the Journal of Craniofacial Surgery using ChatGPT-4o. These articles were evaluated according to the criteria of innovations in clinical practice and compliance with surgical procedures. This study presents interesting findings in terms of the use of artificial intelligence tools in academic content analysis. The authors thought that this study could be a source of inspiration for future studies.
The Time Has Come
Authors: Cooper David K.C. , Riella Leonardo V. , Kawai Tatsuo , Fishman Jay A. , Williams Winfred W. , Elias Nahel , Madsen Joren C. , Pierson Richard N.
Published: September 2024

In vitro studies indicate that kidney transplantation from gene-edited pigs in which expression of all 3 of the known glycan xenoantigens has been deleted may be more challenging in nonhuman primates (NHPs) than it will be in human recipients. Furthermore, pig-to-human xenotransplantation offers several other advantages—(1) the patient can communicate with the surgical team; (2) recipient microbiological monitoring and environment will be clinical-grade; and (3) sophisticated graft monitoring and imaging techniques, (4) therapeutic interventions, eg, dialysis, plasmapheresis, and (5) intensive care can be deployed that are not easily available in NHP laboratory models. We suggest, therefore, that progress to develop safe, informative human clinical trials will be accelerated if pilot clinical cases are initiated. The selection of patients for kidney xenotransplantation can include those who are at high risk of dying imminently, for example, those experiencing increasing vascular access challenges with no realistic alternative therapy available, and those who have been accepted onto the waitlist for an allograft, but who are unlikely ever to receive one. Patients with an increased risk of dying include those with (1) age above 60 years, (2) blood groups O or B, and (3) diabetic nephropathy. UNOS data indicate that an average of 25 patients on the kidney waitlist in the United States die or are removed from the list every day (ie, >9000 each year). Given the improved xenograft survival observed in preclinical studies, we suggest that it is time to plan a small pilot clinical trial for healthy dialysis patients who understand the risks and potential benefits of kidney xenotransplantation.
Proposal of Lactobacillus amylovorus subsp. animalis subsp. nov. and an emended description of Lactobacillus amylovorus
Authors: Yamane Kenji , Tanizawa Yasuhiro , Kobayashi Hisami , Kamizono Tomomi , Kojima Yoichiro , Takagi Hiroki , Tohno Masanori
Published: September 2024

A corrigendum of this article has been published full details can be found at 10.1099/ijsem.0.006564

Seven novel lactic acid bacterial strains (BF125T, BF186, TKL145, YK3, YK6, YK10 and NSK) were isolated from the fresh faeces of Japanese black beef cattle and weanling piglets, spent mushroom substrates, or steeping water of a corn starch production plant. These strains are rod-shaped, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, cytochrome oxidase-negative, facultatively anaerobic, and homofermentative. Strain BF125T did not produce any gas from glucose; both d- and l-lactate were produced as end-products of glucose (D/L, 40 : 60). Growth occurred at 30–45 °C (optimum, 37 °C), pH 5.0–8.0 (optimum, pH 6.0), and with NaCl concentration of 1.0–3.0% (w/v). The G+C content of genomic DNA of strain BF125T was 37.8 mol% (whole-genome analysis). The major fatty acids were C16 : 0, C18 : 1 ω9c, C19 cyclopropane 9, 10, and summed feature 10. The 16S rRNA gene in strain BF125T showed high similarity to that of the type strain of Lactobacillus amylovorus (99.93%), and the other isolates were also identified as L. amylovorus based on these similarities. A phylogenetic tree based on the core genomes of L. amylovorus strains (n=54), including the seven isolates, showed that they could be divided into two clusters. Strains YK3, YK6, YK10, and NSK were in the first cluster, along with the type strain DSM 20531T, while the second cluster included isolates BF125T, BF186, TKL145, and other strains isolated from various animal origins. Phenotypic differences in fermentability were observed for lactose, salicin, and gentiobiose between these two groups. The intergroup digital DNA–DNA hybridization values (72.9–78.6%) and intergroup average nucleotide identity values (95.64–96.92%) were comparable to values calculated using datasets of other valid subspecies of the genus (ex-) Lactobacillus. In light of the physiological, genotypic, and phylogenetic evidence, we propose a novel subspecies of L. amylovorus, named Lactobacillus amylovorus subsp. animalis subsp. nov. (type strain BF125T=MAFF 212522T=DSM 115528T). Our findings also led to the automatic creation of Lactobacillus amylovorus subsp. amylovorus subsp. nov. and an emended description of the species L. amylovorus.
Dynamic imaging of myelin pathology in physiologically preserved human brain tissue using third harmonic generation microscopy
Authors: Meijns Niels R.C. , Blokker Max , Idema Sander , ’t Hart Bert A. , Veta Mitko , Ettema Loes , van Iersel Juliet , Zhang Zhiqing , Schenk Geert J. , Groot Marie Louise , Luchicchi Antonio
Published: September 2024

