bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous targeted and discovery-driven clinical proteotyping using hybrid-PRM/DIA
Authors: Goetze Sandra , van Drogen Audrey , Albinus Jonas B. , Fort Kyle L. , Gandhi Tejas , Robbiani Damiano , Laforte Véronique , Reiter Lukas , Levesque Mitchell P. , Xuan Yue , Wollscheid Bernd 
Published: April 2024

Abstract
Background
Clinical samples are irreplaceable, and their transformation into searchable and reusable digital biobanks is critical for conducting statistically empowered retrospective and integrative research studies. Currently, mainly data-independent acquisition strategies are employed to digitize clinical sample cohorts comprehensively. However, the sensitivity of DIA is limited, which is why selected marker candidates are often additionally measured targeted by parallel reaction monitoring.

Methods
Here, we applied the recently co-developed hybrid-PRM/DIA technology as a new intelligent data acquisition strategy that allows for the comprehensive digitization of rare clinical samples at the proteotype level. Hybrid-PRM/DIA enables enhanced measurement sensitivity for a specific set of analytes of current clinical interest by the intelligent triggering of multiplexed parallel reaction monitoring (MSxPRM) in combination with the discovery-driven digitization of the clinical biospecimen using DIA. Heavy-labeled reference peptides were utilized as triggers for MSxPRM and monitoring of endogenous peptides.

Results
We first evaluated hybrid-PRM/DIA in a clinical context on a pool of 185 selected proteotypic peptides for tumor-associated antigens derived from 64 annotated human protein groups. We demonstrated improved reproducibility and sensitivity for the detection of endogenous peptides, even at lower concentrations near the detection limit. Up to 179 MSxPRM scans were shown not to affect the overall DIA performance. Next, we applied hybrid-PRM/DIA for the integrated digitization of biobanked melanoma samples using a set of 30 AQUA peptides against 28 biomarker candidates with relevance in molecular tumor board evaluations of melanoma patients. Within the DIA-detected approximately 6500 protein groups, the selected marker candidates such as UFO, CDK4, NF1, and PMEL could be monitored consistently and quantitatively using MSxPRM scans, providing additional confidence for supporting future clinical decision-making.

Conclusions
Combining PRM and DIA measurements provides a new strategy for the sensitive and reproducible detection of protein markers from patients currently being discussed in molecular tumor boards in combination with the opportunity to discover new biomarker candidates.
Combination of pregabalin and Amitriptyline in management of chronic idiopathic pain following penile prosthesis implantation: a pilot study
Authors: Shaker Hassan , Said Nouran Omar El , ElSaeed Karim Omar 
Published: April 2024

Abstract
Background
Chronic post-penile prosthesis pain is de novo pain persisting > 2 months post-operatively. This pain is inadequately reported, poorly understood and undermanaged. The purpose of this current pilot study was to improvise a medical approach to alleviate the condition and assess the combination of Pregabalin and Amitriptyline in its management.

Results
The study enrolled 9 patients complaining of idiopathic penile, pelvic, or scrotal pain persisting > 2 months after penile prosthesis implantation. Patients were prescribed pregabalin 75mg/12h (escalated after 1 week to 150mg/12h upon demand) and Amitriptyline 25mg once daily for 3 months. The pain was reassessed after 10, 30 and 100 days. The dose of pregabalin required and the side effects of the medication were noted. Findings revealed a significant decrease in pain duration (p = 0.007), frequency (p < 0.001), and intensity (p < 0.001); in glanular (p = 0.008), shaft pain (p = 0.046) but not scrotal (p = 0.112). Moreover, a significant decrease was found in sharp pain (p = 0.003) and pain aggravated by touch (p = 0.008) but not aching pain (p = 0.277). Additionally, significant improvement was reported in QoL (p < 0.001) and dose escalation of pregabalin to 150mg/12h was required in only 1 case (11%).

