bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the performance of two real-time fluorescent quantitative PCR kits for the detection of SARS-CoV-2 nucleic acid: a study based on large real clinical samples
Authors: Wang Yiting , Li Xuewen , Wang Yifei , Tu Zheyu , Xu Jiancheng , Pan Junqi , Zhou Qi 
Published: November 2022

Abstract
Background
The global pandemic of coronavirus disease 2019 (COVID-19) has led to the development of multiple detection kits by national manufacturers for severe acute respiratory syndrome coronavirus 2 viral nucleic acid testing. The purpose of this study is to evaluate the performance of different kits (i.e., Maccura kit and Sansure kit) in real clinical work using clinical samples, which will help with the optimization of the test kits.

Method
During the past three months (March–May 2022), 1399 pharyngeal swabs from suspected COVID-19 patients have been initially screened using the Maccura kit in Jilin, China, and the test results were verified using the Sansure kit. The cycle threshold (Ct) values generated by the two kits were compared at different viral load levels. Correlation and consistency of the Ct values were investigated using Spearman correlation, Deming regression, and Bland–Altman plots. The cut-off Ct values of the Maccura kit were recalculated by referencing the result of the Sansure kit as a standard. Furthermore, another 163 pharyngeal swabs from suspected COVID-19 patients were collected to verify the new cut-off values.

Results
As a result of the Maccura kit testing, 1192 positive cases and 207 suspected COVID-19 cases were verified. After re-examination by the Sansure kit, 1118 positive cases were confirmed. The difference between the Ct values provided by the two kits was statistically significant, except for the N gene at high viral load. The Ct values obtained from the two kits presented a linear positive correlation. The Maccura kit used new cut-off Ct values of 35.00 (ORF1ab gene) and 35.07 (N gene). Based on that, the validation pass rate for the new cut-off Ct values was 91.41%.

Conclusion
Since the Maccura kit is found to have false positives in actual clinical work, recalculation of the cut-off values can reduce this occurrence. In order to improve the accuracy of the testing, laboratories should use two kits for COVID-19 testing, and the adjusting and optimizing of the kits for their situation are needed.
Aberrant synaptophysin expression in classic Hodgkin lymphoma
Authors: Im Soyoung , Kim Jeong-A. , Park Gyeongsin , Cho Uiju 
Published: November 2022

Abstract
Background
Synaptophysin is an immunohistochemical marker for neuroendocrine differentiation and is widely used in pathologic diagnosis. Its expression in malignant lymphoma has not yet been described. However, we experienced an index case of classic Hodgkin lymphoma with synaptophysin expression. This experience prompted us to investigate synaptophysin expression in classic Hodgkin lymphoma.

Method
Immunohistochemical staining of synaptophysin was performed in 59 diagnosed cases of classic Hodgkin lymphoma, 10 anaplastic large cell lymphomas, 16 diffuse large B-cell lymphomas, and 5 extranodal marginal zone lymphoma of the mucosa-associated tissue. Synaptophysin-positive cases were stained for both chromogranin and CD56a.

Result
Of 59 classic Hodgkin lymphoma cases, 11 (19%) were positive for synaptophysin. None of the anaplastic large cell lymphomas expressed synaptophysin. Synaptophysin showed weak but specific expression in the cytoplasm of the Hodgkin lymphoma tumor cells. Other background inflammatory cells (such as macrophages, B-, and T-lymphocytes) were all negative for synaptophysin expression. Chromogranin and CD56a were not expressed in the synaptophysin-positive classic Hodgkin lymphomas.

Conclusions
Synaptophysin is an integral glycoprotein present in presynaptic vesicles of neurons and neuroendocrine cells. It is a diagnostic marker for neuroendocrine tumors. Aberrant synaptophysin expression has been reported in non-neuroendocrine tumors but not in lymphoma or leukemia. To the best of our knowledge, synaptophysin positivity has only been reported in a single case of precursor T-lymphoblastic leukemia/lymphoma to date. Our study showed that aberrant synaptophysin expression in classic Hodgkin lymphoma is an unexpectedly frequent finding. The mechanism underlying, and prognostic significance of, such aberrant expression is unclear. Thus, in a small biopsy, aberrant synaptophysin expression could be a diagnostic pitfall and should be carefully avoided.
Utilization of cardiac graft with single coronary artery for orthotopic heart transplantation
Authors: Hess Nicholas R. , Keebler Mary E. , Fabrizio Carly A. , Kaczorowski David J. 
Published: November 2022

Abstract
Background
Anomalous coronary arteries arise in a small subset of the population, with each configuration conveying a varying degree of long-term risk. The utilization of cardiac grafts with these anomalies have not been well described.

