bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the trajectory curve of long-term musculoskeletal post-COVID pain symptoms in hospitalized COVID-19 survivors: a multicenter study
Authors: Fernández-de-las-Peñas César , Cancela-Cilleruelo Ignacio , Moro-López-Menchero Paloma , Rodríguez-Jiménez Jorge , Pellicer-Valero Oscar J. , Martín-Guerrero José D. , Arendt-Nielsen Lars 
Published: June 2022

Abstract
This multicenter cohort study investigated the prevalence of musculoskeletal post-COVID pain during the first year after the infection with mosaic plots and an exponential bar plot model and its associated risk factors. Patients hospitalized because of COVID-19 in 5 hospitals of Madrid (Spain) were scheduled for a telephone interview at 2 follow-up periods after hospitalization for collecting data about musculoskeletal post-COVID pain. Hospitalization and clinical data were collected from hospital medical records. From 2000 patients initially recruited, 1593 (44.6% women, age: 61 ± 15 years) were assessed at T0 (hospital admission), T1 (mean: 8.0 ± 1.5 months after discharge), and T2 (mean: 13.2 ± 1.5 months after discharge). The prevalence of musculoskeletal pain (myalgia) was 30.3% (n = 483) at T0, increased to 43.4% (n = 692) at T1, and decreased to 37.8% (n = 603) at T2. The trajectory curve revealed a decreasing prevalence trend of musculoskeletal post-COVID pain the following years after hospitalization. According to the presence of pre-existing pain symptoms, the prevalence of new-onset post-COVID pain was 75.9%. Female sex (odds ratio [OR] 1.593, 95% confidence interval [CI] 1.148-2.211), history of musculoskeletal pain (OR 1.591, 95% CI 1.211-2.07), the presence of myalgia (OR 1.371, 95% CI 1.032-1.821) or headache (OR 2.278, 95% CI 1.622-3.199) at hospitalization, the days of hospitalization (OR 1.013, 95% CI 1.000-1.025), and the presence of post-COVID pain at T1 (OR 11.02, 95% CI 8.493-14.305) were factors associated with musculoskeletal post-COVID pain 1 year after hospitalization. In conclusion, musculoskeletal post-COVID pain remains highly prevalent 1 year after hospitalization. Female sex, previous history of pain symptoms, pain symptoms at onset, and days at hospital were factors associated with musculoskeletal post-COVID pain 1 year after hospitalization.
Combination Tissue Plasminogen Activator and DNase for Loculated Malignant Pleural Effusions
Authors: Chan Chrystal , Sekowski Viktor , Zheng Bo , Li Pen , Stollery Daniel , Veenstra James , Gillson Ashley-Mae 
Published: June 2022

Background:
Indwelling pleural catheters (IPCs) are frequently used for the management of malignant pleural effusions (MPEs), but drainage can be impaired by pleural loculations. We aimed to evaluate the safety and effectiveness of intrapleural tissue plasminogen activator (tPA) versus combination tPA-deoxyribonuclease (DNase) in the treatment of loculated MPE.

Methods:
We performed a retrospective review of patients with confirmed or presumed MPEs requiring IPC insertion. We compared the efficacy of intrapleural tPA, tPA-DNase, and procedural intervention on pleural fluid drainage. Secondary endpoints included the need for future pleural procedures (eg, thoracentesis, IPC reinsertion, chest tube insertion, or surgical intervention), IPC removal due to spontaneous pleurodesis, and IPC-related complications.

Results:
Among 437 patients with MPEs, loculations developed in 81 (19%) patients. Twenty-four (30%) received intrapleural tPA, 46 (57%) received intrapleural tPA-DNase, 4 (5%) underwent a procedural intervention, and 7 (9%) received ongoing medical management. tPA improved pleural drainage in 83% of patients, and tPA-DNase improved pleural drainage in 80% of patients. tPA alone may be associated with increased rates of spontaneous pleurodesis compared with tPA-DNase. There was no difference in complications when comparing tPA, combination tPA-DNase, procedural intervention, and no therapy.

