bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards a single-assay approach: a combined DNA/RNA sequencing panel eliminates diagnostic redundancy and detects clinically-relevant fusions in neuropathology
Authors: Slocum Cheyanne C. , Park Hyeon Jin , Baek Inji , Catalano Jeff , Wells Martin T. , Liechty Benjamin , Mathew Susan , Song Wei , Solomon James P. , Pisapia David J. 
Published: November 2022

AbstractSince the introduction of integrated histological and molecular diagnoses by the 2016 World Health Organization (WHO) Classification of Tumors of the Nervous System, an increasing number of molecular markers have been found to have prognostic significance in infiltrating gliomas, many of which have now become incorporated as diagnostic criteria in the 2021 WHO Classification. This has increased the applicability of targeted-next generation sequencing in the diagnostic work-up of neuropathology specimens and in addition, raises the question of whether targeted sequencing can, in practice, reliably replace older, more traditional diagnostic methods such as immunohistochemistry and fluorescence in-situ hybridization. Here, we demonstrate that the Oncomine Cancer Gene Mutation Panel v2 assay targeted-next generation sequencing panel for solid tumors is not only superior to IHC in detecting mutation in IDH1/2 and TP53 but can also predict 1p/19q co-deletion with high sensitivity and specificity relative to fluorescence in-situ hybridization by looking at average copy number of genes sequenced on 1p, 1q, 19p, and 19q. Along with detecting the same molecular data obtained from older methods, targeted-next generation sequencing with an RNA sequencing component provides additional information regarding the presence of RNA based alterations that have diagnostic significance and possible therapeutic implications. From this work, we advocate for expanded use of targeted-next generation sequencing over more traditional methods for the detection of important molecular alterations as a part of the standard diagnostic work up for CNS neoplasms.
Antibiotics use evaluation among hospitalized adult patients at Jimma Medical Center, southwestern Ethiopia: the way to pave for antimicrobial stewardship
Authors: Dechasa Mesay , Chelkeba Legese , Jorise Amente , Sefera Birbirsa , Melaku Tsegaye 
Published: November 2022

Abstract
Background
An irrational antibiotic use is a common problem in developing countries like Ethiopia, which makes empiric antibiotics use difficult. It is considered to be the greatest health problem in our time and future unless intervened. Therefore, this study aimed to assess the patterns of antibiotics use among hospitalized adult patients to pave the way for antimicrobial stewardship.

Methods
A hospital-based prospective observational study was conducted at Jimma Medical Center, southwestern Ethiopia, from 30 October 2020 to 29 January 2021 with 360 adult hospitalized patients participating. A semi-structured questionnaire and consecutive sampling technique was used for data collection. The data were collected through medical record reviews and patient interviews. The collected data were entered into Epi-data and exported to SPSS® version 23.0 for analysis. Days of therapy (DOT) and essential medicine lists “Access, Watch, and Reserve (AWaRe)” antibiotics classification were used to assess antibiotic use pattern among participants.

Results
The majority of study participants were females (55.3%), attended formal education (59.4%), and live in rural areas (61.4%) with mean age ± (SD) of 37.65 ± (16.75). The overall rate of antibiotics consumption during the study was 111 days of therapy per 100 bed-days and about two-thirds (66%) of the prescribed antibiotics were from the “Watch” group antibiotics. The indicator level of antibiotics use for “Access” group antibiotics was 34% in this study based on the World Health Organization Essential Medicine List. Cephalosporins were the most commonly used class of antibiotics (93.9%).

Conclusion
Higher antibiotics exposure and their consumption frequently observed among adult hospitalized patients in the study setting. There was a rapid increase in “Watch” group antibiotics use and about two-thirds of the prescribed antibiotics were from this group. The third-generation cephalosporin were the most commonly used class of antibiotics. Generally, higher consumption and inappropriate antibiotics use among hospitalized adult patients showed the need for urgent interventions by implementing Antimicrobial Stewardship Programs in hospitals.
Analytical dual quaternion algorithm of the weighted three-dimensional coordinate transformation
Authors: Zeng Huaien , Wang Junjie , Wang Zhihao , Li Siyang , He Haiqing , Chang Guobin , Yang Ronghua 
Published: November 2022

