Miracle-dz/UniFAR-FTUs huggingface dataset:
MS‐Net: Learning to assess the malignant status of a lung nodule by a radiologist and her peers

Abstract Background Automatically assessing the malignant status of lung nodules based on CTscan images can help reduce the workload of radiologists while improving their diagnostic accuracy. Purpose Despite remarkable progress in the automatic diagnosis of pulmonary nodules by deep learning technologies, two significant problems remain outstanding. First, end‐to‐end deep learning solutions tend to neglect the empirical (semantic) features accumulated by radiologists and only rely on automatic features discovered by neural networks to provide the final diagnostic results, leading to questionable reliability, and interpretability. Second, inconsistent diagnosis between radiologists, a widely acknowledged phenomenon in clinical settings, is rarely examined and quantitatively explored by existing machine learning approaches. This paper solves these problems. Methods We propose a novel deep neural network called MS‐Net, which comprises two sequential modules: A feature derivation and initial diagnosis module (FDID), followed by a diagnosis refinement module (DR). Specifically, to take advantage of accumulated empirical features and discovered automatic features, the FDID model of MS‐Net first derives a range of perceptible features and provides two initial diagnoses for lung nodules; then, these results are fed to the subsequent DR module to refine the diagnoses further. In addition, to fully consider the individual and panel diagnosis opinions, we propose a new loss function called collaborative loss, which can collaboratively optimize the individual and her peers’ opinions to provide a more accurate diagnosis. Results We evaluate the performance of the proposed MS‐Net on the Lung Image Database Consortium image collection (LIDC‐IDRI). It achieves 92.4% of accuracy, 92.9% of sensitivity, and 92.0% of specificity when panel labels are the ground truth, which is superior to other state‐of‐the‐art diagnosis models. As a byproduct, the MS‐Net can automatically derive a range of semantic features of lung nodules, increasing the interpretability of the final diagnoses. Conclusions The proposed MS‐Net can provide an automatic and accurate diagnosis of lung nodules, meeting the need for a reliable computer‐aided diagnosis system in clinical practice.
A qualitative study exploring perceptions of people living with HIV using antiretroviral therapy on self-management of healthy nutrition and the related healthcare service in Ethiopia

ABSTRACT In Ethiopia, undernutrition is a quite common health problem among people living with HIV. Unlike in developed countries, nutritional counseling for people living with HIV has not received much attention. This study aimed to explore the perception of people living with HIV on their dietary practice and the existing health care service in Ethiopia. A phenomenological qualitative study was conducted in two hospitals in southern Ethiopia from March to June 2018. A pre-tested interview guide was prepared in English and translated into the Amharic language. The data were collected using key informant interviews, focus group discussions and observations in the ART clinics by six trained nurses. The data were analyzed thematically. Almost all focus group discussion participants mentioned that a healthy diet for ART patients is very important. The majority of the participants mentioned that they were not satisfied with the counseling service given at the ART clinics. Lack of training for health care professionals on nutritional counseling was also reported as a challenge by the nurses themselves. Nutritional counseling given by health care professionals at the ART clinic was poor. Emphasis should be given to the training of healthcare professionals working in ART clinics on nutritional counseling.
Variation in State-Level Mammography Use, 2012 and 2020