Myelin pathology is known to play a central role in disorders such as multiple sclerosis (MS) among others. Despite this, the pathological mechanisms underlying these conditions are often difficult to unravel. Conventional techniques like immunohistochemistry or dye-based approaches, do not provide a temporal characterization of the pathophysiological aberrations responsible for myelin changes in human specimens. Here, to circumvent this curb, we present a label-free, live-cell imaging approach of myelin using recent advancements in nonlinear harmonic generation microscopy applied to physiologically viable human brain tissue from post-mortem donors. Gray and white matter brain tissue from epilepsy surgery and post-mortem donors was excised. To sustain viability of the specimens for several hours, they were subjected to either acute or organotypic slice culture protocols in artificial cerebral spinal fluid. Imaging was performed using a femtosecond pulsed 1060 nm laser to generate second harmonic generation (SHG) and third harmonic generation (THG) signals directly from myelin and axon-like structures without the need to add any labels. Experiments on acute human brain slices and post-mortem human slice cultures reveal that myelin, along with lipid bodies, are the prime sources of THG signal. We show that tissue viability is maintained over extended periods during THG microscopy, and that prolonged THG imaging is able to detect experimentally induced subtle alterations in myelin morphology. Finally, we provide practical evidence that live-cell imaging of myelin with THG microscopy is a sensitive tool to investigate subtle changes in white matter of neurological donors. Overall, our findings support that nonlinear live-cell imaging is a suitable setup for researching myelin morphology in neurological conditions like MS.
Burning glass effect of water droplets triggers an ER-derived calcium response in the chloroplast stroma ofArabidopsis thalianaleaves
Authors: Kuang Dominic , Romand Shanna , Zvereva Anna S. , Marchesano Bianca Maria Orlando , Buratti Stefano , Zheng Ke , Mylle Evelien , Spetea Cornelia , Damme Daniël Van , Wurzinger Bernhard , Schwarzländer Markus , Teige Markus , Costa Alex , Stael Simon
Published: September 2024

Plants require water and light for photosynthesis, but light, when focused by water droplets on leaves, can create high light intensity spots that are harmful to plants. As excessive light intensity can reduce growth or even induce cell death, it is vital for plants to detect and react to changes in light exposure and acclimate to high light stress. Ca2+signaling was previously implicated in high light acclimation. However, the dynamics of free Ca2+concentration in the chloroplast, the primary site of photosynthesis, or in the nucleus and in the cytoplasm, where transcription and translation for long-term acclimation occurs, remain unknown. Here we studied the dynamics and mechanism of the Ca2+response to high light exposure. Focusing light through a glass bead to mimic water droplets triggered an increase of the free Ca2+concentration in the chloroplast stroma ofArabidopsis thaliana. This finding was corroborated using established and newly developed genetically encoded calcium indicators, which revealed a biphasic increase in the stromal free Ca2+concentration when exposed to varying intensities and qualities of light. Among photosynthetic by-products, reactive oxygen and lipophilic species in particular, have been implicated in high light stress acclimation. A H2O2signature was induced, albeit with different dynamics than the Ca2+response, while chemical inhibition of the photosynthetic electron transport points towards singlet oxygen as a potential culprit of the high light-induced increase in stromal free Ca2+concentration. The observed dynamics differed from those of a heat-shock induced Ca2+signature, although temperature had a positive effect on the Ca2+response. Based on Ca2+inhibitor treatments and the free Ca2+concentration dynamics, we suggest that the high light-induced stromal Ca2+is derived from the endoplasmic reticulum rather than from the cytoplasm. In conclusion, inspired by the burning glass effect of water droplets on leaves, we uncovered a Ca2+response that implicates a novel mechanism for plants to acclimate to high light stress—a process that will become increasingly relevant in a changing climate.
Neurons in the medial prefrontal cortex that are not modulated by hippocampal sharp-wave ripples are involved in spatial tuning and signaling upcoming choice
Authors: den Bakker Hanna , Kloosterman Fabian
Published: September 2024