Conclusion:
Both intrapleural tPA and combination tPA-DNase appear to be safe and effective in improving pleural fluid drainage in selected patients with loculated MPE, although further studies are needed.
A Novel Simulator for Teaching Endobronchial Ultrasound–guided Needle Biopsy
Authors: Ahmad Yousef , Domaleski Luke , Kosciuk Patrick , Radchenko Christopher , Flora Arjan , Jandarov Roman , Hellmann Michael 
Published: June 2022

Background:
Endobronchial ultrasound–guided transbronchial needle aspiration (EBUS-TBNA) has become standard for the diagnosis of lung cancer, and there is an increasing need for procedural competence in trainees. We evaluate a low-cost, gelatin-based EBUS-TBNA training simulator to assess pulmonary fellows’ baseline skills and facilitate procedural development.

Methods:
A low-cost ($30) gelatin-based, high-fidelity simulator was created to represent the airways, major vessels, and lymph node stations essential to identify for EBUS-TBNA. Trainees had a baseline skills assessment using the simulator and were then provided a 1-hour didactic session on EBUS-TBNA and additional practice time with the simulator. Trainees then underwent a postsimulation skills assessment using a modified endobronchial ultrasound (EBUS)-Skills and Tasks Assessment Tool (STAT) performance assessment tool. Simulator fidelity and trainee procedural confidence was assessed using a 10-point scale.

Results:
Ten fellows received training on the EBUS-TBNA simulator. First-year trainees scored the lowest on the 18-point performance scale with a mean score of 9, while third-year trainees scored highest with a mean score of 17.5. Mean 18-point performance score improvement after simulator training and didactics was 4.31 points for all trainees with the largest change in first-year trainees amounting to 8.25 points. First-year trainees experienced the greatest improvement in EBUS procedural confidence by a mean of 2.5 points on a 10-point confidence survey.

Conclusion:
A low-cost EBUS simulator effectively differentiated early and advanced learners based on graded procedural performance scores. Simulation-based practice significantly improved learners’ procedural performance, and the degree of improvement correlated with learner inexperience. The simulation significantly increased early learner confidence in EBUS-TBNA technique.
Prophylactic Enoxaparin Against Catheter-Associated Thrombosis in Postoperative Cardiac Children: An Interrupted Time Series Analysis
Authors: Centers Gabriela I. , Hege Kerry M. , Nitu Mara E. , Cristea Ioana A. , Yabrodi Mouhammad , Schade Willis Tina M. , Bhai Hamza , Faustino E. Vincent S. 
Published: June 2022

Objectives:
The effectiveness of pharmacologic prophylaxis against catheter-associated thrombosis in children is unclear. We evaluated the compliance and outcomes associated with a prophylactic enoxaparin protocol in postoperative cardiac children.

Design:
The protocol was implemented as a quality improvement initiative and then analyzed using interrupted time series method. Data collected from November 2014 to December 2018 were divided into preprotocol (period 1), protocol implementation (period 2), and protocol revision (period 3).

Setting:
A 12-bed academic pediatric cardiac ICU.

Patients:
Children less than or equal to 18 years old with congenital heart disease admitted postoperatively with central venous catheter in situ for greater than or equal to 1 day.

Interventions:
Before 2016, prophylactic enoxaparin was administered according to physician preference. In January 2016, an enoxaparin protocol was implemented with a goal anti-Xa range of 0.25–0.49 international units/mL. Protocol was revised in February 2017 to increase the starting dose by 25% for infants less than 1 year old.

Measurements and Main Results:
We analyzed 780 hospitalizations from 636 children. Median percentage of catheter-days on prophylactic enoxaparin was 33% (interquartile range [IQR], 23–47%), 42% (IQR, 30–51%), and 38% (IQR, 35–52%) in periods 1–3, respectively. Percentage of catheter-days on enoxaparin showed immediate increase of 90% (95% CI, 17–210%) between periods 1 and 2 and sustained increase of 2% (95% CI, 0.3–4%) between periods 2 and 3. Median rates of thrombosis per 1,000 catheter-days were 5.8 (IQR, 0–9.3), 3.8 (IQR, 0–12), and 0 (IQR, 0–5.3) in periods 1–3, respectively. Rate of thrombosis showed immediate decrease of 67% (95% CI, 12–87%) between periods 1 and 2 and sustained decrease of 11% (95% CI, 2–18%) between periods 1 and 3.