Objectives: Mammography is a screening tool for early detection of breast cancer. Uptake in screening use in states can be influenced by Medicaid coverage and eligibility policies, public health outreach efforts, and the Centers for Disease Control and Prevention–funded National Breast and Cervical Cancer Early Detection Program. We described state-specific mammography use in 2020 and changes as compared with 2012. Methods: We estimated the proportion of women aged ≥40 years who reported receiving a mammogram in the past 2 years, by age group, state, and demographic and socioeconomic characteristics, using 2020 Behavioral Risk Factor Surveillance System data. We also compared 2020 state estimates with 2012 estimates. Results: The proportion of women aged 50-74 years who received a mammogram in the past 2 years was 78.1% (95% CI, 77.4%-78.8%) in 2020. Across measures of socioeconomic status, mammography use was generally lower among women who did not have health insurance (52.0%; 95% CI, 48.3%-55.6%) than among those who did (79.9%; 95% CI, 79.3%-80.6%) and among those who had a usual source of care (49.4%; 95% CI, 46.1%-52.7%) than among those who did not (81.0%; 95% CI, 80.4%-81.7%). Among women aged 50-74 years, mammography use varied across states, from a low of 65.2% (95% CI, 61.4%-69.0%) in Wyoming to a high of 86.1% (95% CI, 83.8%-88.3%) in Massachusetts. Four states had significant increases in mammography use from 2012 to 2020, and 8 states had significant declines. Conclusion: Mammography use varied widely among states. Use of evidence-based interventions tailored to the needs of local populations and communities may help close gaps in the use of mammography.
An expectation–maximization framework for comprehensive prediction of isoform-specific functions

Abstract Motivation Advances in RNA sequencing technologies have achieved an unprecedented accuracy in the quantification of mRNA isoforms, but our knowledge of isoform-specific functions has lagged behind. There is a need to understand the functional consequences of differential splicing, which could be supported by the generation of accurate and comprehensive isoform-specific gene ontology annotations. Results We present isoform interpretation, a method that uses expectation–maximization to infer isoform-specific functions based on the relationship between sequence and functional isoform similarity. We predicted isoform-specific functional annotations for 85 617 isoforms of 17 900 protein-coding human genes spanning a range of 17 430 distinct gene ontology terms. Comparison with a gold-standard corpus of manually annotated human isoform functions showed that isoform interpretation significantly outperforms state-of-the-art competing methods. We provide experimental evidence that functionally related isoforms predicted by isoform interpretation show a higher degree of domain sharing and expression correlation than functionally related genes. We also show that isoform sequence similarity correlates better with inferred isoform function than with gene-level function. Availability and implementation Source code, documentation, and resource files are freely available under a GNU3 license at https://github.com/TheJacksonLaboratory/isopretEM and https://zenodo.org/record/7594321.
Is the use of Tenofovir Dipivoxil fumarate effective and safe in preventing vertical transmission in pregnant women with chronic HBV with high viral load?

OBJECTIVE In our country, transmission from mother to baby is the most common form of transmission of viral hepatitis B. A high viral load in the mother and HBeAg positivity pose the greatest risk of transmission from mother to baby. The best way to prevent this is to try to eliminate the viral load in the mother by using a strong antiviral such as prenatal TDF in mothers with a high viral load during pregnancy. This study aimed to evaluate the efficacy and safety of TDF in pregnant women with high viral load. PATIENTS AND METHODS Seventy patients with hepatitis B e-antigen positive and negative were included in the retrospective study conducted in our clinic. In 35 cases, pregnant women with HBeAg (+) positive chronic HBV and HBV-DNA levels of 107 copies/mL were between 18 and 27 weeks of pregnancy. The pregnant women took 300 mg of TDF per day. There were 35 untreated HBeAg-negative, chronic HBV patients in the control group. Babies born to HBeAg-positive and HBeAg-negative mothers are given an initial dose of 200 IU of hepatitis B immune globulin (HBIG) and 20 g of recombinant hepatitis B vaccine in the first 12 hours after birth, followed by 4, 8, and 24 weeks. HBsAg and HBV-DNA findings were examined in newborn serum 28 weeks after birth. RESULTS Postpartum 28 weeks, none of the babies born to HBeAg-positive mothers treated with TDF had HBsAg positivity, while 3.5% of babies born to HBeAg-negative mothers and not treated with TDF had HBsAg positivity and immunoprophylaxis failure. There was no statistically significant difference between the treatment and control groups regarding maternal height, weight, gestational age, or congenital malformations (p<0.05). There was no significant difference between the side effects seen in mothers. In the examination performed at the 28th week postpartum, a statistically significant decrease in HBV-DNA levels was observed in mothers who received TDF treatment compared to those who did not (88.5%) (p<0.05). In 31 of the 35 patients receiving TDF treatment, ALT was reported to be normalized in 25 of the 35 patients who did not receive TDF treatment (p<0.05). CONCLUSIONS It has been observed that the use of TDF, which has a strong efficacy and high barrier, in the second and/or third trimester of pregnancy reduces transmission rates without causing side effects in both the mother and the newborn, thereby preventing vertical transmission of viral hepatitis B from the mother to child.
A Molecular and Epidemiological Study of Cholera Outbreak in Sulaymaniyah Province, Iraq, in 2022

