bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of multiple binding sites for LAMP primers across P. falciparum genome improves detection of the parasite from whole blood samples
Authors: Mgawe Cavin , Shilluli Clement , Nyanjom Steven , Odari Eddy , Linnes Jacqueline C. , Kanoi Bernard N. , Gitaka Jesse , Ochola Lucy 
Published: December 2023

IntroductionMalaria remains a significant health concern, particularly in regions with widespread prevalence. As the transmission rates decrease, there is a rise in low-density infections with the causative parasite, P. falciparum, that often escape detection through standard point-of-care diagnostic tools. In-low transmission areas, even few undetected cases can trigger outbreaks, necessitating rapid and sensitive diagnostics. Loop-mediated isothermal Amplification (LAMP) stands out as a nucleic acid technique that can easily utilizes un-processed samples such of saliva, urine, and lysed whole blood templates for a sensitive detection. However, most nucleic acid tests detect genes with few copies per parasite making it difficult to detect low-density parasitaemia.MethodsWe selected Pfr364 multi-copy repeats of the P. falciparum genome as a target for amplification due to their higher copy number, ideal for rapid amplification, addressing amplification drawbacks of limited parasites DNA. We used a sequence clustering approach to design a novel set of LAMP primers, capable of binding to multiple sites. Subsequently, we developed a hydroxynaphthol blue (HNB) colorimetric LAMP assay, using genomic DNA obtained from the 3D7 strain cultivated in vitro. This assay’s performance was validated using archived clinical samples of both whole blood and matched saliva, ensuring accuracy through comparative analysis against gold standard, nested PCR, targeting the 18S RNA gene.ResultsThe HNB-LAMP assay achieved rapid amplification within 15 minutes and exhibited high sensitivity with a limit of detection of 1 parasite. Further, the LAMP assay was robust in whole blood lysed with Triton X-100 and heat-treated saliva clinical samples. Against nested PCR, the assay showed sensitivity of 100% for whole blood and 40% for saliva samples. Moreover, co-analysis with the nested PCR showed a perfect agreement between the two techniques. (K = 0.99 for whole blood, and 0.66 for saliva).ConclusionOur study presents a method for detecting P. falciparum using LAMP, which results in increased sensitivity, shorter assay times, and a simpler workflow than nucleic acid tests relying on conventional DNA extraction and additional equipment for result interpretation. These findings hold great promise for improved malaria diagnosis, especially in settings where low-density parasitaemia is prevalent and rapid and accurate malaria detection is crucial.
The involvement of brain regions associated with lower KPS and shorter survival time predicts a poor prognosis in glioma
Authors: Bao Hongbo , Wang Huan , Sun Qian , Wang Yujie , Liu Hui , Liang Peng , Lv Zhonghua 
Published: December 2023

BackgroundIsocitrate dehydrogenase-wildtype glioblastoma (IDH-wildtype GBM) and IDH-mutant astrocytoma have distinct biological behaviors and clinical outcomes. The location of brain tumors is closely associated not only with clinical symptoms and prognosis but also with key molecular alterations such as IDH. Therefore, we hypothesize that the key brain regions influencing the prognosis of glioblastoma and astrocytoma are likely to differ. This study aims to (1) identify specific regions that are associated with the Karnofsky Performance Scale (KPS) or overall survival (OS) in IDH-wildtype GBM and IDH-mutant astrocytoma and (2) test whether the involvement of these regions could act as a prognostic indicator.MethodsA total of 111 patients with IDH-wildtype GBM and 78 patients with IDH-mutant astrocytoma from the Cancer Imaging Archive database were included in the study. Voxel-based lesion-symptom mapping (VLSM) was used to identify key brain areas for lower KPS and shorter OS. Next, we analyzed the structural and cognitive dysfunction associated with these regions. The survival analysis was carried out using Kaplan–Meier survival curves. Another 72 GBM patients and 48 astrocytoma patients from Harbin Medical University Cancer Hospital were used as a validation cohort.ResultsTumors located in the insular cortex, parahippocampal gyrus, and middle and superior temporal gyrus of the left hemisphere tended to lead to lower KPS and shorter OS in IDH-wildtype GBM. The regions that were significantly correlated with lower KPS in IDH-mutant astrocytoma included the subcallosal cortex and cingulate gyrus. These regions were associated with diverse structural and cognitive impairments. The involvement of these regions was an independent predictor for shorter survival in both GBM and astrocytoma.ConclusionThis study identified the specific regions that were significantly associated with OS or KPS in glioma. The results may help neurosurgeons evaluate patient survival before surgery and understand the pathogenic mechanisms of glioma in depth.
Screening for sleep apnoea risk in testosterone-treated transgender men
Authors: Šnobrová Bára , Burdová Kristina , Weiss Vladimír , Šonka Karel , Weiss Petr 
Published: December 2023