AbstractConsidering that a unit dual quaternion can describe elegantly the rigid transformation including rotation and translation, the point-wise weighted 3D coordinate transformation using a unit dual quaternion is formulated. The constructed transformation model by a unit dual quaternion does not need differential process to eliminate the three translation parameters, while traditional models do. Based on the Lagrangian extremum law, the analytical dual quaternion algorithm (ADQA) of the point-wise weighted 3D coordinate transformation is proved existed and derived in detail. Four numerical cases, including geodetic datum transformation, the registration of LIDAR point clouds, and two simulated cases, are studied. This study shows that ADQA is valid as well as the modified procrustes algorithm (MPA) and the orthonormal matrix algorithm (OMA). ADQA is suitable for the 3D coordinate transformation with point-wise weight and no matter rotation angles are small or big. In addition, the results also indicate that if the distribution of common points degrades from 3D or 2D space to 1D space, the solvable correct transformation parameters decrease. In other words, all common points should not be located on a line. From the perspective of improving the transformation accuracy, high accurate control points (with small errors in the coordinates) should be chosen, and it is preferred to decrease the rotation angles as much as possible.
Graphical Abstract
Expression, characterization, and application potentiality evaluation of recombinant human-like collagen in Pichia pastoris
Authors: Ma Lingling , Liang Xiaolin , Yu Shiqin , Zhou Jingwen 
Published: November 2022

AbstractCollagen is a biofunctional protein that has been widely used in many fields, including but not limited to biomedical, cosmetics and skin care, food, and novel materials. Recombinant collagen has great potential as an alternative to collagen extracted from animals because it avoids the immune response, and the yield and properties are stable. However, challenges remain in the industrial application of recombinant collagen, including improving the expression yield, reducing the cost of purification for industry and expanding applications. In this study, a cloning and recombination method was used to heterologously express the recombinant human-like collagen (RHLC) in Pichia pastoris GS115 using the pPIC9k expression vector. The RHLC expression titre was 2.33 g/L via a 5-L fermenter, and the purification was completed within 48 h and was 98% pure. The characteristics of RHLC were investigated. Furthermore, potential applications for RHLC were explored, such as basal collagen sponge preparation, forming films with chitosan and production of collagen hydrolysed peptides. RHLC has various potential applications due to its triple helical structure, thermostability, good biocompatibility and film-forming ability.
Graphical Abstract
Short-term outcomes in patients with center-involving diabetic macular edema after a single dose of intravitreal bevacizumab
Authors: Turski Christopher A. , Jacobs Mitchell A. , Abou-Jaoude Michelle M. , Fowler Nicholas H. , Harpole Ryan , Altman Emily , Chadwell John B. , Kindl Gabriel , James Hayley R. , Reddy Shivani V. , Maldonado Ramiro S. 
Published: November 2022

Abstract
Background
A significant portion of diabetic macular edema (DME) is refractory to anti-vascular endothelial growth factor (anti-VEGF) agents. This study investigates morphological and functional outcomes to a single intravitreal bevacizumab (IVB) injection in patients with center-involving DME (ciDME) at 4–6 weeks and compares treatment responders and non-responders based on spectral domain optical coherence tomography (SD-OCT) features.

Methods
IRB approved observational, retrospective chart review of patients with ciDME, identified by ICD-10 code, who received IVB and underwent baseline and 4–6 weeks follow-up SD-OCT imaging between January 1, 2016 and January 19, 2021. Patients who had received previous treatment with anti-VEGF or intraocular steroids within 1 year were excluded. Variables included best-corrected visual acuity (BCVA), central subfield thickness (CST) and total macular volume (TMV). Eyes were classified as responders if CST reduction was greater than 10%. OCT scans were graded qualitatively by two masked graders using Imagivault software. Paired Student’s t-tests, Wilcoxon signed rank tests and Chi-Square tests were used for analysis.

Results
A total of 334 prospective subjects were identified, and after applying exclusion criteria 52 eyes from 46 patients (mean age 64.22 ± 8.12 years, 58.7% male) were included. Mean BCVA did not significantly change with treatment, 63.9 ETDRS letters (~ 20/50) at baseline and 65.9 ETDRS letters (~ 20/50) post-treatment (p = 0.07). Mean CST decreased from 466 ± 123 μm at baseline to 402 ± 86 μm post-treatment (p < 0.001). 22 (42.3%) of eyes were categorized as responders and 30 (57.7%) as non-responders. Average change in CST from baseline in responders was -164 μm (p < 0.001) and + 9 μm in non-responders (p = 0.47). Vitreomacular adhesion (VMA) was more prevalent in non-responders (28.7% vs. 4.8%, p = 0.03). In addition, cyst location in the inner nuclear layer (INL) was present more frequently in responders (95.5% vs. 73.3%, p = 0.037) as was subretinal fluid (45.5% vs. 13.3%, p = 0.01).