The hippocampus is known to encode spatial information and reactivate experienced trajectories during sharp-wave ripple events. These events are thought to be key time-points at which information about learned trajectories is transferred to the neocortex for long-term storage. It is unclear, however, how this information may be transferred and integrated in downstream cortical regions. In this study, we performed high-density probe recordings across the full depth of the medial prefrontal cortex and in the hippocampus simultaneously in rats while they were performing a task of spatial navigation. We find that neurons in the medial prefrontal cortex encode spatial information and reliably predict upcoming choice on a maze, and we find that a subset of neurons in the mPFC is modulated by hippocampal sharp-wave ripples. However, the neurons that are involved in predicting upcoming choice are not the neurons that are modulated by hippocampal sharp-wave ripples. This indicates that the integration of spatial information requires the collaboration of different specialized populations of neurons.
Immune Cell Densities Predict Response to Immune Checkpoint-Blockade in Head and Neck Cancer
Authors: Ruiz Torres Daniel A. , Bryan Michael E. , Hirayama Shun , Merkin Ross D. , Evelyn Luciani , Roberts Thomas , Patel Manisha , Park Jong C. , Wirth Lori J. , Sadow Peter M. , Sade-Feldman Moshe , Stott Shannon L. , Faden Daniel L.
Published: September 2024

Immune checkpoint blockade (ICB) is the standard of care for recurrent/metastatic head and neck squamous cell carcinoma (HNSCC), yet efficacy remains low. The current approach for predicting the likelihood of response to ICB is a single proportional biomarker (PD-L1) expressed in immune and tumor cells (Combined Positive Score, CPS) without differentiation by cell type, potentially explaining its limited predictive value. Tertiary Lymphoid Structures (TLS) have shown a stronger association with ICB response than PD-L1. However, their exact composition, size, and spatial biology in HNSCC remain understudied. A detailed understanding of TLS is required for future use as a clinically applicable predictive biomarker. Methods: Pre-ICB tumor tissue sections were obtained from 9 responders (complete response, partial response, or stable disease) and 11 non-responders (progressive disease) classified via RECISTv1.1. A custom multi-immunofluorescence (mIF) staining assay was designed, optimized, and applied to characterize tumor cells (pan-cytokeratin), T cells (CD4, CD8), B cells (CD19, CD20), myeloid cells (CD16, CD56, CD163), dendritic cells (LAMP3), fibroblasts (alpha-Smooth Muscle Actin), proliferative status (Ki67) and immunoregulatory molecules (PD1). Spatial metrics were compared among groups. Serial tissue sections were scored for TLS in both H&E and mIF slides. A machine learning model was employed to measure the effect of these metrics on achieving a response to ICB (SD, PR, or CR). Results: A higher density of B lymphocytes (CD20+) was found in responders compared to non-responders to ICB (p=0.022). A positive correlation was observed between mIF and pathologist identification of TLS (R2= 0.66, p-value= <0.0001). TLS trended toward being more prevalent in responders to ICB (p=0.0906). The presence of TLS within 100 um of the tumor was associated with improved overall (p=0.04) and progression-free survival (p=0.03). A multivariate machine learning model identified TLS density as a leading predictor of response to ICB with 80% accuracy. Conclusion: Immune cell densities and TLS spatial location within the tumor microenvironment play a critical role in the immune response to HNSCC and may potentially outperform CPS as a predictor of ICB response.
Toxoplasma gondiiinfection misdirects placental trophoblast lineage specification
Authors: Cabo Leah F. , Yang Liheng , Gao Mingze , da Silva Rafaela J. , Washington NyJaee N. , Reilly Sarah M. , Megli Christina J. , Coyne Carolyn B. , Boyle Jon P.
Published: September 2024