IntroductionObstructive sleep apnoea (OSA) is more prevalent in men. Several studies suggested that higher testosterone levels were associated with a greater risk of OSA. We aimed to determine whether testosterone administration in transgender men would accentuate symptoms of OSA.MethodsThe study involved 94 adult people undergoing a female-to-male transition with testosterone administration. The participants answered the Berlin Questionnaire (BQ) and a separate question on snoring before starting testosterone treatment and after at least 1 year of being on testosterone treatment.ResultsA higher proportion of participants at the follow-up answered positively to the first category of BQ devoted to snoring. A lower proportion of participants at follow-up answered positively to the second category of BQ devoted to tiredness. The percentage of subjects with a high risk of sleep apnoea, according to BQ, and of those who answered the question on snoring positively did not change significantly.ConclusionAn increased number of transgender men who reported snoring in BQ after testosterone administration indicate a higher risk of OSA development.
Associations of multiple toxic metal exposures with metabolic dysfunction-associated fatty liver disease: NHANES 2011–2018
Authors: Li Yuguang , Liu Zefeng , Chang Yu , Chen Naifei , Zhang Rong , Liu Xiangliang , Song Wei , Lu Jin 
Published: December 2023

BackgroundThe occurrence of metabolic dysfunction-associated fatty liver disease (MASLD) is driven by multiple factors including obesity, hypertension, dyslipidemia, and insulin resistance. However, epidemiological research investigating the association between metal exposure and MASLD occurrence remains limited.MethodsWe conducted a large cross-sectional study with 6,520 participants who were involved in the National Health and Nutrition Examination Survey (NHANES) between 2011 and 2018. Using generalized linear regression, we examined the relationship between five heavy metals (mercury, manganese, lead, selenium, cadmium) and MASLD. Furthermore, restricted cubic spline models and weighted quantile sum (WQS) analysis were employed to characterize the exposure-response relationship between the five metals and MASLD.ResultsHigher blood selenium levels were associated with an increased likelihood of MASLD among US adults. Blood lead exposure was also positively correlated with MASLD risk. However, there was no significant association observed between blood cadmium, mercury, manganese levels, and MASLD risk. Among the five metals, blood cadmium exposure accounted for the highest proportion of MASLD risk.ConclusionOur study indicated the significant association between blood cadmium and lead exposure levels and the occurrence of MASLD in a representative sample of US adults.
Treatment patterns and clinical outcomes in 157 patients with extensive-stage small cell lung cancer: real-world evidence from a single-center retrospective study
Authors: Zheng Yumin , Tan Kexin , Wang Aolin , Lu Xingyu , Dong Huijing , Li Jia , Cui Huijuan 
Published: December 2023