Conclusion
The combination of pregabalin and amitriptyline is very effective in the management of chronic idiopathic pain following penile prosthesis implantation. However, due to the ambiguity and lack of reporting of the condition, we recommend a multicentric contribution to acknowledge the condition, and weigh its prevalence accurately, whilst evaluating the efficacy of our approach.
This study received ethical approval from Ain Shams University Research Ethics Committee (REC) FWA 000017585, on 04/13/2023 (REC-FMASU@med.asu.edu.eg).

Trial registration
no FMASU R98/2023.
CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny
Authors: Kong Garth L. , Nguyen Thai T. , Rosales Wesley K. , Panikar Anjali D. , Cheney John H. W. , Lusardi Theresa A. , Yashar William M. , Curtiss Brittany M. , Carratt Sarah A. , Braun Theodore P. , Maxson Julia E. 
Published: April 2024

Abstract
Background
The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield new insights not revealed with a single modality. For example, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) simultaneously profiles the RNA transcriptome and the surface protein expression. The surface protein markers in CITE-Seq can be used to identify cell populations similar to the iterative filtration process in flow cytometry, also called “gating”, and is an essential step for downstream analyses and data interpretation. While several packages allow users to interactively gate cells, they often do not process multi-omic sequencing datasets and may require writing redundant code to specify gate boundaries. To streamline the gating process, we developed CITEViz which allows users to interactively gate cells in Seurat-processed CITE-Seq data. CITEViz can also visualize basic quality control (QC) metrics allowing for a rapid and holistic evaluation of CITE-Seq data.

Results
We applied CITEViz to a peripheral blood mononuclear cell CITE-Seq dataset and gated for several major blood cell populations (CD14 monocytes, CD4 T cells, CD8 T cells, NK cells, B cells, and platelets) using canonical surface protein markers. The visualization features of CITEViz were used to investigate cellular heterogeneity in CD14 and CD16-expressing monocytes and to detect differential numbers of detected antibodies per patient donor. These results highlight the utility of CITEViz to enable the robust classification of single cell populations.

Conclusions
CITEViz is an R-Shiny app that standardizes the gating workflow in CITE-Seq data for efficient classification of cell populations. Its secondary function is to generate basic feature plots and QC figures specific to multi-omic data. The user interface and internal workflow of CITEViz uniquely work together to produce an organized workflow and sensible data structures for easy data retrieval. This package leverages the strengths of biologists and computational scientists to assess and analyze multi-omic single-cell datasets. In conclusion, CITEViz streamlines the flow cytometry gating workflow in CITE-Seq data to help facilitate novel hypothesis generation.
Sex differences in pain catastrophizing and its relation to the transition from acute pain to chronic pain
Authors: Le Linh H.L. , Brown Vanessa A.V. , Mol Sander , Azijli Kaoutar , Kuijper Martijn M. , Becker Leonie , Koopman Seppe S.H.A. 
Published: April 2024

Abstract
Background and importance
Differences exist between sexes in pain and pain-related outcomes, such as development of chronic pain. Previous studies suggested a higher risk for pain chronification in female patients. Furthermore, pain catastrophizing is an important risk factor for chronification of pain. However, it is unclear whether sex differences in catastrophic thinking could explain the sex differences in pain chronification.

Objectives
The aim of this study was to examine sex differences in pain catastrophizing. Additionally, we investigated pain catastrophizing as a potential mediator of sex differences in the transition of acute to chronic pain.

Design, settings and participants
Adults visiting one of the 15 participating emergency departments in the Netherlands with acute pain-related complaints. Subjects had to meet inclusion criteria and complete questionnaires about their health and pain.

Outcomes measure and analysis
The outcomes in this prospective cohort study were pain catastrophizing (short form pain catastrophizing) and pain chronification at 90 days (Numeric Rating Scale ≥ 1). Data was analysed using univariate and multivariable logistic regression models. Finally, stratified regression analyses were conducted to assess whether differences in pain catastrophizing accounted for observed differences in pain chronification between sexes.

Main results
In total 1,906 patients were included. Females catastrophized pain significantly more than males (p < 0.001). Multiple regression analyses suggested that pain catastrophizing is associated with pain chronification in both sexes.

