bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Qualitative Exploration of Nurse Faculty Experiences Related to the Sudden Unanticipated Death of a Nursing Student
Authors: Colancecco Elise , Farber Janice , Dorney Paulette 
Published: September 2023

Background:
Nurse faculty serve as teachers, role models, and mentors to nursing students. This unique relationship results in a myriad of feelings when a student dies. Limited research exists in examining faculty grief related to the sudden unanticipated death of a nursing student.

Purpose:
To explore the experiences of nurse faculty following the sudden unanticipated death of a nursing student.

Methods:
Researchers conducted a phenomenological qualitative study. The source of qualitative data included a demographic questionnaire and in-depth interviews with 13 participants throughout the geographical regions of the United States.

Results:
Six following themes emerged: (1) leadership response, (2) grief experience, (3) role uncertainty, (4) grief triggers, (5) cannot help but think what if, and (6) acknowledging a life unfulfilled.

Conclusion:
This study yields a rich understanding of the unique grief experiences of nurse faculty, warranting the need for further dialogue, faculty education, policy development, and supportive interventions for faculty and administrative leaders.
Radiologists' Rating for Comparative Qualitative Assessment of Intravoxel Incoherent Motion Using Novel Analysis Methods
Authors: Baidya Kayal Esha , Kandasamy Devasenathipathy , Yadav Richa , Khare Kedar , Bakhshi Sameer , Sharma Raju , Mehndiratta Amit 
Published: September 2023

Objective
The objective was to assess qualitative interpretability and quantitative precision and reproducibility of intravoxel incoherent motion (IVIM) parametric images evaluated using novel IVIM analysis methods for diagnostic accuracy.

Methods
Intravoxel incoherent motion datasets of 55 patients (male/female = 41:14; age = 17.8 ± 5.5 years) with histopathology-proven osteosarcoma were analyzed. Intravoxel incoherent motion parameters—diffusion coefficient (D), perfusion fraction (f), and perfusion coefficient (D*)—were estimated using 5 IVIM analysis methods—(i) biexponential (BE) model, (ii) BE-segmented fitting 2-parameter (BESeg-2), (iii) BE-segmented fitting 1-parameter (BESeg-1), (iv) BE model with total variation penalty function (BE + TV), and (v) BE model with Huber penalty function (BE + HPF). Qualitative scoring in a 5-point Likert scale (uninterpretable: 1; poor: 2; fair: 3; good: 4; excellent: 5) was performed by 2 radiologists for 4 criteria: (a) tumor shape and margin, (b) morphologic correlation, (c) noise suppression, and (d) overall interpretability. Interobserver agreement was evaluated using Spearman rank-order correlation (r
s). Precision and reproducibility were evaluated using within-subject coefficient of variation (wCV) and between-subject coefficient of variation (bCV).

Results
BE + TV and BE + HPF produced significantly (P < 10−3) higher qualitative scores for D (fair–good [3.3–3.8]) than BE (poor [2.3]) and for D* (poor–fair [2.2–2.7]) and f (fair–good [3.2–3.8]) than BE, BESeg-2, and BESeg-1 (D*: uninterpretable–poor [1.3–1.9] and f: poor–fair [1.5–3]). Interobserver agreement for qualitative scoring was r
s = 0.48–0.59, P < 0.009. BE + TV and BE + HPF showed significantly (P < 0.05) improved reproducibility in estimating D (wCV: 24%–31%, bCV: 21%–31% improvement) than the BE method and D* (wCV: 4%–19%, bCV: 5%–19% improvement) and f (wCV: 25%–49%, bCV: 25%–47% improvement) than BE, BESeg-2, and BESeg-1 methods.

