bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disseminated Tuberculosis With an Atypical Cutaneous Manifestation in a Hematopoietic Cell Transplant Patient in the Early Posttransplant Period: Case Report and Review of the Literature
Authors: Czech Mary M , Dioverti Maria Veronica , Karaba Andrew H , Jain Tania , Talluru Sai M , Sunshine Joel C , Kang Jun , Parrish Nikki , Kates Olivia S 
Published: November 2022

Abstract
We describe an unusual case of posttransplant tuberculosis reactivation in a man who underwent allogeneic hematopoietic cell transplant. Concomitant with disseminated adenovirus infection, reactivation of tuberculosis manifested as disseminated, nonfollicular pustules on day +49. Skin biopsy was obtained on day +50. Initial histopathologic evaluation did not suggest mycobacterial infection, but tissue stain showed acid-fast organisms, which were subsequently identified as Mycobacterium tuberculosis. Shortly after the cutaneous presentation of tuberculosis, the patient died on day +52. Our case is among a paucity of reports describing tuberculosis reactivation in hematopoietic cell transplant patients in the early posttransplant period. It highlights the difficulty of diagnosing contemporaneous systemic infections, and it presents a rare and atypical cutaneous manifestation of tuberculosis in a hematopoietic cell transplant patient. Our case and review of the literature emphasize the need for further research to elucidate risk factors associated with early posttransplant reactivation of tuberculosis, and the importance of remaining vigilant for active tuberculosis in hematopoietic cell transplant patients with epidemiologic risk factors.
Rituximab-treated rheumatic patients: B cells predict seroconversion after COVID-19 boost or revaccination in initial vaccine non-responders
Authors: Ammitzbøll Christian , Kragh Thomsen Marianne , Bøgh Andersen Jakob , Jensen Jens Magnus Berth , From Hermansen Marie-Louise , Dahl Johannsen Anders , Larsen Mads Lamm , Mistegaard Clara Elbæk , Mikkelsen Susan , Szabados Fruzsina , Vils Signe Risbøl , Erikstrup Christian , Hauge Ellen-Margrethe , Troldborg Anne 
Published: November 2022

Abstract

Objectives
To investigate the effect of either a booster vaccine (one dose) or revaccination (two doses 3 weeks apart) on the antibody response to the COVID-19 mRNA vaccines in patients with rheumatic disease (RD) treated with rituximab (RTX) who had not produced vaccine-reactive antibodies after the initial two vaccine doses. Further, to examine if B cell levels in peripheral blood predicted seroconversion.

Methods
We included 91 RTX-treated RD patients previously vaccinated against COVID-19. Patients were offered revaccination or a single booster vaccination with an mRNA vaccine. Serum total antibodies against SARS-CoV-2 spike protein were measured before and 6 weeks after the last vaccine dose. B cells (CD19+CD45+) were measured by flow cytometry at inclusion.

Results
Of RD patients with undetectable SARS-CoV-2 antibody levels before inclusion, seroconversion was seen in 38% 6 weeks after the booster dose and 32% after revaccination. Patients receiving revaccination had significantly higher antibody levels than patients receiving a booster dose (P &lt; 0.001). In both univariate and multivariate logistic regression analysis, only B cells higher than 10/µl before boost or revaccination were associated with seroconversion (P = 0.009 and P = 0.01, respectively). Seroconversion was independent of age, gender, diagnosis, cumulative RTX dose, RTX treatment time and time since last RTX treatment.

Conclusion
Continuously impaired humoral response to mRNA vaccines was found in most RTX-treated patients after a booster dose or revaccination. Seroconversion was observed in approximately one-third of the patients. Measurable B cells before boosting or revaccination was the strongest predictor of antibody response after boost or revaccination.
Black Families' Experiences of Developmental Screening: Review of Well-Child Visits to Inform Enhanced Autism Spectrum Disorder Risk Assessment
Authors: Weitlauf Amy S. , Vehorn Alison , Miceli Alexandra , Pinnock Theodora , Dada Yewande , Hine Jeffrey , Warren Zachary 
Published: November 2022

ABSTRACT:

Objective:
Black families face barriers to early diagnosis of autism spectrum disorder (ASD). Most work emphasizes systemic delays to diagnosis rather than how existing screening procedures may affect identification. Our goal was to examine pediatric care visits in which screening was most likely to occur to document behaviors of parents and providers.