Case presentation
An anomalous single coronary artery with the left main coronary artery arising from the right coronary ostium was discovered in a 40-year old male evaluated for cardiac donation. After evaluation, this heart was successfully procured and utilized for orthotopic heart transplantation.

Conclusion
In this report, we demonstrate that in select cases, a cardiac graft with single coronary artery anatomy can be successfully procured and transplanted with excellent outcomes.
Health‐related quality of life and associated factors in people with diabetes at high risk of foot ulceration
Authors: Perrin Byron M. , van Netten Jaap J. , aan de Stegge Wouter B. , Busch‐Westbroek Tessa E. , Bus Sicco A. 
Published: November 2022

AbstractBackgroundThe health‐related quality of life (HRQoL) of people with diabetes‐related foot complications has been increasingly reported, mostly from studies of people with a foot ulcer. The aim of this study was to assess HRQoL and determine factors associated with HRQoL in people with diabetes at high risk of foot ulceration.MethodsIn all, 304 participants enrolled in the Diabetic Foot Temperature Trial (DIATEMP) were included in the cross‐sectional analysis. HRQoL was measured by the RAND® 36‐Item Short Form Health Survey (SF‐36) at baseline. Potential factors associated with HRQoL were analysed using multiple linear regression analyses for the eight domains of the SF‐36.ResultsParticipants were predominantly male (72%), mean age 64.6 (±10.5) years, 77% type 2 diabetes and mean duration of diabetes 20 (±14) years. Mean SF‐36 domain scores for the General Health (49.2 ± 20.1), Role Physical (50.9 ± 44.7), Physical Function (58.5 ± 27.9) and Vitality domains (59.8 ± 21.6) were lower compared to the Mental Health (78.4 ± 18.0), Social Functioning (75.3 ± 24.2), Role Emotional (73.5 ± 38.9) and Bodily Pain (67.0 ± 27.0) domains. HRQoL was lower than Dutch population‐based and general diabetes samples, but higher than in samples with an ulcer. Use of a walking aid was associated with lower HRQoL across all 8 SF‐36 domains (β range − 0.20 to − 0.50), non‐Caucasian descent was associated with lower HRQoL in 5 domains (β range − 0.13 to − 0.17). Not working, higher BMI and younger age were associated with lower HRQoL in 3 domains.ConclusionsPeople at high risk of diabetes‐related foot ulceration have reduced HRQoL that varies across domains, with the physical domains most affected. Assessing mobility, ethnicity, BMI and job status may be useful in daily practice to screen for people who might benefit from interventions targeting HRQoL.Trial registrationNetherlands Trial Registration: NTR5403. Registered on 8 September 2015.
Improvement of attention deficit/hyperactivity disorder (ADHD) in three adult men during testosterone treatment: a case series
Authors: Rogne Ane , Hassel Bjørnar 
Published: November 2022

Abstract
Background
Attention deficit/hyperactivity disorder (ADHD) entails inattention, impulsivity, and restlessness at a disabling level. The pharmacological treatment of ADHD rests on the use of centrally acting stimulants, such as methylphenidate and D-amphetamine. In some patients, these drugs cause side effects that preclude their use.

Case presentation
We present three adult male, Caucasian, ADHD patients (24, 37, and 43 years old) whose ADHD symptoms improved during treatment with testosterone. The first patient experienced loss of libido during treatment with methylphenidate; for this, he was offered a trial of testosterone. Unexpectedly, his ADHD symptoms improved with testosterone treatment, and this effect continued with testosterone as monotherapy. The two other patients, who also had side effects from centrally acting stimulants, received testosterone monotherapy with similar results. The effect has now continued for 4.5–5 years at the same doses: 10–60 mg testosterone/day, administered as a skin gel. Prior to testosterone treatment, the patients had serum levels of testosterone in the low–normal range: 12–16 nmol/L (age-specific reference range: 10.4–32.6 nmol/L). The testosterone/sex hormone-binding globulin ratio was low in two patients (0.32 and 0.34; age-specific reference range: 0.38–1.1), suggesting low free serum levels of testosterone. Serum testosterone levels and testosterone/sex hormone-binding globulin ratios increased with testosterone treatment in all patients, but remained within reference values.