Pregnancy is a critical point of vulnerability to infection and other insults that could compromise proper fetal development. The placenta acts as a protective and nutrient-permeable barrier to most infectious agents, but a few are capable of bypassing its defenses. Remarkably little is known about how exposure to these select pathogens might impact ongoing placental development. Here we demonstrate thatToxoplasma gondiientirely misdirects the developmental program of trophoblast stem cells. Infection of progenitor cytotrophoblasts prevents fusion and differentiation to infection-resistant syncytiotrophoblast. Rather,T. gondiielicits a unique transcriptional identity that polarizes cytotrophoblasts to the infection-permissive extravillous trophoblast fate. Strong evidence of developmental disruption is found in multiple orthogonal models, including trophoblast stem cells, trophoblast organoids, and chorionic villi. Manipulation of cell fate by the parasite is most dramatic in trophoblast organoids, where we see robust outgrowth of HLA-G(+) extravillous trophoblasts. Collectively, these data show thatToxoplasmaantagonizes differentiation of an infection-resistant cell type by inducing formation of an infection-permissive cell type, therefore potentiating its own transmission to the fetus.
Inter-strain variation in intra-chromosomal rates of recombination inCaenorhabditis elegans
Authors: Matharage Dharani U. , Cutler Riley , Khadgi Anamica , Dapper Amy L.
Published: September 2024

Meiotic recombination results in the exchange of genetic material between homologous chromosomes. One consequence of meiotic recombination is the production of novel combination of alleles. Recombination rate varies dramatically within and between species, populations, sexes and individuals. Although, the role of PRDM9 in intra-chromosomal variation in crossovers is extensively studied, variation in recombination rate and the cellular and evolutionary dynamics that influence recombination is not well understood due to the complexity of the recombination landscape, intrinsic variation in recombination, and the limited experimental approaches. Though, there has only been limited research regarding the variation in recombination rates inCaenorhabditis elegans, observations from previous studies bring out the potential ofC. elegansto be a convenient system for studying intra-chromosomal variation in recombination rate that avoid many of the common pitfalls. Therefore, we investigated the variation in intra-chromosomal patterns of recombination rates in two distinct populations ofC. elegansin one of the two high recombination regions of chromosome IV. We used phenotypic fluorescent markers which are inserted in chromosome IV to estimate the recombination rate of the two most genetically distinct strains, N2 and CB4856. We identified statistically significant differences in recombination rate between the two strains, with a 3% higher frequency of recombinant offspring in CB4856 in this focal region. Additionally, we did not find any evidence of sex differences in recombination rate (heterochiasmy). Moreover, we looked at the plasticity of recombination rate in response to stressful conditions in the twoC. elegansstrains. Here we observed a significant decrease in the recombination rate in both strains when exposed to stressful conditions. These results open the door to usingC. elegansto study evolution and genetics of variation in recombination rate.
Accuracy of the National Early Warning Score version 2 (NEWS2) in predicting need for time-critical treatment: Retrospective observational cohort study
Authors: Goodacre Steve , Sutton Laura , Fuller Gordon , Trimble Ashleigh , Pilbery Richard
Published: September 2024

Background

Initial emergency department (ED) assessment can use early warning scores to identify and prioritise patients who need time-critical treatment. We aimed to determine the accuracy of the National Early Warning Score version 2 (NEWS2) for predicting the need for time-critical treatment.

Methods

We undertook a single centre retrospective observational cohort study. We randomly selected 4000 adults who attended a tertiary hospital ED in 2022 and had NEWS2 routinely recorded on electronic patient records. The first NEWS2 score and vital signs were extracted from electronic records. Research nurses selected cases that received a potentially time-critical treatment. Two independent clinical experts then determined whether time-critical treatment was or should have been received, using an expert consensus derived list of interventions. We used receiver operating characteristic (ROC) analysis and calculated sensitivity and specified at pre-defined thresholds to evaluate the accuracy of NEWS2 for predicting need for time-critical intervention.

Results

After excluding ten patients who received their intervention before NEWS2 recording, 164/3990 (4.1%) needed time-critical treatment and 71/3990 (1.8%) died within seven days. NEWS2 predicted need for time-critical treatment with a c-statistic of 0.807 (95% confidence interval 0.765 to 0.849) and death within seven days with a c-statistic of 0.865 (0.813, 0.917). NEWS2>4 predicted need for time-critical treatment with sensitivity of 0.518 (0.442, 0.593) and positive predictive value of 0.258 (0.213, 0.307). Patients needing emergency surgery, antibiotics for open fractures, insulin infusion, or manipulation of limb-threatening injuries frequently had NEWS2≤4. Patients with NEWS2>4 who did not need time-critical treatment frequently scored three points on NEWS2 for their respiratory rate, conscious level, or receiving supplemental oxygen.