Conclusions
This study reported differences between sexes in catastrophic cognitions in the development of chronic pain. This is possibly of clinical importance to identify high-risk patients and ensure an early intervention to prevent the transition from acute to chronic pain.
Classification system for primary care provider eConsults about medications for older adults with frailty
Authors: Schneider T , Farrell B , Karunananthan S , Afkham A , Keely E , Liddy C , McCarthy L. M. 
Published: April 2024

Abstract
Background
Providing primary care for people with frailty can be challenging due to an increased risk of adverse outcomes and use of potentially inappropriate medications which may exacerbate characteristics of frailty. eConsult is a service where primary care providers can receive timely specialist advice for their patients through a secure web-based application. We aimed to develop a classification system to characterize medication-focused eConsult questions for older adults with frailty and assess its usability.

Methods
A classification system was developed and refined over three cycles of improvement through a cross-sectional study of 35 cases categorized as medication-focused from cases submitted in 2019 for patients aged 65 or older with frailty through the Champlain BASE eConsult service (Ontario, Canada). The final classification system was then applied to each case.

Results
The classification system contains 5 sections: (1) case descriptives; (2) intent and type of question; (3) medication recommendations and additional information in the response; (4) medication classification; and (5) potentially inappropriate medications. Among the 35 medication-focused cases, the most common specialties consulted were endocrinology (9 cases, 26%) and cardiology (5 cases, 14%). Medication histories were available for 29 cases (83%). Many patients were prescribed potentially inappropriate medications based on explicit tools (AGS Beers Criteria®, STOPPFall, Anticholinergic Cognitive Burden Scale, ThinkCascades) yet few consults inquired about these medications.

Conclusion
A classification system to describe medication-related eConsult cases for patients experiencing frailty was developed and applied to 35 eConsult cases. It can be applied to more cases to identify professional development opportunities and enhancements for eConsult services.
Safety and efficacy of a low-dose combination of midazolam, alfentanil, and propofol for deep sedation of elderly patients undergoing ERCP
Authors: Zhang Yanping , Zhang Ning , Hu Jing , Liu Changlin , Li Guanjun 
Published: April 2024

Abstract
Background
Proper sedation of patients, particularly elderly individuals, who are more susceptible to sedation-related complications, is of significant importance in endoscopic retrograde cholangiopancreatography (ERCP). This study aims to assess the safety and efficacy of a low-dose combination of midazolam, alfentanil, and propofol for deep sedation in elderly patients undergoing ERCP, compared to a group of middle-aged patients.

Methods
The medical records of 610 patients with common bile duct stones who underwent elective ERCP under deep sedation with a three-drug regimen, including midazolam, alfentanil, and propofol at Shandong Provincial Third Hospital from January 2023 to September 2023 were retrospectively reviewed in this study. Patients were categorized into three groups: middle-aged (50–64 years, n = 202), elderly (65–79 years, n = 216), and very elderly (≥ 80 years, n = 192). Intraoperative vital signs and complications were compared among these groups.

Results
The three groups showed no significant difference in terms of intraoperative variation of systolic blood pressure (P = 0.291), diastolic blood pressure (P = 0.737), heart rate (P = 0.107), peripheral oxygen saturation (P = 0.188), bispectral index (P = 0.158), and the occurrence of sedation-related adverse events including hypotension (P = 0.170) and hypoxemia (P = 0.423).

Conclusion
The results suggest that a low-dose three-drug regimen consisting of midazolam, alfentanil, and propofol seems safe and effective for deep sedation of elderly and very elderly patients undergoing ERCP procedures. However, further studies are required to verify these findings and clarify the benefits and risks of this method.
Comparison of lifestyle, cognitive function, mental health, and quality of life between hospitalized older adults with COVID-19 and non-COVID-19 in South Korea: a cross-sectional study
Authors: Jung Jae Hyu , Park Ji-Hyuk , Park Kang-Hyun 
Published: April 2024

Abstract
Background
The coronavirus disease (COVID-19) pandemic has greatly impacted older adults, resulting in many deaths. The impact of lifestyle and mental health on vulnerable groups, such as older adults, can be large and long lasting. Therefore, this study aimed to investigate the effects of COVID-19 confirmation on cognition, lifestyle, mental health, and quality of life in adults aged 55 years.