Conclusion
The short-term response to a single IVB was sub-optimal with structural but no functional improvements. Greater baseline CST, presence of INL cysts and subretinal fluid may represent factors indicative of a better treatment response.
Using patient-reported outcome measures to assess psychological well-being in a non-representative US general population during the COVID-19 pandemic
Authors: Kaur Manraj N. , Tsangaris Elena , Dey Tanujit , Deibert Shelby , Kueper Janina , Edelen Maria , Pusic Andrea L. 
Published: November 2022

AbstractPurposeThe impact of the COVID-19 pandemic on psychological well-being will likely be long-lasting. Efforts directed towards monitoring the onset and progression of distress and mental health disorders are needed to identify and prioritize at-risk populations. This study assesses the psychological well-being of the United States (US) general population during the early phase of the COVID-19 COVID-19 pandemic using validated patient-reported outcome measures (PROMs).MethodsA cross-sectional study design was used. Adults (18 years or older) who could read and write in English were recruited through Prolific in May 2020. Participants completed a REDCap survey including demographic and health-related questions and three PROMs measuring global health (PROMIS-10 Global Health), anxiety [Generalized Anxiety Disorder Scale-7 (GAD-7)], and depression [Patient Health Questionnaire-9 (PHQ-9)]. A multivariable linear regression was used to identify key factors associated with worse psychological well-being.ResultsMean age of the 2023 participants was 31.92 ± 11.57 years (range, 18–82). Participants were mainly White (64.7%, n = 1309), female (52.2%, n = 1057), working full-time before the pandemic (43.5%, n = 879), and completed a college, trade, or university degree (40.7%, n = 823). Most participants reported mild to severe anxiety (57.3%, n = 1158) and depression (60%, n = 1276) on the GAD-7 and PHQ-9, respectively. Patient characteristics associated with worse psychological well-being included: age ≤ 39 years, non-White, female or gender diverse, BMI ≥ 30, uninsured, annual income ≤ $49,999 (USD), lower educational attainment, and belief that COVID-19 is deadlier than flu.ConclusionPROMs can be used to assess and monitor psychological well-being during the COVID-19 pandemic and to inform the planning and delivery of targeted public health interventions to support at-risk populations.
Transverse myelitis with positive dengue virus serology: a case report
Authors: Jafri Lubna , Hameed Sajid , Shakeel Erum , Shaikh Naeemuddin , Kanwar Dureshahwar 
Published: November 2022

Abstract
Background
Transverse myelitis is an inflammation of the spinal cord that spreads along the horizontal plane of a section of the spinal cord. Arboviruses, including dengue virus, are rare but known causative factors. However, this association and underlying pathophysiology is unclear. We report a case of transverse myelitis in a patient with a dengue viral infection.

Case presentation
A 38-year-old man presented with fever followed by acute paraplegia and urinary retention. His workup was positive for serum IgM antibodies against dengue virus and imaging of the spine showed inflammation in multiple sections of the spinal cord. A diagnosis of TM secondary to a dengue infection was made. He was managed with high dose of methylprednisolone for 5 days followed by oral tapering dose. The weakness subsequently improved with full recovery on follow-up visits.

Conclusions
TM secondary to acute dengue infection is a rarely reported consequence. Timely diagnosis and treatment can cause significant reduction in the otherwise resultant morbidity.
Experimental validation of a portable tidal volume indicator for bag valve mask ventilation
Authors: Maxey Benjamin S. , White Luke A. , Solitro Giovanni F. , Conrad Steven A. , Alexander J. Steven 
Published: November 2022

Abstract
Introduction
Short-term emergency ventilation is most typically accomplished through bag valve mask (BVM) techniques. BVMs like the AMBU® bag are cost-effective and highly portable but are also highly prone to user error, especially in high-stress emergent situations. Inaccurate and inappropriate ventilation has the potential to inflict great injury to patients through hyper- and hypoventilation. Here, we present the BVM Emergency Narration-Guided Instrument (BENGI) – a tidal volume feedback monitoring device that provides instantaneous visual and audio feedback on delivered tidal volumes, respiratory rates, and inspiratory/expiratory times. Providing feedback on the depth and regularity of respirations enables providers to deliver more consistent and accurate tidal volumes and rates. We describe the design, assembly, and validation of the BENGI as a practical tool to reduce manual ventilation-induced lung injury.