Methods:
We examined 18- to 36-month primary care visits in our electronic health record system (n = 99) of thirty-nine 4- and 8-year-old Black children later diagnosed with ASD. We extracted qualitative and quantitative data and engaged in consensus coding. We captured whether formal screening occurred, the content of concerns of parents and providers, and referral patterns for follow-up care or evaluation.

Results:
Consistent with existing work, we found differences in parent and provider concerns and discrepancies in referral rates. Parents often endorsed concerns about language, sleeping or eating habits, behavior, or motor skills rather than ASD, but specific mention of ASD as a concern increased over time. Referrals for follow-up care were more likely when providers, not parents alone, expressed concerns about patient development.

Conclusion:
Pediatric providers cannot place the burden on families to raise autism concerns. Although some level of developmental risk was noted at most visits for children later diagnosed with ASD, referrals were only made when providers were also concerned, and most of these were for speech-language evaluation. Ongoing work is necessary to better understand how existing care systems interact with diverse families to inform the creation of inclusive screening practices that mitigate diagnostic delays.
Implementing the Get SET Early Model in a Community Setting to Lower the Age of ASD Diagnosis
Authors: Smith Christopher J. , James Stephen , Skepnek Erica , Leuthe Eileen , Outhier Lisa Elder , Avelar Delia , Barnes Cynthia Carter , Bacon Elizabeth , Pierce Karen 
Published: November 2022

Objective:
The objective of this study was to implement a validated, university-based early detection program, the Get SET Early model, in a community-based setting. Get SET was developed to improve
S

creening,
E

valuation, and
T

reatment referral practices. Specifically, its purpose was to lower the age of diagnosis and enable toddlers with autism spectrum disorder (ASD) to begin treatment by 36 months.

Methods:
One hundred nine pediatric health care providers were recruited to administer the Communication and Symbolic Behavior Scales Developmental Profile Infant-Toddler Checklist at 12-month, 18-month, and 24-month well-baby visits and referred toddlers whose scores indicated the need for a developmental evaluation. Licensed psychologists were trained to provide diagnostic evaluations to toddlers as young as 12 months. Mean age of diagnosis was compared with current population rates.

Results:
In 4 years, 45,504 screens were administered at well-baby visits, and 648 children were evaluated at least 1 time. The overall median age for ASD diagnosis was 22 months, which is significantly lower than the median age reported by the CDC (57 months). For children screened at 12 months, the age of first diagnosis was significantly lower at 15 months. Of the 350 children who completed at least 1 follow-up evaluation, 323 were diagnosed with ASD or another delay, and 239 (74%) were enrolled in a treatment program.

Conclusion:
Toddlers with ASD were diagnosed nearly 3 years earlier than the most recent CDC report, which allowed children to start a treatment program by 36 months. Overall, Get SET Early was an effective strategy for improving the current approach to screening, evaluation, and treatment. Efforts to demonstrate sustainability are underway.
Modern indications for referral for kidney and pancreas transplantation
Authors: Fridell Jonathan A. , Stratta Robert J. 
Published: November 2022

Purpose of reviewPancreas transplantation (PTx) is currently the only therapy that can predictably achieve sustained euglycemia independent of exogenous insulin administration in patients with insulin-dependent diabetes mellitus. This procedure involves a complex abdominal operation and lifetime dependence on immunosuppressive medications. Therefore, PTx is most frequently performed in combination with other organs, usually a kidney transplant for end stage diabetic nephropathy. Less frequently, solitary PTx may be indicated in patients with potentially life-threatening complications of diabetes mellitus. There remains confusion and misperceptions regarding indications and timing of patient referral for PTx.Recent findingsIn this review, the referral, evaluation, and listing process for PTx is described, including a detailed discussion of candidate assessment, indications, contraindications, and outcomes.SummaryBecause the progression of diabetic kidney disease may be less predictable than other forms of kidney failure, early referral for planning of renal and/or pancreas transplantation is paramount to optimize patient care and allow for possible preemptive transplantation.
Paradigm shift in lifestyle modification for solitary kidney after donor nephrectomy
Authors: Tantisattamo Ekamol , Kalantar-Zadeh Kamyar 
Published: November 2022