Conclusion

NEWS2 has modest accuracy for predicting need for time-critical treatment. We have identified time-critical interventions that frequently have low NEWS2 scores and NEWS2 parameters than may overestimate need for time-critical intervention.
Cumulative local recurrence rate is a misleading and non-representative outcome measure for early breast cancer trials
Authors: Vaidya Jayant S , Bulsara Max , Vaidya Uma J , Morgan David , Douek Michael , Bernstein Marcelle , Brew-Graves Chris , Williams Norman R , Tobias Jeffrey S
Published: September 2024

In many breast cancer radiotherapy trials, the results are presented in the form of cumulative incidence rates of local recurrence or Kaplan-Meier plots, in which deaths are censored. Censoring - using patients’ length of follow up until the point when they had last been seen alive – is included in the statistical model, under the correct assumption that they will continue to have a risk of developing a local recurrence. Censoring should be non-informative and balanced. However, if shorter follow up is unbalanced between treatments, or if shorter follow up is due to death (from whatever cause), these assumptions and therefore the model is no longer valid. It is therefore ambiguous to statistically ignore deaths when reporting local recurrence, by censoring them. We illustrate, with examples from randomised trials, why and how such graphs cannot give patients and clinicians a clear indication of the effects of treatments or prognosis. For instance, in one of these examples, 60% of patients were alive at 10 years, so those alive without a local recurrence should inevitably be lower than 60%, rather than the 90% estimated using the above method. The simple way to avoid this error is to turn the analysis on its head, by reporting chances of success rather than failure, by reporting the probability of being free of local recurrence (i.e. both death and local recurrence are events). This estimate truly represents what really happens to patients in terms of local control and the relative effectiveness of treatment(s) comprehensively. It also conforms with the recommendations of ICH-GCP, European (DATECAN) and American (STEEP) guidelines.
Insulin-dependence as a Predictor of Shortened Cancer-specific Survival in Pancreatic Neuroendocrine Tumors: A Multi-Institutional Study from the United States Neuroendocrine Study Group
Authors: Mirza Muhammad Bilal , Baechle Jordan J , Smith Paula Marincola , Ali Danish , Dillhoff Mary , Poultsides George , Rocha Flavio G. , Cho Clifford S. , Winslow Emily R. , Fields Ryan C. , Maithel Shishir K. , Idrees Kamran
Published: September 2024

Introduction

PNETs are rare pancreatic malignancies originating from islet cells and exhibit a strong co-occurrence with Diabetes Mellitus (DM), associated with worse survival outcomes. However, studies have yet to delineate the impact of insulin dependent (IDDM) and non -insulin dependent (NIDDM) on poor oncological outcomes.

Methods

Utilizing the U.S. Neuroendocrine Tumor Study Group database (1999-2016), we performed a retrospective cohort study of adult patients who underwent primary surgical resection of PNETs. Patients were categorized based on preoperative diagnosis into non-DM, NIDDM, and IDDM cohorts. We used the Kaplan-Meier method and log-rank test to study cancer-specific survival (CSS). Cox proportional Hazards models were used to assess the impact of IDDM on CSS.

Results

Of the 1,122 patients included in the analysis, 870 (77%) were non-DM, 168 (15%) were NIDDM, and 84 (8%) were IDDM. The groups were similar in tumor stage and grade. However, they differed in sex, BMI, age, ASA class, tumor location, preoperative HbA1c and serum glucose (p-value <0.05). Patients with IDDM had significantly decreased 5-year CSS compared to patients without IDDM (CSS: IDDM 85%, NIDDM 94%, non-DM 93%, NIDDM + non-DM 93%;P<0.01). On multivariate analysis, IDDM was independently associated with worse CSS (HR 2.27, 95% Confidence Interval 1.15-4.45,P=0.02).

Conclusion

Insulin dependence is associated with worse cancer-specific survival in PNET patients following surgical resection compared to PNET patients with NIDDM or without DM.
Sex and age differences in cardiovascular risk factors and lifestyle at the onset of diabetes mellitus: a cross-sectional study in Spanish Primary Health Care
Authors: Vich-Pérez P , Taulero-Escalera B , García-Espinosa V , Villanova-Cuadra L , Regueiro-Toribio P , Sevilla-Machuca I , Timoner-Aguilera J , Martínez-Grandmontagne M , Abós-Pueyo T , Álvarez-Hernandez-Cañizares C , Reviriego-Jaén G , Serrano-López-Hazas A , Gala-Molina I , Sanz-Pascual M , Salinero-Fort MA
Published: September 2024

Aims

To describe the main characteristics of patients recently diagnosed with diabetes mellitus in terms of comorbidities, cardiovascular risk factors and healthy lifestyle by sex and age group.