Methods
The prototype BENGI was assembled with custom 3D-printed housing and commercially available electronic components. A mass flow sensor in the central channel of the device measures air flow, which is used to calculate tidal volume. Tidal volumes are displayed via an LED ring affixed to the top of the BENGI. Additional feedback is provided through a speaker in the device. Central processing is accomplished through an Arduino microcontroller. Validation of the BENGI was accomplished using benchtop simulation with a clinical ventilator, BVM, and manikin test lung. Known respiratory quantities were delivered by the ventilator which were then compared to measurements from the BENGI to validate the accuracy of flow measurements, tidal volume calculations, and audio cue triggers.

Results
BENGI tidal volume measurements were found to lie within 4% of true delivered tidal volume values (95% CI of 0.53 to 3.7%) when breaths were delivered with 1-s inspiratory times, with similar performance for breaths delivered with 0.5-s inspiratory times (95% CI of 1.1 to 6.7%) and 2-s inspiratory times (95% CI of –1.1 to 2.3%). Audio cues “Bag faster” (1.84 to 2.03 s), “Bag slower” (0.35 to 0.41 s), and “Leak detected” (43 to 50%) were triggered close to target trigger values (2.00 s, 0.50 s, and 50%, respectively) across varying tidal volumes.

Conclusions
The BENGI achieved its proposed goals of accurately measuring and reporting tidal volumes delivered through BVM systems, providing immediate feedback on the quality of respiratory performance through audio and visual cues. The BENGI has the potential to reduce manual ventilation-induced lung injury and improve patient outcomes by providing accurate feedback on ventilatory parameters.
Toxic myocarditis presenting as an acute coronary syndrome
Authors: Kalekar Tushar , Kapoor Reetika , Soman Nikhith , Singh Tejvir , Mohanan Karthik 
Published: November 2022

Abstract
Background
Acute myocarditis is one of the causes of acute non-ischemic myocardial injury mimicking acute coronary syndrome (ACS) on presentation. It is usually underdiagnosed due to the non-specificity of presenting symptoms, elevated troponin levels, and abnormal ECG (electrocardiogram) findings. Delayed contrast-enhanced cardiac MRI (CMR) is known as the gold standard imaging modality for differentiating acute non-ischemic myocardial injury from infarcted myocardium. The most frequent cause of myocarditis is viral infections, but further infrequent causes include other infectious pathogens, toxins, hypersensitivity drug reactions, and autoimmune diseases. Cannabis is one of the most abused illicit and recreational drugs in the world among adolescents and adults. Also, many reports of marijuana-associated cardiovascular risks have been established previously, mainly presenting as arrhythmias, myocardial infarction, and myocarditis.

Case presentation
A 19-year-old female, complaining of radiating chest pain to the left arm and jaw, along with associated sweating for 1 day. Initial work-up showed elevated troponin levels with ST segment elevation on ECG. On further investigation, CMR showed findings of myocarditis and negative virology work-up led to a work-up of proper history, which revealed marijuana abuse, with a history of consumption 3 days before presentation. Hence, it was diagnosed as toxic myocarditis secondary to presumed cannabis abuse and treated for same.

Conclusions
Non-ischemic myocardial injury causes like myocarditis should be considered in young patients especially, who are presenting to emergency with ACS. CMR should be used as a first line diagnostic imaging modality (based on its availability) in cases mimicking an ACS or suspected myocarditis, especially in young patients. Though viral etiology is considered the most common cause of myocarditis, less common causes such as toxic myocarditis must be considered in cases of young individuals presenting with ACS in an emergency.
Theoretical model of recovery following a suicidal episode (COURAGE): scoping review and narrative synthesis
Authors: Sokol Yosef , Levin Chynna , Linzer Mairav , Rosensweig Chayim , Hubner Shifra , Gromatsky Molly , Walsh Samantha , Dixon Lisa , Goodman Marianne 
Published: November 2022

Background
Despite a significant need, there are currently no rigorously developed empirically based models for what personal recovery from a suicidal episode looks like.