Methods
The sample consisted of 111 people in the COVID group and 189 people in the non-COVID group aged over 55 years in South Korea. An online survey was conducted between January and May 2022. Participants responded to the following assessment tools: Yonsei Lifestyle Profile, Prospective and Retrospective Memory (PRMQ), Subjective Memory Complaints Questionnaire (SMCQ), Visual Analogue Scale, Patient Health Questionnaire-9 (PHQ-9), Insomnia Severity Index (ISI), Fear of COVID-19 Scale (FCV-19 S), and the World Health Organization Quality of Life Scale abbreviated version (WHOQOL-BREF). Differences in lifestyle, cognition, depression, anxiety, and quality of life were compared between the two groups.

Results
There were significant differences in physical activity, diet, the total score of the PRMQ, PM (a sub-score of the PRMQ), PHQ-9, Korean version of the ISI (ISI-K), and WHOQOL-BREF scores between the COVID and non-COVID groups. However, there were no significant differences in activity participation, Self-Rating Anxiety Scale (SAS), or FCV-19 S between groups.

Conclusions
The study confirms that COVID-19 negatively affects memory, physical activity, diet, quality of life, depression, and insomnia in the older adults. Therefore, this study implicated that prevention and intervention strategies required improving the memory, lifestyle, and mental health of older adults with COVID-19.

Trial registration
The study was conducted in accordance with the Declaration of Helsinki, and approved by the Institutional Review Board of Yonsei university in Korea (Registration number: 1041849-202112-SB-226-03, Date of registration: 01042022).
Can a prolonged healing pressure injury be benefited by using an AI mattress? A case study
Authors: Ni Tung Fang , Wang Jyh-Liang , Chen Chih-Kuang , Shih De Fen , Wang Jeng 
Published: April 2024

Abstract
Background
Pressure injuries are a common and serious issue for bedridden residents in long-term-care facilities. Areas of bony prominences, such as the scapula, sacrum, and heels, are more likely to develop pressure injuries. The management of pressure injury wounds include dressing changes, repositioning, away from moisture, decreasing the occurrence of friction and shear, and more. Some supportive surfaces are also used for pressure injury cases such as gel pads, alternating pressure air mattresses, and air-fluidized beds. The aim of this case study was to determine whether the use of an artificial intelligent mattress can improve a nursing home resident with prolonged pressure injury.

Case presentation
A retrospective study design was conducted for this case study. A 79-year-old male developed a pressure injury in the sacrum. His pressure injury was initially at stage 4, with a score of 12 by the Braden scale. The PUSH score was 16. During 5.5 months of routine care plus the use of the traditional alternative air mattress, in the nursing home, the wound stayed in stage 3 but the PUSH score increased up to 11. An artificial intelligence mattress utilizing 3D InterSoft was used to detect the bony prominences and redistribute the external pressure of the skin. It implements a color guided schematic of 26 colors to indicate the amount of pressure of the skin.

Results
The wound size was decreased and all eczema on the resident’s back diminished. The PUSH score was down to 6, as the artificial intelligent mattress was added into the routine care. The staff also reported that the resident’s quality of sleep improved and moaning decreased. The hemiplegic side is at greater risk of developing pressure injury.

Conclusions
This novice device appeared to accelerate wound healing in this case. In the future, more cases should be tested, and different care models or mattress can be explored.
Preoperative prediction of microsatellite instability status in colorectal cancer based on a multiphasic enhanced CT radiomics nomogram model
Authors: Bian Xuelian , Sun Qi , Wang Mi , Dong Hanyun , Dai Xiaoxiao , Zhang Liyuan , Fan Guohua , Chen Guangqiang 
Published: April 2024

Abstract
Background
To investigate the value of a nomogram model based on the combination of clinical-CT features and multiphasic enhanced CT radiomics for the preoperative prediction of the microsatellite instability (MSI) status in colorectal cancer (CRC) patients.