Abstract Cholera is a disease caused by a Gram-negative bacterium Vibrio cholerae and is among the significant threats to global public health. The disease is mainly spread in the hot months of the year; low sanitation and lack of clean water are the major causes of the disease. In this study, we conducted a molecular and epidemiological study of the recent outbreak in the city of Sulaymaniyah in Iraq. Based on the bacteriological, serological, and molecular identification of the bacterium, it was shown that V. cholerae O1 serotype Ogawa caused the disease. Additionally, the number of positive cholera cases were higher in June compared to July (391 positive cases in June and 23 in July). Moreover, the majority (> 60%) of the cholera cases were recorded among 20–44-year-old people in both months; however, there was no significant difference in the patient genders diagnosed every month. Overall, this is the first report on the recent cholera outbreak in the city of Sulaimaniyah in Iraq.
Constraints on accessing abstract source information : instantiation of principles facilitates children's analogical transfer

An abstract principle provided as source information alone often fails to enhance analogical transfer. Two experiments were conducted to investigate the circumstances under which an abstract statement promotes analogical problem solving in children. External instantiation (providing concrete examples, with similar or dissimilar surface features along with an abstract statement) and internal instantiation (encouraging learners to generate concrete examples of the abstract statement) were equally effective in facilitating transfer. Adding explicit causal relations in the source statements did not significantly enhance transfer. These results suggest that abstract information by itself is less accessible because it lacks superficial features similar to the target problem and lacks example-specific contextual information. Educational implications of the effects of external and internal instantiations are discussed.
Tumor Necrosis Receptor Superfamily Interact with Fusion and Fission of Mitochondria of Adipose Tissue in Obese Patients without Type 2 Diabetes

Interactions between receptors and ligands of the tumor necrosis factor superfamily (TNFSF) provide costimulatory signals that control the survival, proliferation, differentiation, and effector function of immune cells. All components of the TNF superfamily are associated with NF-kB functions that are not limited to cell death and may promote survival in the face of adipose tissue inflammation in obesity. Inflammation dysfunction of mitochondria is a key factor associated with insulin resistance in obesity. The aim of the study was to analyze the relationship of soluble forms of receptors and ligands of the TNF superfamily in blood plasma with mitochondrial dynamics in adipose tissue (greater omentum (GO) and subcutaneous adipose tissue (Sat)) of obese patients with and without type 2 diabetes mellitus (T2DM). Increased plasma sTNF-R1, sTNF-R2, sTNFRSF8 receptors, and ligands TNFSF12, TNFSF13, TNFSF13B are characteristic of obese patients without T2DM. The TNF-a levels in blood plasma were associated with a decrease in MFN2 gene expression in GO and IL-10 in blood plasma. The TNFSF12 levels contributed to a decrease in glucose levels, a decrease in BMI, and an increase in IL-10 levels by influencing the MFN2 gene expression in GO, which supports mitochondrial fusion.
Novel Measures of Arterial Hemodynamics and Wave Reflections Associated With Clinical Outcomes in Patients With Heart Failure.