BackgroundImmune checkpoint inhibitors (ICIs) have changed the therapeutic options for extensive-stage small-cell lung cancer (ES-SCLC). In this real-world study, we analyzed the treatment patterns in patients with ES-SCLC and evaluated the efficacy of chemotherapy combined with immunotherapy as first-line therapy.MethodsA retrospective analysis was performed on patients with ES-SCLC who received treatment at China-Japan Friendship Hospital (Beijing, China) between August 1, 2020, and April 30, 2023. The treatment patterns appeared in the form of Sunburst Chart and Sankey diagram. The survival analyses were conducted by Kaplan-Meier curves.ResultsA total of 157 patients with ES-SCLC were retrospectively included. According to first-line therapy, patients were divided into the chemotherapy (CT) group (n=82) and chemo-immunotherapy (CIT) group (n=75). The median treatment lines were 2[1, 2] and cycles were 8[5, 12], respectively. 82 patients received the second line of therapy, followed by 37 for the third, 15 for the fourth, 11 for the fifth, and 5 for the sixth. Overall, the treatment patterns involved 11 options including 12 chemotherapy regimens, 11 ICIs, and 4 targeted agents. The second-line treatment pattern had the most options (9) and regimens (43). In the first 3 lines, chemotherapy was the largest proportion of treatment options. The addition of ICIs prolonged progression-free survival from 6.77 (95% confidence interval [CI], 6.00-7.87) to 7.33 (95% CI, 6.03-9.80) months (hazard ratio [HR]=0.67, 95% CI, 0.47-0.95; P=0.025), overall survival from 12.97 (10.90-23.3) to 14.33 (12.67-NA) months without statistically significant difference (HR=0.86, 95% CI, 0.55-1.34; P=0.505).ConclusionThe treatment options of patients with ES-SCLC are more diversified. Combination therapy is the current trend, where chemotherapy is the cornerstone. Meanwhile, ICIs participate in almost all lines of treatment. However, the clinical efficacy remains barely satisfactory. We are urgently expecting more breakthrough therapies except immunology will be applied in the clinic.
Diagnostic utility of lung ultrasound in predicting the need for surfactant therapy in preterm neonates with respiratory distress
Authors: Singh Pari , Patnaik Suprabha , Verma Arjun , Garegrat Reema , Maheshwari Rajesh , Suryawanshi Pradeep 
Published: December 2023

BackgroundLung ultrasound is an accurate and early predictor for surfactant replacement therapy in respiratory distress syndrome (RDS) as compared to clinical parameters and chest x-ray. However, lung pathologies for respiratory distress at birth have overlapping symptomatology and low middle-income countries have a higher incidence of congenital pneumonia, in addition to RDS, making the immediate diagnosis difficult. Thus, there is a need for assessing a cutoff for lung ultrasound scores in the given setting.ObjectivesThe primary objective was to determine the diagnostic accuracy of the lung ultrasound score (LUS) in predicting the need for surfactant therapy in preterm neonates with respiratory distress. Secondary objectives were to correlate LUS with corresponding oxygen saturation to the fraction of inspired oxygen ratio (SpO2/FiO2), arterial/Alveolar oxygen pressure ratio (a/A), and chest x-ray (CXR) findings.MethodologyA prospective observational study was carried out at a tertiary-level neonatal intensive care unit in India in 2022 enrolling 100 neonates &lt;34 weeks gestational age with respiratory distress at birth. After initial stabilization of the neonate, LUS was performed and baseline parameters were noted. Surfactant was administered as per the 2019 European Consensus guidelines and LUS was repeated after 6 h of therapy.ResultsThe mean gestation of enrolled neonates was 31.06 ± 2.12 weeks and the mean birthweight was 1,412 ± 391 g. Approximately 58% were diagnosed with RDS and 30% had congenital pneumonia. Surfactant was administered to 40% of neonates. The cutoff LUS for surfactant therapy was 7 [area under the curve (AUC) 0.977; 95% CI, 0.947–1; P &lt; 0.001; with sensitivity 92.5%, specificity 96.67%, PPV 94.87%, and NPV 95.08%] and the cutoff LUS for the second dose of surfactant was 10 (AUC 0.964; 95% CI, 0.913–1; P &lt; 0.001). The score decreased by 3.24 (2.44–4.05) after 6 h of the first dose and correlated significantly with SpO2/FiO2 ratio (−0.750), a/A ratio (−0.650), and CXR findings (0.801).ConclusionThe study predicted an optimal LUS cutoff of 7 and 10 for the need for the first dose of surfactant and re-treatment, respectively, in neonates &lt;34 weeks gestational age with respiratory distress.
Online information and availability of three doping substances (anabolic agents) in sports: role of pharmacies
Authors: Garcia Juan F. , Seco-Calvo Jesús , Arribalzaga Soledad , Díez Raquel , Lopez Cristina , Fernandez M. Nelida , Garcia Juan J. , Diez M. Jose , de la Puente Raul , Sierra Matilde , Sahagún Ana M. 
Published: December 2023