Purpose of review
Living donor kidney transplantation potentially leads to long-term complications including chronic kidney disease, end-stage kidney disease, elevated blood pressure, and pregnancy-associated hypertension. Given living donors generally do not have underlying medical conditions, lifestyle modifications, particularly dietary interventions may prevent those complications and improve their health outcomes.

Recent findings
Glomerular hyperfiltration occurs as physiologic adaptation during an initial postdonor nephrectomy period. In the long-term, these adaptations may become pathologic consequences resulting from hyperfiltration-mediated kidney injury and ultimately secondary focal segmental glomerulosclerosis in the solitary kidney. Dietary interventions to slow a decline in kidney function include low protein intake of <0.8 g/kg/day and low sodium consumption of 2–4 g/day as well as certain health dietary patterns. There is no evidence regarding the quantity and quality of protein that can be recommended for living kidney donors and the same for sodium. Plant Dominant (PLADO) diets, Dietary Approaches to Stop Hypertension (DASH), Mediterranean, and vegetarian diets may be favorable for living kidney donors with solitary kidney but the evidence is still lacking.

Summary
Although dietary interventions may provide benefits and kidney health for living kidney donors, further studies including clinical trials are required to incorporate them into clinical practice guidelines.
Postburn Reconstruction of the Face and Neck
Authors: Sabapathy S. Raja , Shanmugakrishnan R. Raja , Ramkumar Sanjai , Muthukumar Vamseedharan , Senthilkumaran M. , Bharathi R. Ravindra 
Published: November 2022

Learning Objectives:
After studying this article, the participant should be able to: 1. Understand the cardinal principles in the management of postburn deformities in the face and neck. 2. Understand reconstruction of specific subsites in the face and neck affected by burn contracture. 3. Acquire knowledge about the various techniques of burn reconstruction of the face and neck. 4. Grasp technical nuances and select appropriate surgical options for individual cases.

Summary:
Postburn contractures in the face and neck region are multifactorial in origin and difficult to prevent in extensive burns. Facial burns lead to distortion of anatomical landmarks, causing aesthetic, functional, and psychological problems. Each subunit of the face is unique in structure; thus, the surgeon needs to adjust the timing of surgery and the technique according to region and the severity of contracture. Contracture of one unit, especially that of the neck and forehead, can exaggerate the contracture in neighboring subunits. The role of these extrinsic influences must be considered while sequencing surgical procedures. The burn surgeon must be adept in all reconstructive surgery techniques from skin grafting to tissue expanders to microsurgery to obtain the best outcomes. Surgery must be followed up with long-term physical therapy and psychological rehabilitation to help burn survivors with head and neck contractures to integrate back into society.
Bioschemas Training Profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources
Authors: Jael Castro Leyla , Palagi Patricia M. , Beard Niall , Attwood Teresa K. , Brazas Michelle D. 
Published: November 2022

AbstractStand-alone life science training events and e-learning solutions are amongst the most sought-after modes of training because they address both point-of-need learning and the limited timeframes available for ‘upskilling’. Yet, finding relevant life sciences training courses and materials is challenging because such resources are not marked up for Internet searches in a consistent way. This absence of mark-up standards to facilitate discovery, re-use and aggregation of training resources limits their usefulness and knowledge-translation potential. Through a joint effort between the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET), the Bioschemas Training community and the ELIXIR FAIR Training Focus Group, a set of Bioschemas Training profiles has been developed, published and implemented for life sciences training courses and materials. Here, we describe our development approach and methods, which were based on the Bioschemas model, and present the results for the three Bioschemas Training profiles:TrainingMaterial, CourseandCourseInstance. Several implementation challenges were encountered, which we discuss alongside potential solutions. Over time, continued implementation of these Bioschemas Training profiles by training providers will obviate the barriers to skill development, facilitating both the discovery of relevant training events to meet individuals’ learning needs, and the discovery and re-use of training and instructional materials.
Inferring Spatially Resolved Transcriptomics Data from Whole Slide Images for the Assessment of Colorectal Tumor Metastasis: A Feasibility Study
Authors: Fatemi Michael , Feng Eric , Sharma Cyril , Azher Zarif , Goel Tarushii , Ramwala Ojas , Palisoul Scott , Barney Rachael , Perreard Laurent , Kolling Fred , Salas Lucas A. , Christensen Brock C. , Tsongalis Gregory , Vaickus Louis , Levy Joshua J. 
Published: November 2022