Conclusions
BE + TV and BE + HPF demonstrated qualitatively and quantitatively improved IVIM parameter estimation and may be considered for clinical use further.
Enlarging 18F-FDG–Avid Solitary Pulmonary Nodule: A Distinctly Unusual Presentation of Cytomegalovirus Infection in a Patient Receiving Chemotherapy
Authors: Zamora Edgar , Edema Ukuemi , Zuckier Lionel S. 
Published: September 2023

Abstract
Rapidly growing lung lesions, particularly in immunocompromised patients, invoke consideration of an infectious etiology. Aspergillomas, for example, can appear as round nodules with soft tissue attenuation, often associated with cavitation, and are variably 18F-FDG avid. In contrast, cytomegalovirus, which may also evidence 18F-FDG uptake, typically manifests as ground-glass opacities, symmetrically distributed small pulmonary nodules, or confluent consolidations, with lower lobe predilection. We describe a patient treated for lymphoma presenting with a solitary enlarging FDG-avid lung nodule, which was determined on resection to be focal cytomegalovirus infection, a distinctly uncommon presentation of this pathogen, more typical of fungal or mycobacterial disease.
Cooperative progression of colitis and leukemia modulated by clonal hematopoiesis via PTX3/IL-1β pro-inflammatory signaling
Authors: He Hang , Wen Yuchen , Yu Hanzhi , Liu Jingjing , Huo Qingran , Jin Wenyan , Wang Zhiqin , Du Guohui , Du Jun , Wang Huaquan , Zhao Zhigang , Cai Zhigang 
Published: September 2023

AbstractClonal hematopoiesis (CH) is considered an important risk factor for all-cause mortality and the development of multiple chronic diseases including hematological neoplasms, cardiovascular diseases, and potentially a range of autoimmune or immune-deficiency diseases. Mutations inTET2are one of the first identified, most important, and prevalent genetic drivers of CH. However, cooperative factors and mechanisms underlyingTET2-deficiency related CH (TedCH) remain largely unknown. Recently, it has been suggested that certain diseases occurred before TedCH and promote TedCH trajectory on the contrary, indicating that diseases in non-hematopoietic organs may act as environmental non-genetic drivers of CH. To clarify the relationships between immune-dysfunctional diseases and CH, here we tested the impact of various challenges on TedCH. We found that expedited TedCH depended on establishment of an inflammatory environment. Primary or chimericTet2-mutant mice spontaneously developed co-symptoms reminiscent of human chronic colitis and myeloid leukemia, which was exacerbated by feeding with DSS, an experimental inducer of ulcerative colitis. Single cell RNA-seq (scRNA-seq) analysis reveals in depth the damage of colon in theTet2-mutant mice in physiological conditions or fed with DSS, along with increase of dysbacteriosis indicated by gut microbiome analysis. Results from colon scRNA-seq from both mouse and human highlight the important roles of PTX3/IL-1β pro-inflammatory signaling in promoting colitis or leukemia. Finally, TedCH trajectory and inflammation in colon and bone marrow were ameliorated by treatment of IL-1R1 inhibitor Anakinra. Our study suggests that PTX3/IL-1β signaling and clonal hematopoiesis cooperate and play important roles in gut-bone marrow axis and related diseases including colitis and leukemia.HighlightsCertain environmental factors, such as Dextran Sulfate Sodium (DSS), an experimental inducer of ulcerative colitis, promote TedCHColitis and leukemia are spontaneously and simultaneously developed inTet2-defficient primary or chimeric mice, along with increased pathogenic gut microbiomes, indicating an aberrant gut-bone marrow axis in the mutant mice.Single cell RNA-seq analysis reveals enhanced PTX3, a soluble pattern recognition molecule and IL-1β pro-inflammatory signaling in colitis and leukemia.TheIn vivofunction of the PTX3/IL-1β pro-inflammatory signaling in TedCH is indicated in human colitis and validated in experimental settings.
Disruption of immunoglobulin heavy and light chain assembly by antisense oligonucleotides impairs protein homeostasis and myeloma cell survival
Authors: Horiot Catherine , Roussel Murielle , Praité Antoine , Pollet Justine , Bender Sébastien , Sirac Christophe , Bonaud Amélie , Delpy Laurent 
Published: September 2023

