Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS

According to WHO 2019, Hepatocellular carcinoma (HCC) is the fourth highest cause of cancer death worldwide. More precise diagnostic models are needed to enhance early HCC and cirrhosis quick diagnosis, treatment, and survival. Breath biomarkers known as volatile organic compounds (VOCs) in exhaled air can be used to make rapid, precise, and painless diagnoses. Gas chromatography and mass spectrometry (GCMS) are utilized to diagnose HCC and cirrhosis VOCs. In this investigation, metabolically generated VOCs in breath samples (n = 35) of HCC, (n = 35) cirrhotic, and (n = 30) controls were detected via GCMS and SPME. Moreover, this study also aims to identify diagnostic VOCs for distinction among HCC and cirrhosis liver conditions, which are most closely related, and cause misleading during diagnosis. However, using gas chromatography-mass spectrometry (GC-MS) to quantify volatile organic compounds (VOCs) is time-consuming and error-prone since it requires an expert. To verify GC-MS data analysis, we present an in-house R-based array of machine learning models that applies deep learning pattern recognition to automatically discover VOCs from raw data, without human intervention. All-machine learning diagnostic model offers 80% sensitivity, 90% specificity, and 95% accuracy, with an AUC of 0.9586. Our results demonstrated the validity and utility of GCMS-SMPE in combination with innovative ML models for early detection of HCC and cirrhosis-specific VOCs considered as potential diagnostic breath biomarkers and showed differentiation among HCC and cirrhosis. With these useful insights, we can build handheld e-nose sensors to detect HCC and cirrhosis through breath analysis and this unique approach can help in diagnosis by reducing integration time and costs without compromising accuracy or consistency.
Endothelial function assessment by flow-mediated dilation of the brachial artery in acute kidney injury and chronic kidney disease

Background: Endothelial dysfunction has a significant role in the pathogenesis of cardiovascular events in patients with kidney dysfunction. The present study aimed to compare the level of endothelial dysfunction in patients with chronic kidney disease (CKD) and acute kidney injury (AKI) by brachial artery flow-mediated dilation (FMD) technique. Also, we sought to find whether this non-invasive technique may assist in accurately distinguishing the acute or chronic nature of kidney failure in patients presenting with uremia for the first time. Methods: Demographic and medical characteristics, and laboratory and renal ultrasonography data of the patients with AKI and CKD were collected and compared with a control group. Brachial artery FMD was measured using a Toshiba aplio 300 device with a 7.5 MHz linear probe. Results: In a total of 175 patients with a mean (SD) age of 55.96(15.54) years, FMD% was significantly lower in the CKD and AKI patients compared to the control group (Mean±SD: 16.28%±10.52%), 16.28 %±4.35%, and 24.24±5.71, respectively, p<0.001). Among the different causes of AKI, contrast-induced nephropathy (10.78%±1.75%), volume depletion (14.87%±1.22%), and post-renal AKI (15.96%±1.54%) had the lowest levels of FMD. Also, a significant correlation between FMD and eGFR (r=0.26, P<0.001), serum Hb (r=0.18, P=0.013), Na (r=0.19, P=0.011), BUN (r=-0.21, P=0.005) and Cr (r=- 0.13, P=0.084) was reported. Conclusion: Compared to the control group, CKD and AKI patients showed greater levels of endothelial dysfunction as evidenced by lower brachial artery FMD. However, the FMD technique did not appear to be a practical method in differentiating CKD and AKI in patients presenting with uremia for the first time.
Detecting macromolecular differences of the CSF in low disability multiple sclerosis using quantitative MT MRI at 3T