Background: The Internet has become an important source for easy access to doping substances, where people and athletes may acquire, outside pharmacies and without a (medical) prescription. These online websites do not always offer quality-assured products, and are outside the regular distribution channels of medicines. The aim of this study was to estimate the availability and accessible information on the Internet about the sale of three doping substances (oxandrolone, DHEA, androstenedione).Methods: Cross-sectional exploratory study, being an observation at a point in time of the online availability of these three doping substances (WADA S1 category: anabolic agents), purchased from Spain, Puerto Rico, Canada, United States, Ukraine and Russia. The characteristics of the websites, the countries the webs sold to, the pharmaceutical forms offered and the recommendations for its use were analyzed by using a computer tool designed ad hoc.Results: There were significant differences between countries in the number of webpages that sold the products (Chi-square test, p &lt; 0.05). Oxandrolone was available for purchase mainly when buying from Spain (27.12%) and Ukraine (26.58%), in websites dedicated to sports (77.26%). For DHEA, most of the pages offered it if the search was done from Canada (23.34%) and Russia (21.44%). Products containing androstenedione or DHEA are claimed to enhance sports performance or for sports use without providing details. Compared to the total number of websites checked, the proportion of pharmacies offering these products was low, ranging from 4.86% for DHEA to 15.79% for androstenedione.Conclusion: The three substances selected are easily available without control through the Internet. Only a small number of websites offering them were online pharmacies, and requested a prescription. Most of the doping substances are purchased from the country where they are requested. Product information described benefits for sports performance, but did not do the same with their side effects. It would be advisable for these products to be sold through pharmacies, to guarantee their quality and provide evidence-based information on their safe use, benefits and risks, and only with a prescription. Athletes should be encouraged to consult health professionals about those supplements suitable for their type of training and sports objectives.
Thyroid function, renal function, and depression: an association study
Authors: Liang Hai , Wang Jin-min , Wei Xiao-qian , Su Xiao-qin , Zhang Bi-xia 
Published: December 2023

ObjectiveTo investigate the correlations between thyroid function, renal function, and depression.MethodsClinical data of 67 patients with Major depressive disorder (MDD) and 36 healthy control subjects between 2018 and 2021 were collected to compare thyroid and renal function. Thyroid and renal functions of depressed patients were then correlated with the Hamilton Depression Rating Scale (HAMD) and the Hamilton Anxiety Rating Scale (HAMA).Spearman correlation analysis was used to find the correlation between renal function, thyroid function, and depression. A logistic regression was performed to find significant predictors of depression.ResultsTriiodothyronine protamine (T3), thyroxine (T4), free triiodothyronine protamine (FT3), uric acid, sodium, and anion gap were lower in the MDD group than in the control group (p &lt; 0.05). Correlation analysis of thyroid function, renal function, and factor terms of HAMD in the MDD group suggested that diurnal variation, hopelessness, and depression level were positively correlated with thyrotropin (TSH) (p &lt; 0.05). Cognitive disturbance, retardation, and depression level were negatively correlated with creatinine (p &lt; 0.05). Diurnal variation was negatively correlated with sodium ion (p &lt; 0.01); hopelessness and depression level were positively correlated with chloride ion (p &lt; 0.05); diurnal variation, retardation, and depression level were negatively correlated with anion gap (p &lt; 0.05). Diurnal variation (p &lt; 0.01) and retardation (p &lt; 0.05) were negatively correlated with osmolality. Cognitive disturbance and depression level were positively correlated with estimated glomerular filtration rate (eGFR) (p &lt; 0.05). In the MDD group, correlation analysis of thyroid function, renal function, and HAMA factor terms suggested that the total HAMA score and anxiety level were positively correlated with chloride ion (p &lt; 0.05); psychic anxiety, total HAMA score, and anxiety level were negatively correlated with anion gap (p &lt; 0.05). Furthermore, a low level of anion gap was an independent risk factor for depression and anxiety levels (p &lt; 0.05).ConclusionLow thyroid function and reduced waste metabolized by the kidneys in patients with MDD suggest a low intake and low metabolism in depressed patients. In addition, subtle fluctuations in the anion gap in depressed patients were strongly correlated with the degree of depression and anxiety.
Mindfulness to improve the mental health of university students. A systematic review and meta-analysis
Authors: González-Martín Ana María , Aibar-Almazán Agustín , Rivas-Campo Yulieth , Castellote-Caballero Yolanda , Carcelén-Fraile María del Carmen 
Published: December 2023