Conclusion
These cases suggest that a moderately reduced serum level of free testosterone may contribute to the ADHD symptoms of some adult male ADHD patients, and that testosterone treatment may be of value for these patients.
Using government data to understand the use and availability of medicines for hypertension and diabetes: lessons from Peru
Authors: Tenorio-Mucha Janeth , Lazo-Porras María , Zafra Jessica , Ewen Margaret , Beran David 
Published: November 2022

Abstract
Background
Regular measurement of the availability and use of key medicines for non-communicable diseases allows the tracking of progress to achieve equitable access to medicines. Using a country-level public sector monitoring system for medicine supply, we aim to evaluate the availability and use of losartan 50 mg tablets and metformin 850 mg tablets between 2015 and 2020 investigating the impact of different policy changes and the COVID-19 pandemic.

Methods
Data from the Peruvian National System of Medicine Supply were analyzed using an interrupted time series analysis with known and unknown structural breaks. The outcomes assessed were medicine use (monthly doses dispensed at facilities over time) and medicine availability (proportion of facilities that reported having the medicine available).

Results
The use of losartan and metformin at the primary level of care had a linear increasing trend over the period of analysis. In secondary and tertiary levels of care, there were no increases but some significant level and trend changes of doses dispensed at different times between 2017 to 2019, but none were related to the change of procurement procedures. At all levels of care, the COVID-19 onset in April 2020 caused an abrupt drop in doses dispensed especially at the primary level. Regarding availability, we found an increasing linear trend in the primary level of care for both medicines. In secondary and tertiary levels of care, the availability fluctuated between 40 and 95%. The onset of the COVID-19 pandemic did not significantly impact medicine availability, except for losartan in the tertiary level of care.

Conclusion
The availability and proper dispensing of first-line medicines for hypertension and diabetes is an essential factor for sustainable and equitable treatment. Health care systems need to be prepared for forecasting the increasing demand of medicines for chronic diseases, but also to maintain effective medicine supply chains during humanitarian crisis like pandemics.
MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
Authors: Nata’ala Muhammad Kabiru , Avila Santos Anderson P. , Coelho Kasmanas Jonas , Bartholomäus Alexander , Saraiva João Pedro , Godinho Silva Sandra , Keller-Costa Tina , Costa Rodrigo , Gomes Newton C. M. , Ponce de Leon Ferreira de Carvalho André Carlos , Stadler Peter F. , Sipoli Sanches Danilo , Nunes da Rocha Ulisses 
Published: November 2022

Abstract
Background
Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.

Results
In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as ‘ocean’. The ‘Quick Search’ and ‘Advanced Search’ tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the MarineMetagenomeDB web app to select estuarine metagenomes for potential large-scale microbial biogeography studies.

Conclusion
The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/.
Exercise-induced Brugada pattern and ventricular tachycardia during Capecitabine treatment
Authors: Strobel George B. , Ponamgi Shiva P. , Roka Attila , Aboeata Ahmed S. A. 
Published: November 2022

AbstractWe report the case of a 59-year-old female patient with no previous cardiovascular disease treated for Breast cancer with Capecitabine. Shortly after starting treatment, she developed recurrent angina. An exercise stress echocardiogram was performed, which induced a type 1 Brugada pattern 12 s of a non-sustained pleomorphic ventricular tachycardia ensued.
Algebraic topology-based machine learning using MRI predicts outcomes in primary sclerosing cholangitis
Authors: Singh Yashbir , Jons William A. , Eaton John E. , Vesterhus Mette , Karlsen Tom , Bjoerk Ida , Abildgaard Andreas , Jorgensen Kristin Kaasen , Folseraas Trine , Little Derek , Gulamhusein Aliya F. , Petrovic Kosta , Negard Anne , Conte Gian Marco , Sobek Joseph D. , Jagtap Jaidip , Venkatesh Sudhakar K. , Gores Gregory J. , LaRusso Nicholas F. , Lazaridis Konstantinos N. , Erickson Bradley J. 
Published: November 2022

Abstract
Background
Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease that can lead to cirrhosis and hepatic decompensation. However, predicting future outcomes in patients with PSC is challenging. Our aim was to extract magnetic resonance imaging (MRI) features that predict the development of hepatic decompensation by applying algebraic topology-based machine learning (ML).