Methods
A total of 347 patients with a pathological diagnosis of colorectal adenocarcinoma, including 276 microsatellite stabilized (MSS) patients and 71 MSI patients (243 training and 104 testing), were included. Univariate and multivariate regression analyses were used to identify the clinical-CT features of CRC patients linked with MSI status to build a clinical model. Radiomics features were extracted from arterial phase (AP), venous phase (VP), and delayed phase (DP) CT images. Different radiomics models for the single phase and multiphase (three-phase combination) were developed to determine the optimal phase. A nomogram model that combines clinical-CT features and the optimal phasic radscore was also created.

Results
Platelet (PLT), systemic immune inflammation index (SII), tumour location, enhancement pattern, and AP contrast ratio (ACR) were independent predictors of MSI status in CRC patients. Among the AP, VP, DP, and three-phase combination models, the three-phase combination model was selected as the best radiomics model. The best MSI prediction efficacy was demonstrated by the nomogram model built from the combination of clinical-CT features and the three-phase combination model, with AUCs of 0.894 and 0.839 in the training and testing datasets, respectively.

Conclusion
The nomogram model based on the combination of clinical-CT features and three-phase combination radiomics features can be used as an auxiliary tool for the preoperative prediction of the MSI status in CRC patients.
Post-bariatric pregnancy is associated with vitamin K1 deficiency, a case control study
Authors: Bechensteen Brit Torunn , Sithiravel Cindhya , Strøm-Roum Ellen Marie , Ruud Heidi Kathrine , Kravdal Gunnhild , Winther Jacob A. , Valderhaug Tone G. 
Published: April 2024

Abstract
Background
Maternal obesity is associated with adverse outcome for pregnancy and childbirths. While bariatric surgery may improve fertility and reduce the risk of certain pregnancy-related complications such as hypertension and gestational diabetes mellitus, there is a lack of evidence on the optimal nutritional monitoring and supplementation strategies in pregnancy following bariatric surgery. We aimed to assess the impact of bariatric surgery on micronutrients in post-bariatric pregnancy and possible differences between gastric bypass surgery and sleeve gastrectomy.

Methods
In this prospective case control study, we recruited 204 pregnant women (bariatric surgery n = 59 [gastric bypass surgery n = 26, sleeve gastrectomy n = 31, missing n = 2] and controls n = 145) from Akershus university hospital in Norway. Women with previous bariatric surgery were consecutively invited to study participation at referral to the clinic for morbid obesity and the controls were recruited from the routine ultrasound screening in gestational week 17–20. A clinical questionnaire was completed and blood samples were drawn at mean gestational week 20.4 (SD 4.5).

Results
The women with bariatric surgery had a higher pre-pregnant BMI than controls (30.8 [SD 6.0] vs. 25.2 [5.4] kg/m2, p < 0.001). There were no differences between groups regarding maternal weight gain (bariatric surgery 13.3 kg (9.6) vs. control 14.8 kg (6.5), p = 0.228) or development of gestational diabetes (n = 3 [5%] vs. n = 7 [5%], p = 1.000). Mean levels of vitamin K1 was lower after bariatric surgery compared with controls (0.29 [0.35] vs. 0.61 [0.65] ng/mL, p < 0.001). Multiadjusted regression analyses revealed an inverse relationship between bariatric surgery and vitamin K1 (B -0.26 ng/mL [95% CI -0.51, -0.04], p = 0.047) with a fivefold increased risk of vitamin K1 deficiency in post-bariatric pregnancies compared with controls (OR 5.69 [1.05, 30.77] p = 0.044). Compared with sleeve gastrectomy, having a previous gastric bypass surgery was associated with higher risk of vitamin K1 deficiency (OR 17.1 [1.31, 223.3], p = 0.030).

Conclusion
Post-bariatric pregnancy is negatively associated with vitamin K1 with a higher risk of vitamin K1 deficiency in pregnancies after gastric bypass surgery compared with after sleeve gastrectomy. Vitamin K1 deficiency in post-bariatric pregnancy have potential risk of hypocoaguble state in mother and child and should be explored in future studies.