Methods

A cross-sectional, multicenter, observational study of 681 patients aged >30 years diagnosed with diabetes mellitus in the previous 4 years was performed. The patients were treated in primary care centers in Madrid (Spain). The variables were obtained from their electronic medical records, physical examination, complete analysis, and lifestyle questionnaires.

Results

The main comorbidities were: hypercholesterolemia (64.4%; 95% CI, 60.6-68.2), hypertension (55.2%; 95% CI, 51.3-59.1), obesity (58.9%; 95% CI, 55.2-62.6), metabolic syndrome (58.5%; 95% CI, 54.6-62.5); and hypertriglyceridemia (25.3%; 95% CI, 21.9-28.7). Despite being newly diagnosed, 7.6% (95% CI, 5.4-9.8) had microalbuminuria, and 10.3% (95% CI, 8.0-12.6) cardiovascular disease. The main unhealthy lifestyles were: low physical activity (52%; 95% CI, 48.1-55.9), alcohol consumption (47.7%; 95% CI, 44.0-51.5) and smoking (19.2%; 95% CI, 16.2-22.3). Compared with men, women had more morbid obesity (9.7% vs 4.6%, p=.014), worse lipid profile (total cholesterol: 184 (IQR, 158-207) vs. 165 (IQR, 144-192), p<.01), less treatment with metformin (74.8% vs. 84.4%, p<.01) and antiplatelet agents (8.1% vs.18.6%, p<.01), but women had fewer comorbidities. Patients with a high educational level (OR= 1.90, 95% CI, 1.28-2.81)) and those >60 years (OR= 1.49; 95% CI, 1.01-2.21) were more adherent to the Mediterranean diet, and the older ones did less intense exercise (OR= 0.34, 95% CI, 0.16-0.75). Normal blood pressure was associated with Mediterranean diet (OR= 1.52; 95% CI, 1.05-2.21) and high physical activity (OR= 4.03; 95% CI, 1.69-9.61); and body mass index was inversely associated with physical activity (OR= 0.92; 95% CI, 0.85-0.99).

Conclusions

Patients newly diagnosed with diabetes mellitus have crucial cardiovascular risk factors and comorbidities at the onset of the disease. These can be modified through a healthy lifestyle.
Improving Deceased Donor Kidney Utilization: Predicting Risk of Nonuse with Interpretable Models
Authors: Li Ruoting , Tunc Sait , Ozaltin Osman , Ellis Matthew J.
Published: September 2024

Background

Despite the increasing disparity between the number of patients awaiting kidney transplants and the availability of deceased donor kidneys, a significant number of donated kidneys go unused. Early identification of organs at high risk of nonuse can facilitate effective allocation interventions, ensuring these organs are offered to patients who could potentially benefit from them. While several machine learning models have been developed to predict nonuse risk, the complexity of these models compromises their practical implementation.

Methods

We propose implementable nonuse risk prediction models that consist of a minimal set of variables, including the Kidney Donor Risk Index (KDRI), along with factors selected by machine learning models or transplantation experts. Our approach takes into account the influence of Organ Procurement Organization (OPO) behavior on kidney disposition.

Results

The proposed models demonstrate competitive performance compared to more complex models that involve a large number of variables. Importantly, they maintain simplicity and interpretability.