Background Arterial stiffness and earlier wave reflections can increase afterload and impair cardiovascular function. Most prior studies have been performed in patients with preserved left ventricular function. We describe novel measures of pulsatile arterial hemodynamics and their association with clinical outcomes in patients with heart failure with reduced ejection fraction. Methods and Results Participants with heart failure with reduced ejection fraction (n=137, median age 56 years, 49% women, 58% Black) and age-matched healthy controls (n=124) underwent measurements of large artery stiffness and pulsatile arterial hemodynamics. Carotid-femoral pulse wave velocity and augmentation index were assessed using radial applanation tonometry. Pressure-flow analyses derived reflected wave transit time, the systolic pressure-time integral imposed by proximal aortic characteristic impedance, and the pressure-time integral from wave reflection (wasted pressure effort). Cox proportional hazards models defined associations between hemodynamic measures and (1) all-cause death and (2) a combined end point of left ventricular assist device implant, heart transplant, and death, at 2 years adjusted for race, BNP (B-type natriuretic peptide), and the Meta-Analysis Global Group in Chronic Heart Failure Risk Score. Compared with controls, participants with heart failure with reduced ejection fraction exhibited similar carotid-femoral pulse wave velocity (6.8±1.6 versus 7.0±1.6 m/s, P=0.40) but higher augmentation index normalized to a heart rate of 75 bpm (13±2% versus 22±2%, P<0.001). Shorter reflected wave transit time (ie, earlier wave reflection arrival to the proximal aorta) was associated with an increased risk of death (adjusted hazard ratio [aHR] 1.67 [95% CI 1.03-1.63]) and the combined end point of death/left ventricular assist device/heart transplant (aHR, 1.61 [95% CI, 1.06-2.44]) at 2 years. Wasted pressure effort/proximal aortic characteristic impedance, representing the proportion of systolic load from wave reflection versus aortic root characteristic impedance, was univariately associated with death (hazard ratio (HR), 1.44 [95% CI, 1.05-1.97]) and with death/left ventricular assist device/heart transplant on univariate (HR, 1.42 [95% CI, 1.07-1.88]) and multivariable (aHR, 1.40 [95% CI, 1.02-1.93]) analysis. Conclusions Increased left ventricular systolic load from premature wave reflections is associated with adverse clinical outcomes in patients with heart failure with reduced ejection fraction.
Long-Term Outcomes of Depression Treatment With Hypnotherapy or Cognitive Behavioral Therapy

Abstract In a recent randomized controlled trial of mild to moderate depression, hypnotherapy (HT) was noninferior to cognitive behavioral therapy (CBT) after 6 months of outpatient treatment. In the present article, we extended the results in a secondary analysis and investigated how HT compares with CBT 1) during the course of the self-rated depressive symptoms throughout the 12-month follow-ups, 2) with regard to the rates of full remission, and 3) for the time to remission after treatment. Of the 152 randomized patients with current depression, 136 were available for the follow-up analyses. The course of self-rated depressive symptoms during follow-ups was analyzed with linear mixed-effects models. Time to a full remission, defined as eight consecutive weeks without depression, was compared between groups in a survival analysis. The self-reported depressive symptoms could be maintained on a low symptom level during the 12-month follow-up for both HT and CBT. Overall, both treatments achieved comparably high long-term remission rates of 73% after a median of 30 weeks. Outpatient psychotherapy with HT achieved good long-term results mostly comparable to CBT.
Epigenetic Regulation of Inflammatory Mechanisms and a Psychological Symptom Cluster in Patients Receiving Chemotherapy