Background Imaging investigation of cerebrospinal fluid (CSF) in multiple sclerosis (MS) is understudied. Development of noninvasive methods to detect pathological CSF changes would have a profound effect on MS diagnosis and would offer insight into MS pathophysiology and mechanisms of neurological impairment. Objective We propose magnetization transfer (MT) MRI as a tool to detect macromolecular changes in spinal CSF. Methods MT and quantitative MT (qMT) data were acquired in the cervical region in 27 people with relapsing-remitting multiple sclerosis (pwRRMS) and 38 age and sex-matched healthy controls (HCs). MT ratio (MTR), the B1, B0, and R1 corrected qMT-derived pool size ratio (PSR) were quantified in the spinal cord and CSF of each group. Results Both CSF MTR and CSF qMT-derived PSR were significantly increased in pwRRMS compared to HC (p = 0.027 and p = 0.020, respectively). CSF PSR of pwRRMS was correlated to Expanded Disability Status Scale Scores (p = 0.045, R = 0.352). Conclusion Our findings demonstrate increased CSF macromolecular content in pwRRMS and link CSF macromolecular content with clinical impairment. This highlights the potential role of CSF in processing products of demyelination.
Physical inactivity 5–8 years after anterior cruciate ligament reconstruction is associated with knee-related self-efficacy and psychological readiness to return to sport

Objectives To investigate whether patient demographics and patient-reported outcomes (PROs), respectively, are associated with physical inactivity (PI) 5–8 years after primary anterior cruciate ligament reconstruction (ACLR). Methods This case control observational study included individuals who had undergone primary ACLR between the ages of 15 and 65 years and had responded to PROs 18 months postoperatively. These individuals were asked to answer a questionnaire regarding their present level of physical activity (PA) at 5–8 years after ACLR. Patient-demographic data and results from the Knee injury and Osteoarthritis Outcome Score, the Knee Self-Efficacy Scale and the ACL Return to Sport (RTS) after Injury scale from 18 months after ACLR were extracted from a rehabilitation-specific register. Univariable logistic regression analyses were performed with PI (<150 min PA per week/≥150 min PA/week) as the dependent variable. Results Of 292 eligible participants, 173 (47% women; mean±SD age = 31±11 years) responded to the PA questionnaire. In all, 14% (n=25; 28% women) were classified as physically inactive. Participants with lower levels of present and future self-efficacy, OR 1.35 (CI 1.05 to 1.72) and OR 1.20 (CI 1.12 to 1.45), and lower levels of psychological readiness to RTS, OR 1.19 (CI 1 to 1.43), at the 18-month follow-up, had higher odds of being physically inactive 5–8 years after ACLR. None of the patient demographic variables was able to predict PI. Conclusion Lower levels of knee-related self-efficacy and psychological readiness to RTS, 18 months after ACLR, were associated with PI 5–8 years after surgery.
Transitional Care from Hospital to Cardiac Rehabilitation During COVID-19: The Perspectives of Older Adults and Their Healthcare Providers

Transitional care to cardiac rehabilitation during the pandemic was a complex process for older adults, with additional challenges for decision-making and participation. This study aimed to explore the perspectives of older adults and health providers on transitional care from the hospital to cardiac rehabilitation, focusing on patient participation in decision-making. A qualitative exploratory design was used. Semi-structured interviews were conducted with 15 older adults and 6 healthcare providers. Document analysis and reflexive journaling were used to support triangulation of findings. Six themes emerged from the data, related to insufficient follow-up from providers, the importance of patients’ emotional and psychological health and the support provided by family members, the need for information tailored to patients’ needs and spaces for participation in decision-making, as well as challenges during COVID-19, including delayed medical procedures, rushed discharge and isolating hospital stays. The findings of this study indicated a number of potential gaps in the provision of transitional care services as reported by older adults who had a cardiovascular event, often during the first few weeks post hospital discharge.
A CASE OF FAMILIAL MEDITERRANEAN FEVER PRESENTING WITH ISOLATED DRY PLEURITIS

Familial Mediterranean fever (FMF), a hereditary disease which is characterised by self limited attacks of fever and serositis, is especially common in Mediterranean region. Colchicine is the most effective drug in preventing the recurrent attacks of the disesae. Since it is a rare condition, we present a patient with FMF who had pleural involvement without radiologic findings.
A novel sophorolipids extraction method by yeast fermentation process for enhanced skin efficacy

Oriental herbs have been used as medicines in the folk remedy for their numerous phytochemicals and bioactivities. In this study, we have selected five Korean traditional medical herbs and applied bio conversion extraction technology, named it as Bioconversion Oji complex, to identify phytochemicals and evaluate skin related efficacies.
Burden of prostate cancer and relationship with the human development index (HDI) in Asia: A study of Global Burden disease in 2019