ABSTRACTMultiple myeloma (MM) is related to the accumulation of malignant plasma cells (PCs) in the bone marrow. MM accounts for approximatively 10% of hematological malignancies and despite major improvement in therapies and outcomes, relapses will virtually occur in all patients. Usually, the disease goes along with an excess production of a monoclonal immunoglobulin (Ig) component by the tumor PC clone. However, many questions remain regarding the consequences of a deregulated Ig production on PC survival. Recent advances in RNA-based therapy using antisense oligonucleotides (ASO) prompted us to examine the impact of altered Ig heavy to light chain (HC/LC) ratios in MM cells. We designed a pan IgG subclasses specific ASO targeting a consensus sequence found in the polyadenylation signal (PAS) of all secretedIGHGmRNAs (IgG-ASO). Remarkably, treatment with this compound strongly decreased IgG secretion in MM cell lines and patient cells. Consistent with a deregulated HC/LC ratio, a dose-dependent excess of free-LCs (as monomers and dimers) was observed in myeloma cells treated with IgG-ASO, compared to an irrevelant control ASO (CTRL). RNA-seq profiles further indicated that the expression of genes involved in cellular metabolism, unfolded protein response (UPR) and cell death pathways were altered after treatment with IgG-ASO. Interestingly, impaired survival of primary IgG-expressing cells isolated from MM patients was achieved upon treatment with IgG-ASO, whereas no major effect was observed for healthy cells. Altogether, our data provide evidence for efficient inhibition of IgG secretion upon ASO treatment and suggest that an excess of free-LC due to disruption of HC/LC stoichiometry is toxic for MM cells expressing complete Ig. Such RNA-based strategies targeting PC in an Ig isotype-dependent manner could open new avenues for selective therapeutic approaches in PC dyscrasias.
Delivering biochemicals with precision using bioelectronic devices enhanced with feedback control
Authors: Marquez Giovanny , Dechiraju Harika , Baniya Prabhat , Li Houpu , Tebyani Maryam , Pansodtee Pattawong , Jafari Mohammad , Teodorescu Mircea , Rolandi Marco , Gomez Marcella 
Published: September 2023

AbstractPrecision medicine tailors treatment in a way that accounts for variations in patient response. Treatment strategies can be determined based on factors such as genetic mutations, age, and diet. Another way of implementing precision medicine in a dynamic fashion is through bioelectronics equipped with real-time sensing and intelligent actuation. Bioelectronic devices such as ion pumps can be utilized to deliver therapeutic drugs. To be able to perform precision medicine, medical devices need to be able to deliver drugs with high precision. For this, closed-loop control is required to be able to change the treatment strategy as new information about the response and progression of the biological system is received. To this end, a sliding mode controller is utilized given its ability to perform satisfactory control actions when there is model uncertainty. The controller is used in an experiment with the goal of delivering a pre-determined dosage of fluoxetine throughout a period of time.
Passive surveillance for shrimp pathogens inPenaeus vannameisubmitted from 3 Regions of Latin America
Authors: Intriago Pablo , Medina Andres , Cercado Nicole , Arteaga Kelly , Montenegro Alejandra , Burgos Milena , Espinoza Jorge , Brock James A , McIntosh Robins , Flegel Tim 
Published: September 2023

ABSTRACTMultiple PCR analyzes were performed using 19 different primer sets to open and broaden the search spectrum for shrimp pathogens. In addition, multiple primer pairs for 10 pathogens were compared to see if there were differences in selectivity or sensitivity among them. Some pathogens that did not present histological lesions were detected. The most important outcome was that selection of appropriate primers was the most critical factor in obtaining reliable results. We found high variability in results among primers and we learned it was prudent to seasonally assess among them for the best set selection. It is important to understand that a PCR positive test result alone does not confirm the presence of a viable pathogen or a disease state. Nor, as might be expected, does it mean that the positive PCR test results will be necessarily accompanied by histological lesions characteristic of the targeted pathogen. However, the use of appropriately selected primers sets can reveal whether there is an evolution in the result spectrum over time and if some pathogens disappear or reappear or new ones emerge. In general, most shrimp presented coinfections that consisted of the presence of WzSV8, DHPV, chronic midgut inflammation and tubule distension/epithelial atrophy consistent with Pir A/B toxicity. Also included were RLB/NHPB, microsporidia, striated muscle necrosis, gregarines in the hindgut caecum (gametocyte stage, and not associated with tegumental glands but glands that line the mouth and anus) and encysted, presumed nematode larvae. WzSV8 was newly discovered in gonads. Histological changes and the presence of spheroids in the lymphoid organ were considered as healthy host responses of often unidentified cause.
Manifestations, Diagnosis and Treatment of Osseous Rosai-Dorfman Disease: A Systematic Review
Authors: Agarwal Abhimanyu , Abozeed Mostafa 
Published: September 2023