Methods
We conducted a retrospective multicenter study among adults with large duct PSC who underwent MRI. A topological data analysis-inspired nonlinear framework was used to predict the risk of hepatic decompensation, which was motivated by algebraic topology theory-based ML. The topological representations (persistence images) were employed as input for classification to predict who developed early hepatic decompensation within one year after their baseline MRI.

Results
We reviewed 590 patients; 298 were excluded due to poor image quality or inadequate liver coverage, leaving 292 potentially eligible subjects, of which 169 subjects were included in the study. We trained our model using contrast-enhanced delayed phase T1-weighted images on a single center derivation cohort consisting of 54 patients (hepatic decompensation, n = 21; no hepatic decompensation, n = 33) and a multicenter independent validation cohort of 115 individuals (hepatic decompensation, n = 31; no hepatic decompensation, n = 84). When our model was applied in the independent validation cohort, it remained predictive of early hepatic decompensation (area under the receiver operating characteristic curve = 0.84).

Conclusions
Algebraic topology-based ML is a methodological approach that can predict outcomes in patients with PSC and has the potential for application in other chronic liver diseases.
Are remote psychotherapy/remediation efforts accessible and feasible in patients with schizophrenia? A narrative review
Authors: Datta Reetobaan , Vishwanath Rashmi , Shenoy Sonia 
Published: November 2022

Abstract
Background
Cognitive remediation (CR) therapy provides an effective way to improve cognitive impairments in schizophrenia. With the advent of telehealth services, especially during COVID 19 pandemic, a suitable alternative can be found in computer and cell phone-based mental health interventions. Previous studies have proven that remote mental health interventions have by and large been successful. Remote psychotherapy/CR services can now be accessed through smartphone apps, iPads, laptops and wearable devices. This has the advantage of reaching a wider population in resource-limited settings. The lack of access to technology, difficulty in using these online interventions and lack of privacy provide impediments to the delivery of care through these online platforms. Further, as some previous studies have shown, there may be a high rate of dropout in people using remote mental health resources. We aim to look at the factors, which influence the accessibility of remote mental health interventions in schizophrenia. Additionally, we test the feasibility of these interventions and look at how they compare and the potential they hold for implementation in future clinical settings.

Results
We found remote cognitive remediation to be both accessible and feasible. Concerning features, however, are the high attrition rates and the concentration of the studies in Western populations.

Conclusions
Remote interventions are a viable alternative to in-person psychotherapy when in-person resources may not always be present. They are efficacious in improving health outcomes among patients with schizophrenia. Further research into the widespread implementation of remote CR will be beneficial in informing clinical decision-making.
Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome
Authors: Smith Rebecca H. , Glendinning Laura , Walker Alan W. , Watson Mick 
Published: November 2022

AbstractMicrobiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observed that adding cultured reference genomes from the rumen to the reference database greatly improved classification rate and accuracy. We also demonstrated that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.
Brewing and biochemical characterization of Camellia japonica petal wine with comprehensive discussion on metabolomics
Authors: Majumder Soumya , Ghosh Arindam , Chakraborty Sourav , Bhattacharya Malay 
Published: November 2022

AbstractA novel wine has been developed fromCamellia japonica’s petal by fermenting the decoction withSaccharomyces cerevisiaeor brewer’s yeast. pH, brix, specific gravity and alcohol percentage were tested to study the physicochemical properties of the wine. Qualitative tests indicated presence of phenols such as flavonoids, coumarins; protein; glycosides; glycerin; terpenoids; steroids; and fatty acids in the wine. Total phenol content was found high in the decoction and in its fermented form as well. In vitro biological activities such as antioxidant activity, antidiabetic activity and lipid peroxidation inhibition power were assessed in samples. Furthermore, GC-MS analysis helped to detect volatiles present in the unfermented decoction and understand the effect of fermentation on its changing metabolome while column chromatography assisted the separation of solvent-based fractions. Notable outcomes from this study were detection of bioactive compound quinic acid in the decoction and a proposed pathway of its metabolic breakdown after fermentation. Results of this research revealed biochemical and physicochemical acceptability of this wine prepared from an underutilized flower.Graphical Abstract