AbstractOver 150,000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50,000 individuals will die from CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. Tumor metastasis is the primary factor related to the risk of recurrence and mortality. Yet, screening for nodal and distant metastasis is costly, and invasive and incomplete resection may hamper adequate assessment. Signatures of the tumor-immune microenvironment (TIME) at the primary site can provide valuable insights into the aggressiveness of the tumor and the effectiveness of various treatment options. Spatially-resolved transcriptomics technologies offer an unprecedented characterization of TIME through high multiplexing, yet their scope is constrained by cost. Meanwhile, it has long been suspected that histological, cytological and macroarchitectural tissue characteristics correlate well with molecular information (e.g., gene expression). Thus, a method for predicting transcriptomics data through inference of RNA patterns from whole slide images (WSI) is a key step in studying metastasis at scale. In this work, we collected and preprocessed Visium spatial transcriptomics data (17,943 genes at up to 5,000 spots per patient sampled in a honeycomb pattern) from tissue across four stage-III matched colorectal cancer patients. We compare and prototype several convolutional, Transformer, and graph convolutional neural networks to predict spatial RNA patterns under the hypothesis that the transformer and graph-based approaches better capture relevant spatial tissue architecture. We further analyzed the model’s ability to recapitulate spatial autocorrelation statistics using SPARK and SpatialDE. Overall, results indicate that the transformer and graph-based approaches were unable to outperform the convolutional neural network architecture, though they exhibited optimal performance for relevant disease-associated genes. Initial findings suggest that different neural networks that operate on different scales are relevant for capturing distinct disease pathways (e.g., epithelial to mesenchymal transition). We add further evidence that deep learning models can accurately predict gene expression in whole slide images and comment on understudied factors which may increase its external applicability (e.g., tissue context). Our preliminary work will motivate further investigation of inference for molecular patterns from whole slide images as metastasis predictors and in other applications.
SARS-CoV-2 Spike Protein Induces Hemagglutination: Implications for COVID-19 Morbidities and Therapeutics and for Vaccine Adverse Effects
Authors: Boschi Celine , Scheim David E. , Bancod Audrey , Millitello Muriel , Bideau Marion Le , Colson Philippe , Fantini Jacques , Scola Bernard La 
Published: November 2022

ABSTRACTExperimental findings for SARS-CoV-2 related to the glycan biochemistry of coronaviruses indicate that attachments from spike protein to glycoconjugates on the surfaces of red blood cells (RBCs), other blood cells and endothelial cells are key to the infectivity and morbidity of COVID-19. To provide further insight into these glycan attachments and their potential clinical relevance, the classic hemagglutination (HA) assay was applied using spike protein from the Wuhan, Alpha, Delta and Omicron B.1.1.529 lineages of SARS-CoV-2 mixed with human RBCs. The electrostatic potential of the central region of spike protein from these four lineages was studied through molecular modeling simulations. Inhibition of spike protein-induced HA was tested using the macrocyclic lactone ivermectin (IVM), which is indicated to bind strongly to SARS-CoV-2 spike protein glycan sites. The results of these experiments were, first, that spike protein from these four lineages of SARS-CoV-2 induced HA. Omicron induced HA at a significantly lower threshold concentration of spike protein than for the three prior lineages and was much more electropositive on its central spike protein region. IVM blocked HA when added to RBCs prior to spike protein and reversed HA when added afterwards. These results validate and extend prior findings on the role of glycan bindings of viral spike protein in COVID-19. They furthermore suggest therapeutic options using competitive glycan-binding agents such as IVM and may help elucidate rare serious adverse effects (AEs) associated with COVID-19 mRNA vaccines which use spike protein as the generated antigen.
Population genomics, resistance, pathogenic potential, and mobile genetic elements of carbapenem-resistantKlebsiella pneumoniaecausing infections in Chile
Authors: Veloso Marcelo , Acosta Joaquín , Arros Patricio , Berríos-Pastén Camilo , Rojas Roberto , Varas Macarena , Allende Miguel L. , Chávez Francisco P. , Araya Pamela , Hormazábal Juan Carlos , Lagos Rosalba , Marcoleta Andrés E. 
Published: November 2022