Background A psychological symptom cluster is the most common cluster identified in oncology patients. Although inflammatory mechanisms are hypothesized to underlie this cluster, epigenetic contributions are unknown. Objectives This study’s purpose was to evaluate associations between the occurrence of a psychological symptom cluster and levels of DNA methylation for inflammatory genes in a heterogeneous sample of patients with cancer receiving chemotherapy. Methods Prior to their second or third cycle of chemotherapy, 1,071 patients reported the occurrence of 38 symptoms using the Memorial Symptom Assessment Scale. A psychological cluster was identified using exploratory factor analysis. Differential methylation analyses were performed in two independent samples using Illumina Infinium 450K and EPIC microarrays. Expression-associated CpG (eCpG) loci in the promoter region of 114 inflammatory genes on the 450K and 112 genes on the EPIC microarray were evaluated for associations with the psychological cluster. Robust rank aggregation was used to identify differentially methylated genes across both samples. Significance was assessed using a false discovery rate of 0.05 under the Benjamini–Hochberg procedure. Results Cluster of differentiation 40 (CD40) was differentially methylated across both samples. All six promoter eCpGs for CD40 that were identified across both samples were hypomethylated in the psychological cluster group. Conclusions This study is the first to suggest associations between a psychological symptom cluster and differential DNA methylation of a gene involved in tissue inflammation and cell-mediated immunity. Our findings suggest that increased CD40 expression through hypomethylation of promoter eCpG loci is involved in the occurrence of a psychological symptom cluster in patients receiving chemotherapy. These findings suggest a direction for mechanistic studies.
Electron-phonon coupling in La3In under pressure

Conventional superconducting parameters Eliashberg spectral function, phonon DOS, average electron-phonon coupling constant & superconducting transition temperature of La3In were calculated at ambient and applied positive hydrostatic pressure. Ambient pressure electron-phonon coupling constant was found to be 1.43 and superconducting transition temperature was calculated to be 8.7 K which is close to the experimental reported value of 9.5 K. Logarithmic average phonon frequency at ambient pressure was found to be 6.21 × 10−3 eV. Phonon dispersion relations for the ambient and applied positive hydrostatic pressure were calculated to confirm the dynamical stability of La3In under positive pressure. Acoustic modes of vibrations were found to mediate most of the electron-phonon-electron interaction with a very small contribution from optical modes of vibrations. Fermi surface at ambient pressure was also calculated and employed in explaining the large value of the calculated electron-phonon coupling constant. The effect of spin–orbit coupling on electronic, phonon and superconducting properties of La3In was also studied.
Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae

Abstract The Paf1 complex (Paf1C) is a conserved transcription elongation factor that regulates transcription elongation efficiency, facilitates co-transcriptional histone modifications, and impacts molecular processes linked to RNA synthesis, such as polyA site selection. Coupling of the activities of Paf1C to transcription elongation requires its association with RNA polymerase II (Pol II). Mutational studies in yeast identified Paf1C subunits Cdc73 and Rtf1 as important mediators of Paf1C association with Pol II on active genes. While the interaction between Rtf1 and the general elongation factor Spt5 is relatively well-understood, the interactions involving Cdc73 have not been fully elucidated. Using a site-specific protein cross-linking strategy in yeast cells, we identified direct interactions between Cdc73 and two components of the Pol II elongation complex, the elongation factor Spt6 and the largest subunit of Pol II. Both of these interactions require the tandem SH2 domain of Spt6. We also show that Cdc73 and Spt6 can interact in vitro and that rapid depletion of Spt6 dissociates Paf1 from chromatin, altering patterns of Paf1C-dependent histone modifications genome-wide. These results reveal interactions between Cdc73 and the Pol II elongation complex and identify Spt6 as a key factor contributing to the occupancy of Paf1C at active genes in Saccharomyces cerevisiae.
High‐speed reflectance confocal microscopy of human skin at 1251–1342 nm

Reflectance confocal microscopy (RCM) is an imaging method that can noninvasively visualize microscopic features of the human skin. The utility of RCM can be further improved by increasing imaging speed. In this paper, we report high‐speed RCM imaging of human skin with a frame rate that is over 10 times faster and an area imaging rate that is 6–9 times faster than those of commercially available RCM devices.