Aims
To develop a theoretical model of personal recovery after a suicidal episode, based on a comprehensive literature review and stakeholder feedback.

Method
A scoping review of all empirical studies on this topic was conducted, followed by a thematic analysis to create a preliminary framework. Consultation-based revisions were then made based on feedback from a stakeholder panel to develop the final theoretical model.

Results
The final model comprised seven themes: choosing life, optimising identity, understanding oneself, rediscovering meaning, acceptance, growing connectedness and empowerment (acronym ‘COURAGE’). Although there are some similarities between COURAGE and other models of personal recovery, there are components, such as ‘choosing life’ and ‘understanding oneself’, that are specific to recovery after an acute suicidal episode.

Conclusions
To our knowledge, this is the first study to use a comprehensive literature review with stakeholder feedback to develop a conceptual model of personal recovery after an acute suicidal episode. This model has important implications for both researchers and clinicians to consider. Looking ahead, COURAGE can inform the reconceptualisation of assessment, research and clinical care of individuals who have experienced a suicidal episode.
Oncology Informatics for Lynch Syndrome Research and Care: A Literature Review
Authors: Dehghani Soufi Mahsa , Rezaei Hachesu Peyman , Ferdousi Reza 
Published: November 2022

PURPOSE This study aims to review and evaluate available informatics platforms for research and management purposes of Lynch syndrome (LS) to identify gaps and needs for future development. METHODS LS informatics tools were identified through literature search in four publication databases (1 and Scopus). First, the LS and functional elements of every informatics tools for LS were introduced. Then, current existing LS informatics tools were reviewed and explained. RESULTS A detailed review of implemented studies shows that many types of informatics platforms are available for LS management (ie, prediction model, clinical decision support system, database website, and other tools for research and management purposes of LS). Moreover, several dimensions of existing LS informatics tools were discussed and features and positive findings were reported. CONCLUSION Reviewing the literature reveals that several LS informatics tools were focused on gene-specific estimate, cancer risk prediction, identifying/screening patients, supporting personalized care of individuals with LS, and storing mismatch repair mutations information. Nevertheless, these platforms do not fully cover the care and research purposes. For instance, future developments of LS tools require more attention to dynamic knowledgebase, extra-colonic lynch–related cancers on the basis of precision medicine, variants of unknown significance, and support from diagnosis to surveillance for patient follow-up. Insights and recommendations provided in this study could help researchers and developers to meet the existing challenges in future developments.
Lipophilic Nitrile N-Oxide for Catalyst-Free Surface Modification of Nanoemulsions as Light-Harvesting Nanoantennas
Authors: Kaneko Masuomi , Nakayama Taku , Seki Hitomi , Yamamoto Shinkuro , Uemura Takumi , Inoue Keiji , Hadano Shingo , Watanabe Shigeru , Niko Yosuke 
Published: November 2022

Abstract
The therapeutic and diagnostic applications of nanoemulsions (NEs) are restricted by a lack of suitable methods to modify their surfaces, specifically the surfactant-stabilized oil–water interface. Herein, we developed a modification technique using a lipophilic nitrile N-oxide compound (LipoCNO). LipoCNO-loaded NEs underwent efficient 1,3-dipolar cycloaddition with functional molecules bearing a terminal C=C or C≡C bond under mild, catalyst-free conditions at the oil–water interface, thus producing surface-functionalized NEs that could be used without purification. To exemplify the applicability of this technique, NEs encapsulating fluorescent molecules (Cy3.5LP) and LipoCNO were surface functionalized with pheophorbide a (PpA), a singlet-oxygen-generating photosensitizer. These NEs acted as light-harvesting nanoantennas, with the excitation energy gathered by Cy3.5LP in the NEs migrating to PpA on the NE surfaces via Förster resonance energy transfer. This system showed 7–18 times more efficient singlet oxygen generation than direct PpA excitation. Furthermore, PpA-functionalized dye-loaded NEs induced cancer cell death under photoillumination. These results highlight the utility of LipoCNO for functionalizing NE surfaces toward the realization of new biological applications.