Conclusions:
The temporal association between increase in percentage of catheter-days on enoxaparin and decrease in rate of thrombosis suggests the effectiveness of prophylactic enoxaparin.
Comparative Clinical Outcomes With Scale-up of Dolutegravir as First-Line Antiretroviral Therapy in Ukraine
Authors: Dumchev Kostyantyn , Kiriazova Tetiana , Riabokon Serhiy , Shost Alyona , Parrish Canada , Shapoval Anna , Germanovych Myroslava , Penner Jeremy , Beste Jason , Puttkammer Nancy 
Published: June 2022

Background:
Achievement of the UNAIDS 95-95-95 targets requires ARV regimens that are easy to use, well-tolerated, and cost-effective. Dolutegravir (DTG)-based regimens are efficacious and less costly than other common first-line regimens. This study assessed real-world effectiveness of DTG regimens in treatment-naive people living with HIV in Ukraine.

Methods:
We extracted data from the national Medical Information System on all adult patients who initiated antiretroviral therapy (ART) with DTG, lopinavir/ritonavir, or efavirenz (EFV) between October 2017 and June 2018, at 23 large clinics in 12 regions of Ukraine. Viral suppression at 12 ± 3 months and retention at 12 months after treatment initiation were the outcomes of interest.

Results:
Of total 1057 patients, 721 had a viral load test within the window of interest, and 652 (90%) had viral load of ≤ 200 copies/mL. The proportion with suppression was lower in the EFV group [aOR = 0.4 (95% confidence interval: 0.2 to 0.8)] and not different in the LPV group [aOR = 1.6 (0.5 to 4.9)] compared with the DTG group. A 24-month or longer gap between diagnosis and treatment was associated with lower odds of suppression [aOR = 0.4 (0.2 to 0.8)]. Treatment retention was 90% (957/1057), with no significant difference by regimen group. History of injecting drug use was associated with decreased retention [aOR = 0.5 (0.3 to 0.8)].

Conclusions:
DTG-based regimens were comparable with LPV and more effective than EFV in achieving viral suppression among ART-naive patients in a multisite cohort in Ukraine. Treatment retention was equally high in all 3 groups. This evidence from Ukraine supports the ART Optimization Initiative as a strategy to improve efficiency of the ART program without negatively affecting patient clinical outcomes.
A National Assessment of Alzheimer Disease and Antipsychotic Medication Prescribing Among Older Adults in Ambulatory Care Settings
Authors: Tidmore Laura M. , Skrepnek Grant H. 
Published: June 2022

Objective:
The objective of this study was to assess antipsychotic prescribing within ambulatory settings in the United States among older adults with Alzheimer disease after adjusting for demographic, provider, and clinical factors.

Methods:
This cross-sectional cohort study utilized Centers for Disease Control’s (CDC) National Ambulatory Medical Care Survey (NAMCS) ambulatory care data from 2014 to 2016 among visits 65 years old or older with any listed diagnosis of Alzheimer. Multivariable logistic regression analyses assessed the association between the outcome of antipsychotic prescribing after controlling for numerous demographic, provider, and clinical covariates. An extension of the Oacaxa-Blinder decomposition was used to assess observed differentials.

Results:
An estimated 15,471,125 ambulatory visits involving Alzheimer disease among those 65 years old or older occurred from 2014 to 2016. Antipsychotics were prescribed in 9.3% of these visits, equating to 6.81 times higher multivariable-adjusted odds relative to non-Alzheimer visits (95% confidence interval: 2.86-16.20, P<0.001). The decomposition analysis indicated that the study’s predictor variables explained 15.6% of the outcome gap between Alzheimer versus non-Alzheimer visits.

Conclusions:
Despite potential mortality risks with antipsychotics in adults 65 years old or older with Alzheimer disease and recommendations discouraging their use, this nationally representative study observed significantly higher odds of prescribing independent of demographic, provider, and clinical characteristics. Polypharmacy may be a risk factor that warrants continued assessment regarding the appropriateness of antipsychotic prescribing in this vulnerable population.
Stability of steady-state visual evoked potential contrast response functions
Authors: Ash Ryan T. , Nix Kerry , Norcia Anthony M. 
Published: June 2022