ObjectivesThis systematic review and meta-analysis was to analyze the effects of a mindfulness program on mental health in university students.MethodsA systematic review was conducted using the databases Pubmed, Scopus, Web of Science and CINAHL. The selected studies had to incorporate a mindfulness intervention in university students. The methodological quality of the collected articles was evaluated using the PEDro scale.ResultsWe initially identified 321 studies, of which 21 were included in this review. The interventions focused on mindfulness with durations ranging from 8 weeks to 3 months. The results demonstrated significant effects of a mindfulness intervention on mental health in university students.ConclusionThis systematic review and meta-analysis found that mindfulness is effective for improving the mental health of college students.Systematic Review Registrationidentifier: CRD42023441453.
classLog: Logistic regression for the classification of genetic sequences
Authors: Zeller Michael A. , Arendsee Zebulun W. , Smith Gavin J.D. , Anderson Tavis K. 
Published: December 2023

IntroductionSequencing and phylogenetic classification have become a common task in human and animal diagnostic laboratories. It is routine to sequence pathogens to identify genetic variations of diagnostic significance and to use these data in realtime genomic contact tracing and surveillance. Under this paradigm, unprecedented volumes of data are generated that require rapid analysis to provide meaningful inference. MethodsWe present a machine learning logistic regression pipeline that can assign classifications to genetic sequence data. The pipeline implements an intuitive and customizable approach to developing a trained prediction model that runs in linear time complexity, generating accurate output rapidly, even with incomplete data. Our approach was benchmarked against porcine respiratory and reproductive syndrome virus (PRRSv) and swine H1 influenza A virus (IAV) datasets. Trained classifiers were tested against sequences and simulated datasets that artificially degraded sequence quality at 0, 10, 20, 30, and 40%. ResultsWhen applied to a poor-quality sequence data, the classifier achieved between &gt;85% to 95% accuracy for the PRRSv and the swine H1 IAV HA dataset and this increased to near perfect accuracy when using the full dataset. The model also identifies amino acid positions used to determine genetic clade identity through a feature selection ranking within the model. These positions can be mapped onto a maximum-likelihood phylogenetic tree, allowing for the inference of clade defining mutations. DiscussionOur approach is implemented as a python package with code available at https://github.com/flu-crew/classLog.
Eicosanoids and Related Metabolites Associated with ESKD in a Community-Based Cohort
Authors: Surapaneni Aditya L. , Schlosser Pascal , Rhee Eugene P. , Cheng Susan , Jain Mohit , Alotaiabi Mona , Coresh Josef , Grams Morgan E. 
Published: December 2023

Key Points

High-throughput eicosanoid profiling can identify metabolites that may play a protective role in the development of kidney disease.In contrast to many other nonlipid metabolites, eicosanoid levels are minimally related with kidney filtration cross-sectionally.

Background
Eicosanoids are derivatives of polyunsaturated fatty acids and participate in the inflammatory response and the maintenance of endothelial function. Specific eicosanoids have been linked to various diseases, including hypertension and asthma, and may also reduce renal blood flow. A systematic investigation of eicosanoid-related metabolites and adverse kidney outcomes could identify key mediators of kidney disease and inform ongoing work in drug development.

Methods
Profiling of eicosanoid-related metabolites was performed in 9650 participants in the Atherosclerosis Risk in Communities Study (visit 2; mean age, 57 years). The associations between metabolite levels and the development of ESKD was investigated using Cox proportional hazards regression (n=256 events; median follow-up, 25.5 years). Metabolites with statistically significant associations with ESKD were evaluated for a potential causal role using bidirectional Mendelian randomization techniques, linking genetic instruments for eicosanoid levels to genomewide association study summary statistics of eGFR.

Results
The 223 eicosanoid-related metabolites that were profiled and passed quality control (QC) were generally uncorrelated with eGFR in cross-sectional analyses (median Spearman correlation, −0.03; IQR, −0.05 to 0.002). In models adjusted for multiple covariates, including baseline eGFR, three metabolites had statistically significant associations with ESKD (P value < 0.05/223). These included a hydroxyoctadecenoic acid, a dihydroxydocosapentaenoic acid, and arachidonic acid, with higher levels of the former two protective against ESKD and higher levels of arachidonic acid having a positive association with risk of ESKD. Mendelian randomization analyses suggested a causal role for the hydroxyoctadecenoic and arachidonic acid in determining eGFR. Spectral analysis identified the former metabolite as either 11-hydroxy-9-octadecenoic acid or 10-hydroxy-11-octadecenoic acid.

Conclusions
High-throughput eicosanoid profiling can identify metabolites that may play a protective role in the development of kidney disease.