ABSTRACTBACKGROUNDWe hypothesize that lymphadenopathy and extraosseous manifestation affect the management protocol and our aim is to aid in development of standardized diagnosis and treatment protocols.METHODSPubMed and Google Scholar were searched from January 2012 through December 2022 using keywords “Rosai-Dorfman”, “Rosai and Dorfman,” and “bone“. Out of 98 researches, meta-analysis of 51 full-text studies involving 53 individuals with osseous RDD was conducted.RESULTSA significant association was found between lymphadenopathy with steroid therapy (OR: 20.125, 95%CI: 3.02, 134.09, P=0.0004). Extraosseous RDD showed significant association with steroid therapy (P=0.0145), T1-isointense MRI (OR: 0.173, 95%CI: 0.0304, 0.986, P=0.035), T1-hyperintense MRI (OR: 0.16, 95%CI: 0.0314, 0.815, P=0.019) and T2-hyperintense MRI (OR: 0.115, 95%CI= 0.0206, 0.6456, P=0.007).CONCLUSIONOsseous RDD is rare and lacks standardized diagnosis and treatment protocols. Patients with lymphadenopathy were 9 times more likely to receive steroids, and those with extraosseous manifestations were less likely to undergo MRI. RDD is often not initially considered in differential diagnoses, leading to worsened conditions. We propose that further testing is required in affected individuals to develop standardized protocols.Key PointsRevealed variations in osseous and extraosseous involvement and immunohistochemistry played a crucial role in diagnosis.Found association of lymphadenopathy and extraosseous involvement with steroid therapy and diagnostic modalities of RDD.Limitations include reliance on case reports (low-quality evidence), potential inclusion bias in reported data.
Effects of kinesthetic cues supported by physiotherapist during a motor training intervention with virtual reality-based games on functioning in people with Parkinson’s disease: A prospective, single-blinded, parallel-group, randomized clinical trial
Authors: Igarasi Barbosa Pamela Yuki , Falconi Amarilis , D’Alencar Matheus , Okamoto Erika , Pimentel Piemonte Maria Elisa 
Published: September 2023

AbstractBackgroundIt’s been suggested that kinesthetic cues (KC) could be a useful tool in helping individuals improve their motor learning process by facilitating muscle activation. However, while virtual reality-based games (VRG) are becoming more popular as a intervention tool, the potential effects of KC on this kind of intervention have yet to be investigated in people with Parkinson’s disease (PwPD). Therefore, this study aimed to compare the effects of motor intervention using VRG coupled or not with KC provided by a physiotherapist (PT) during training on the functioning of PwPD.MethodsThirty-eight PwPD in 1-3 Hoehn and Yahr (HY) stage were randomized into two groups: (1) VRG with KC Group (KCG), where KC was provided by manual assistance of a PT, and (2) VRG with NO KC group (NKCG), where no PT manual assistance was provided during the training. Both groups received 8 individual sessions with 50 minutes, twice a week, for 4 weeks: 10 minutes for warm-up and 40 minutes to play 4 games fromXBOX 360withKinect®system. Outcomes were evaluated at three time points: (1) before training (BT), (2) 1 week after training (AT), and 8 weeks after that as follow-up (FU). To reach a comprehensive evaluation of functioning, several outcomes were adopted and categorized according to International Classification of Functioning Disability and Health (ICF): Geriatric Depression Scale (GDS); Montreal Cognitive Assessment (MOCA); Unified Parkinson Disease Rating Scale (UPDRS) - section 3 (UPDRS-III); and Rapid Turns Test (RTT) used to assess motor and non-motor alteration into Function domain; Balance Evaluation Systems Test (BESTest); Falls Efficacy Scale International (FES-I); Thirty-Second Walk Test (30sWT); Six-Minute Walk Test (6mWT); 5 Times Sit to Stand Test; and UPDRS section II (UPDRS-II) used to assess motor performance into Activity domain, and finally, the Parkinson Disease Questionnaire (PDQ-39) to assess quality of life into Participation domain.ResultsANOVA for repeated measures showed a significant effect for evaluation-time factor only (p-value<.001), (no effect for group or evaluation-time X group interaction) for all measures of three ICF domains, excluding GDS and 6mWT. The Tukey post-hoc test confirmed significant improvements in AT that remained at FU. Conclusions: A motor intervention using VRG can improve the functioning in terms of Function, Activity, and Participation of PwPD, regardless of the KC provided by PT during the training.
Insights intoPhakopsora pachyrhizieffector-effector interactions
Authors: Qi Mingsheng , Yu Haiyue , Bredow Melissa , Chicowski Aline Sartor , Fields Letícia Dias , Whitham Steven A. 
Published: September 2023