ABSTRACTA repeated measure of neural activity that is stable over time when unperturbed is needed to be able to meaningfully measure neuroplastic changes in the brain. With sensory-evoked potentials in particular, repeated presentation of stimuli can generate neuroplasticity by itself under certain conditions. We assessed the repeated-measure within-day and across-day stability of the steady-state visual-evoked potential (ssVEP), a high signal-to-noise electrophysiological readout of neural activity in human visual cortex, in preparation for studies of visual cortical neuroplasticity. Steady-state VEP contrast-sweep responses were measured daily for 4 days (four 20-trial blocks per day, 22 participants). Response amplitudes were stable in individual participants, with measured across-block and across-day coefficients of variation (CV= SD / Mean) of 12±1% and 19±2%, respectively. No consistent changes in response amplitude were observed either across blocks or across days. We conclude that contrast-sweep steady-state VEPs provide a stable human neurophysiological measure well-suited for repeated-measures studies.
Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2
Authors: Hassouneh Sayf Al-Deen , Trujillo Alexa , Ali Sobur , Cella Eleonora , Johnston Catherine , DeRuff Katherine C. , Sabeti Pardis C. , Azarian Taj 
Published: June 2022

AbstractViral genomic surveillance has been integral in the global response to the SARS-CoV-2 pandemic. Surveillance efforts rely on the availability of representative clinical specimens from ongoing testing activities. However, testing practices have recently shifted due to the widespread availability and use of rapid antigen tests, which could lead to gaps in future monitoring efforts. As such, genomic surveillance strategies must adapt to include laboratory workflows that are robust to sample type. To that end, we compare the results of RT-qPCR and viral genome sequencing using samples from positive BinaxNOW™ COVID-19 Antigen Card swabs (N=555) to those obtained from previously collected nasopharyngeal (NP) swabs used for nucleic acid amplification testing (N=135). We show that swabs obtained from antigen cards are comparable in performance to clinical excess samples from NP swabs, providing a viable alternative. This validation permits the reliable expansion of viral genomic surveillance to cases identified in the clinic or home setting where rapid antigen tests are used.
Stratifying elicited antibody dynamics after two doses of SARS-CoV-2 vaccine in a community-based cohort in Fukushima, Japan
Authors: Nakamura Naotoshi , Kobashi Yurie , Kim Kwang Su , Tani Yuta , Shimazu Yuzo , Zhao Tianchen , Nishikawa Yoshitaka , Omata Fumiya , Kawashima Moe , Yoshida Makoto , Abe Toshiki , Saito Yoshika , Senoo Yuki , Nonaka Saori , Takita Morihito , Yamamoto Chika , Kawamura Takeshi , Sugiyama Akira , Nakayama Aya , Kaneko Yudai , Park Hyeongki , Jeong Yong Dam , Tatematsu Daiki , Akao Marwa , Sato Yoshitaka , Iwanami Shoya , Fujita Yasuhisa , Wakui Masatoshi , Aihara Kazuyuki , Kodama Tatsuhiko , Shibuya Kenji , Iwami Shingo , Tsubokura Masaharu 
Published: June 2022

AbstractRecent studies have provided insights into the effect of vaccine boosters on recall immunity. Given the limited global supply of COVID-19 vaccines, identifying vulnerable populations with lower sustained vaccine-elicited antibody titers is important for targeting individuals for booster vaccinations. Here we investigated longitudinal data in a cohort of 2,526 people in Fukushima, Japan, from April 2021 to December 2021. Antibody titers following two doses of a COVID-19 vaccine were repeatedly monitored and information on lifestyle habits, comorbidities, adverse reactions, and medication use was collected. Using mathematical modeling and machine learning, we stratified the time-course patterns of antibody titers and identified vulnerable populations with low sustained antibody titers. Moreover, we showed that only 5.7% of the participants in our cohort were part of the “durable” population with high sustained antibody titers, which suggests that this durable population might be overlooked in small cohorts. We also found large variation in antibody waning within our cohort. There is a potential usefulness of our approach for identifying the neglected vulnerable population.
The di-symbiotic systems in the aphids Sipha maydis and Peryphillus lyropictus provide a contrasting picture of recent co-obligate nutritional endosymbiosis in aphids
Authors: Renoz François , Ambroise Jérôme , Bearzatto Bertrand , Fakhour Samir , Parisot Nicolas , Lopes Mélanie Ribeiro , Gala Jean-Luc , Calevro Federica , Hance Thierry 
Published: June 2022