ABSTRACTMultidrug and carbapenem-resistantK. pneumoniae(CR-Kp) are considered critical threats to global health and key traffickers of resistance genes to other pathogens. In Chile, although a sustained increase in CR-Kpinfections has been observed, few strains have been described at the genomic level, lacking molecular details of their resistance and virulence determinants and the mobile elements mediating their dissemination. In this work, we studied the antimicrobial resistance and performed a comparative genomics analysis of ten CR-Kpisolates from the Chilean surveillance of carbapenem-resistantEnterobacteriaceae. High resistance to most of the antibiotics tested was observed among the isolates, five ST25, three ST11, one ST45, and one ST505, which harbored a total of 44 plasmids, many of them predicted to be conjugative and carrying genes conferring resistance to a variety of antibiotic, metals, and disinfectants. Ten plasmids encoding either KPC-2, NDM-1, or NDM-7 carbapenemases were characterized, including novel plasmids with increased resistance gene load and a novel genetic environment forblaKPC-2gene. This corresponds to the first report of ST25 and ST45Kpproducing NDM-7 in South America, and of an ST505 CR-Kpworldwide, producing both NDM-7 and KPC-2. Moreover, we characterized a variety of genomic islands carrying virulence and fitness factors. These results provide baseline knowledge for the detailed understanding of molecular and genetic determinants behind antibiotic resistance and virulence ofK. pneumoniaein Chile and South America.
Tissue- and sex-specific DNA damage tracks aging in rodents and humans
Authors: Guilbaud Axel , Ghanegolmohammadi Farzan , Wang Yijun , Leng Jiapeng , Kreymerman Alexander , Varela Jacqueline Gamboa , Garbern Jessica , Elwell Hannah , Cao Fang , Ricci-Blair Elisabeth M. , Liang Cui , Balamkundu Seetharamsingh , Vidoudez Charles , DeMott Michael S. , Bedi Kenneth , Margulies Kenneth B. , Bennett David A. , Palmer Abraham A. , Barkley-Levenson Amanda , Lee Richard T. , Dedon Peter C. 
Published: November 2022

SummaryDNA damage causes genomic instability underlying many human diseases. Traditional approaches to DNA damage analysis provide minimal insights into the spectrum of disease-driving DNA lesions and the mechanisms causing imbalances in damage formation and repair. Here we used untargeted mass spectrometry-based adductomics1to discover 114 putative DNA lesions and modifications consistently detected in humans and two independent analyses in rats, showing species-, tissue-, age-, and sex-biases. As evidence of methodologic rigor, 10 selected adductomic signals were structurally validated as epigenetic marks: 5-MdC, 5-HMdC, 5-FdC; DNA damage products:N2-CMdG, 1,N6ε-dA, 3,N4-εdC, M1dG,O6/N2-MdG, and 8-Oxo-dG; and established analytical artifacts: cyclobutane dimers of 2’-deoxycytosine. With steady-state levels of putative DNA adducts integrating multiple cell types in each tissue, there was strong age-dependent variation for many putative adducts, includingN2-CMdG, 5-HMdC, and 8-Oxo-dG in rats and 1,N6ε-dA in human heart, as well as sex biases for 67 putative adducts in rat tissues. These results demonstrate the potential of untargeted adductomic analysis for defining DNA adducts as disease determinants, assigning substrates to DNA repair pathways, discovering new metabolically-driven DNA lesions, and quantifying inter-individual variation in DNA damage and repair across populations.