AbstractThe multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, where some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions amongPhakopsora pachyrhizieffector candidates (PpECs).P. pachyrhizihaustorial transcriptome analysis identified a collection of predictedPpECs. Among these,PpEC23 was found to interact withPpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast-two-hybrid screen to explore protein-protein interactions betweenPpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly,PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRP), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain withinPpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature ofPpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions amongP. pachyrhizieffector-effector interactions.
Accurate Prediction of Antibody Function and Structure Using Bio-Inspired Antibody Language Model
Authors: Jing Hongtai , Gao Zhengtao , Xu Sheng , Shen Tao , Peng Zhangzhi , He Shwai , You Tao , Ye Shuang , Lin Wei , Sun Siqi 
Published: September 2023

AbstractIn recent decades, antibodies have emerged as indispensable therapeutics for combating diseases, particularly viral infections. However, their development has been hindered by limited structural information and labor-intensive engineering processes. Fortunately, significant advancements in deep learning methods have facilitated the precise prediction of protein structure and function by leveraging co-evolution information from homologous proteins. Despite these advances, predicting the conformation of antibodies remains challenging due to their unique evolution and the high flexibility of their antigen-binding regions. Here, to address this challenge, we present the Bio-inspired Anti-body Language Model (BALM). This model is trained on a vast dataset comprising 336 million 40% non-redundant unlabeled antibody sequences, capturing both unique and conserved properties specific to antibodies. Notably, BALM showcases exceptional performance across four antigen-binding prediction tasks. Moreover, we introduce BALMFold, an end-to-end method derived from BALM, capable of swiftly predicting full atomic antibody structures from individual sequences. Remarkably, BALMFold outperforms those well-established methods like AlphaFold2, IgFold, ESMFold, and OmegaFold in the antibody benchmark, demonstrating significant potential to advance innovative engineering and streamline therapeutic antibody development by reducing the need for unnecessary trials.
Sexual antagonism and sex determination in three syngnathid species alongside a male pregnancy gradient
Authors: Dubin Arseny , Parker Jamie , Böhne Astrid , Roth Olivia 
Published: September 2023

AbstractThe allocation of energy towards gamete production, parental care, mate choice, sex roles, and sexual dimorphism generates divergence in selection pressures between the sexes, leading to opposing fitness strategies and sexual antagonism (SA). Due to the shared genetic makeup, a single genomic locus can contain a gene or allele with differing fitness impacts on each sex. This intralocus sexual conflict can be resolved via intersex bias in gene expression and/or formation of sex-linked genomic regions, that may also regulate sex determination. Sex determination (SD) encompasses environmental SD (ESD), monogenic SD, and polygenic SD. Occasionally, shifts from one SD locus to another can occur. While the precise mechanisms driving these shifts are unknown, SA is believed to be a major contributor. To investigate the link between SA and SD, we selected three syngnathid species along the gradient of male pregnancy that evolved with different sex roles and intensities of sexual dimorphism. By looking at intersex genetic divergence (Fst) and sex-biased expression patterns, we uncovered that sex role and mate competition, rather than male pregnancy, primarily drive SA. Furthermore, we identified processes related to non-coding RNAs and biased allele expression as mediators of SA. Most notably, we discovered intraspecies sex chromosome polymorphism inHippocampus erectus. Overall, we report important details on the interplay between SA and SD, and suggest that understanding SA and its resolution mechanisms is crucial for unraveling the evolution of SD in diverse species.