Conclusions

Our results provide accurate risk predictions, offer valuable insights into key factors contributing to kidney nonuse, and underscore significant variations among OPOs in the allocation of hard-to-place kidneys. These findings can inform the design of effective organ allocation interventions, increasing the likelihood of transplantation for hard-to-place kidneys.
Identification of Proteins Influencing CRISPR-Associated Transposases for Enhanced Genome Editing
Authors: Song Leo C.T. , Alker Amanda T.P. , Oromí-Bosch Agnès , Swartz Sophia E. , Martinson Jonathan N.V. , Arora Jigyasa , Wang Abby M. , Rovinsky Rachel , Smith Sara J. , Pierce Emily C. , Deutschbauer Adam M. , Doudna Jennifer A. , Cress Brady F. , Rubin Benjamin E.
Published: September 2024

CRISPR-Associated Transposases (CASTs) hold tremendous potential for microbial genome editing due to their ability to integrate large DNA cargos in a programmable and site-specific manner. However, the widespread application of CASTs has been hindered by their low efficiency in diverse, non-model bacteria. In an effort to address this shortcoming, we conducted the first genome-wide screen for host factors impactingVibrio choleraeCAST (VchCAST) activity and used the findings to increaseVchCAST editing efficiency. A genome-wide loss-of-function mutant library inE. coliwas screened to identify 15 genes that impact typeVchCAST transposition. Of these, seven factors were validated to improveVchCAST activity and two were found to be inhibitory. Informed by homologous recombination involved effectors, RecD and RecA, we tested the λ-Red recombineering system in ourVchCAST editing vectors, which increased its insertion meditated-editing efficiency by 25.7-fold inE. coliwhile maintaining high target specificity and similar insertion arrangements. Furthermore, λ-Red-enhancedVchCAST achieved increased editing efficiency in the industrially important bacteriaPseudomonas putidaand the emerging pathogenKlebsiella michiganensis. This study improves understanding of factors impactingVchCAST activity and enhances its efficiency as a bacterial genome editor.

GRAPHICAL ABSTRACT
ABHD11 mediated deglutarylation regulates the TCA cycle and T cell metabolism
Authors: Grice Guinevere L , Minogue Eleanor , Coates Hudson W , Debela Mekdes , Kaneider-Kaser Nicole , Antrobus P Robin , Johnson Randall S , Nathan James A
Published: September 2024

Glutarate is an intermediate of amino acid catabolism and an important metabolite for reprogramming T cell immunity, exerting its effects by inhibition of histone demethylase enzymes or through glutarylation. However, how distinct glutarate modifications are regulated is unclear. Here, we uncover a deglutarylation pathway that couples amino acid catabolism to tricarboxylic acid (TCA) cycle function. By examining how glutarate can form conjugates with lipoate, an essential mitochondrial modification for the TCA cycle, we find that Alpha Beta Hydrolase Domain 11 (ABHD11) protects against the formation of glutaryl-lipoyl adducts. Mechanistically, ABHD11 acts as a thioesterase to selectively remove glutaryl adducts from lipoate, maintaining integrity of the TCA cycle. Functionally, ABHD11 influences the metabolic reprogramming of human T cells, increasing central memory T cell formation and attenuating oxidative phosphorylation. These results uncover ABHD11 as a selective deglutarylating enzyme and highlight that targeting ABHD11 offers a potential approach to metabolically reprogramme cytotoxic T cells.
Essential and dual effects of Notch activity on a natural transdifferentiation event
Authors: Daniele Thomas , Cury Jeanne , Morin Marie-Charlotte , Ahier Arnaud , Isaia Davide , Jarriault Sophie
Published: September 2024

Cell identity can be reprogrammed, naturally or experimentally, albeit with low frequency. Why given cells, but not their neighbours, undergo a cell identity conversion remains unclear. We find that Notch signalling plays a key role to promote natural transdifferentiation inC. elegans. Endogenous Notch signal endows a cell with the competence to transdifferentiate by promoting plasticity factors expression (hlh-16/Oligandsem-4/Sall). Strikingly, exogenous Notch can trigger ectopic transdifferentiationin vivo. However, Notch signalling can both promote and block transdifferentiation depending on its activation timing. Notch only promotes transdifferentiation during an early precise window of opportunity and signal duration must be tightly controlled in time. Our findings emphasise the importance of temporality and dynamics of the underlying molecular events preceding the initiation of natural cell reprogramming. Finally, our results support a model where both an extrinsic signal and the intrinsic cellular context combine to empower a cell with the competence to transdifferentiate.
The histone methyltransferase DOT1B is dispensable for stage differentiation and macrophage infection inLeishmania mexicana
Authors: Eisenhuth Nicole , Rauh Elisa Theres , Mitnacht Melina , Debus Andrea , Butter Falk , Schleicher Ulrike , Pruzinova Katerina , Volf Petr , Janzen Christian J.
Published: September 2024