AbstractDependence on multiple nutritional bacterial symbionts forming a metabolic unit has repeatedly evolved in many insect species that feed on nutritionally unbalanced diets such as plant sap. This is the case for aphids of the subfamilies Lachninae and Chaitophorinae, which have evolved di-symbiotic systems in which the ancient obligate nutritional symbiont Buchnera aphidicola is metabolically complemented by an additional nutritional symbiont acquired more recently. Deciphering how different symbionts integrate both metabolically and anatomically in such systems is crucial to understanding how complex nutritional symbiotic systems function and evolve. In this study, we sequenced and analyzed the genomes of the symbionts B. aphidicola and Serratia symbiotica associated with the Chaitophorinae aphids Sipha maydis and Periphyllus lyropictus. Our results show that, in these two species, B. aphidicola and S. symbiotica complement each other metabolically (and their hosts) for the biosynthesis of essential amino acids and vitamins but with distinct metabolic reactions supported by each symbiont depending on the host species. Furthermore, the S. symbiotica symbiont associated with S. maydis appears to be strictly compartmentalized into the specialized host cells housing symbionts in aphids, the bacteriocytes, whereas the S. symbiotica symbiont associated with P. lyropictus exhibits a highly invasive phenotype, presumably because it is capable of expressing a larger set of virulence factors, including a complete flagellum for bacterial motility. Such contrasting levels of metabolic and anatomical integration for two S. symbiotica symbionts that were recently acquired as nutritional co-obligate partners reflect distinct coevolutionary processes specific to each association.
The prevalence of mental ill-health in women during pregnancy and after childbirth during the Covid-19 pandemic: a Systematic review and Meta-analysis
Authors: Delanerolle Gayathri , McCauley Mary , Hirsch Martin , Zheng Yutian , Cong Xu , Cavalini Heitor , Shetty Ashish , Rathod Shanaya , Shi Jian Qing , Hapangama Dharani K , Phiri Peter 
Published: June 2022

AbstractBackgroundSevere Acute Respiratory Syndrome Coronavirus (SARS-CoV) is a respiratory disease causing coronavirus. SARS-CoV has caused the Middle East Respiratory Syndrome (MERS), SARS-CoV in Hong King and SARS-CoV-2 (COVID-19). COVID-19, to date, have had the highest mortality and morbidity globally, thus reaching the pandemic status. In comparison to research conducted to explore the impact of pandemics on the general wellbeing, there appears to be a paucity on its association with women’s mental health. Many pregnant women have reported that the pandemic negatively impacted their mental health.AimThis study aimed is to explore the prevalence of the impact of the COVID-19, MERS and SARS pandemics on the mental health of pregnant women.MethodA study protocol was developed and published in PROSPERO (CRD42021235356) to explore a number of key objectives. For the purpose of this study PubMed, Science direct, Ovid PsycINFO and EMBASE databases were searched from December 2000 – July 2021. The search results were screened, first by title, and then by abstract. A meta-analysis was conducted to report the findings.ResultsThere were no studies reporting the mental health impact due to MERS and SARS. We systematically identified 316 studies that reported on the mental health of women that were pregnant and soon after birth. The meta-analysis indicated 24.9% (21.37%-29.02%) of pregnant women reported symptoms of depression, 32.8% (29.05% to 37.21%) anxiety, 29.44% (18.21% - 47.61%) stress, 27.93% (9.05%-86.15 %) PTSD, and 24.38% (11.89%-49.96%) sleep disorders during the COVID-19 pandemic. Furthermore, the I2 test showed a high heterogeneity value.ConclusionThe importance of managing the mental health during pregnancy and after-delivery improves the quality of life and wellbeing of mothers. Developing an evidence based mental health framework as part of pandemic preparedness to help pregnant women would improve the quality of care received during challenging times.
Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation
Authors: Cartes Jorge Avila , Anand Santosh , Ciccolella Simone , Bonizzoni Paola , Della Vedova Gianluca 
Published: June 2022

AbstractBackgroundSince the beginning of the COVID-19 pandemic there has been an explosion of sequencing of the SARS-CoV-2 virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus, most notably the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade.ResultsIn this paper, we leverage the Frequency Chaos Game Representation (FCGR) and Convolutional Neural Networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieves an 96.29% overall accuracy, while a similar tool, Covidex, obtained a 77, 12% overall accuracy. As far as we know, our method is the first using Deep Learning and FCGR for intra-species classification. Furthermore, by using some feature importance methods CouGaR-g allows to identify k-mers that matches SARS-CoV-2 marker variants.ConclusionsBy combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on Random Forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants.AvailabilityThe trained models can be tested online providing a FASTA file (with one or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.