Conserved histone methyltransferases of the DOT1 family are involved in replication regulation, cell cycle progression, stage differentiation and gene regulation in trypanosomatids. However, the specific functions of these enzymes depend on the host evasion strategies of the parasites. In his study, we investigated the role of DOT1B inLeishmania mexicana, focusing on life cycle progression and infectivity. In contrast toTrypanosoma brucei, in which DOT1B is essential for the differentiation of mammal-infective bloodstream forms to insect procyclic forms,L. mexicanaDOT1B (LmxDOT1B) is not critical for the differentiation of promastigotes to amastigotesin vitro. Additionally, there are no significant differences in the ability to infect or differentiate in macrophages or sand fly vectors between theLmxDOT1B-depleted and control strains. These findings highlight the divergency of the function of DOT1B in these related parasites, suggesting genus-specific adaptations in the use of histone modifications for life cycle progression and host adaptation processes.
Integrated single-cell atlas of human atherosclerotic plaques
Authors: Traeuble K. , Munz M. , Pauli J. , Sachs N. , Vafadarnejad E. , Carrillo-Roa T. , Maegdefessel L. , Kastner P. , Heinig M.
Published: September 2024

Atherosclerosis, a major cause of cardiovascular diseases, is characterized by the buildup of lipids and chronic inflammation in the arteries, leading to plaque formation and potential rupture. The underlying causal immune mechanisms and alterations in structural cell composition and plasticity driving plaque progression remain incompletely defined. Recent advances in single-cell transcriptomics (scRNA-seq) have provided deeper insights into the roles of immune and non-immune cells in atherosclerosis. However, existing public scRNA-seq datasets often lack comprehensive cell type coverage and consistent annotations, posing challenges for downstream analyses. In this study, we present an integrated single-cell atlas of human atherosclerotic plaques, encompassing 261,747 high-quality annotated cells from carotid, coronary, and femoral arteries. By benchmarking and applying the best-performing data integration method, scPoli, we achieved robust cell type annotations validated by expert consensus and surface protein measurements. This comprehensive atlas enables accurate automatic cell type annotation of new datasets, optimal experimental design, and deconvolution of existing as well as novel bulk RNA-seq data to comprehensively determine cell type proportions in human atherosclerotic lesions. It facilitates future studies by providing an interactive WebUI for easy data annotation and experimental design, while supporting various downstream applications, including integration of genetic association studies and experimental planning.
Multiplexed nanopore amplicon sequencing to distinguish recrudescence from new infection in antimalarial drug trials
Authors: Holzschuh Aurel , Lerch Anita , Nsanzabana Christian
Published: September 2024

Background

The assessment of antimalarial drug efficacy againstPlasmodium falciparumrequires PCR correction to distinguish recrudescence from new infections by comparing parasite genotypes before treatment and in recurrent infections. Nanopore sequencing offers a low-cost, portable, scalable, and rapid alternative to traditional methods, supporting the expansion and decentralization of sequencing in endemic, resource-limited settings, potentially providing rapid PCR-corrected drug failure estimates.

Methods

We optimized a multiplexed AmpSeq panel targeting six microhaplotypes for high and uniform coverage. We assessed sensitivity and specificity for detecting minority clones in polyclonal infections and evaluated genetic diversity across the microhaplotype markers. We used mixtures of fourP. falciparumlaboratory strains at different ratios and 20 paired patient samples from a clinical trial. A custom bioinformatics workflow was used to infer haplotypes from polyclonal infections, including minority clones, with defined cut-off criteria for accurate haplotype calling.

Findings

The nanopore AmpSeq assay achieved uniform and high read coverage across all six microhaplotype markers (median coverage: 12,989× to 15,440× for laboratory strain mixtures and 7,011× to 11,600× for patients’ samples, respectively). We found high sensitivity in detecting minority clones (up to 50:1:1:1 in the 3D7:K1:HB3:FCB1 laboratory strain mixtures) and high specificity with less than 0.01% of all reads being false-positive haplotypes. Genetic diversity in the markers used was high (HE≥ 0.98 and up to 31 unique haplotypes in 20 paired samples withcpmp), and concordant results in classifying new infections and recrudescence across all markers used were observed in 18 (90%) of 20 paired samples.

Interpretation

Our study demonstrates the feasibility of nanopore AmpSeq for distinguishing recrudescence from new infections in clinical trials.

Funding

Swiss Tropical and Public Health Institute.