Background: Prostate cancer (PC) ranks as the second most commonly diagnosed neoplasia and the fifth cause of death in men with cancer, with an increasing trend in incidence. Methods: All accessible data sources from the 2019 Global Burden of Disease study were used to estimate the prevalence, mortality and disability-adjusted life years (DALY) and burden prostate cancer in Asia from 1990 to 2019. We estimated all-cause and cause-specific mortality, years of life lost (YLLs), years lived with disability (YLDs) and DALYs. All estimates were presented as counts and age-standardized rates per 100 000 population, with uncertainty intervals (UIs). Concentration Index analysis and Concentration Curve were used to determine the relationship between Prostate cancer burden and human development index. Results: The results showed that the percentage of changes in the incidence in 1990-2019 was positive in all countries of the Asian continent except for Afghanistan and Kyrgyzstan. The results of the concentration index showed that the incidence and mortality of prostate cancer is more concentrated in countries with a high HDI level. Examining the DALY, YLL and YLD index also showed the value of concentration index, which shows that DALY, YLL and YLD of prostate cancer are more concentrated in countries with high HDI level. Conclusion: Given that burden of prostate cancer are increasing in most Asian countries and are mostly concentrated in the HDI drawers, obtaining accurate estimates in these countries to prepare for the potential change in public health burden due to this disease which is very important.
Horizontal displacement of carbon associated with agriculture and its impacts on atmospheric CO2

The growth of crops represents a sink of atmospheric CO2, whereas biomass is consumed by humans and housed animals, yielding respiratory sources of CO2. This process induces a lateral displacement of carbon and creates geographic patterns of CO2 sources and sinks at the surface of the globe. We estimated the global carbon flux harvested in croplands to be 1290 TgC/yr. Most of this carbon is transported into domestic trade, whereas a small fraction (13%) enters into international trade circuits. We then calculated the global patterns of CO2 fluxes associated with food and feedstuff trade, using country‐based agricultural statistics and activity maps of human and housed animal population densities. The CO2 flux maps show regional dipoles of sources and sinks in Asia and North America. The effect of these fluxes on atmospheric CO2 was simulated using a global atmospheric transport model. The mean latitudinal CO2 gradients induced by the displacement of crop products are fairly small (≈0.2 ppm) compared with observations (4–5 ppm), indicating that this process has a only a small influence in explaining the latitudinal distribution of CO2 fluxes. On the other hand, the simulated longitudinal mean atmospheric CO2 gradients at northern midlatitudes (≈ up to 0.5 ppm) are comparable to the ones measured between atmospheric stations, suggesting that CO2 fluxes from crop products trade are an important component of continental‐ and regional‐scale CO2 budgets. Thus they should be accounted for as prior information in regional inversions.
Determinants of practice for providing decision coaching to facilitate informed values-based decision-making: protocol for a mixed-methods systematic review

Introduction Decision coaching is a non-directive approach to support patients to prepare for making health decisions. It is used to facilitate patients’ involvement in informed values-based decision-making and use of evidence-based health information. A recent systematic review revealed low certainty evidence for its effectiveness with and without evidence-based information. However, there may be opportunities to improve the study and use of decision coaching in clinical practice by systematically investigating its determinants of practice. We aim to conduct a systematic review to identify and synthesise the determinants of practice for providing decision coaching to facilitate patient involvement in decision-making from multiple perspectives that influence its use. Methods and analysis We will conduct a mixed-methods systematic review guided by the Cochrane’ Handbook of Systematic Reviews. We will include studies reporting determinants of practice influencing decision coaching with or without evidence-based patient information with adults making a health decision for themselves or a family member. Systematic literature searches will be conducted in Medline, EMBASE, Cochrane CENTRAL and PsycINFO via Ovid and CINAHL via EBSCO including quantitative, qualitative and mixed-methods study designs. Additionally, experts in the field will be contacted. Two reviewers will independently screen and extract data. We will synthesise determinants using deductive and inductive qualitative content analysis and a coding frame developed specifically for this review based on a taxonomy of barriers and enablers of shared decision-making mapped onto the major domains of the Consolidated Framework for Implementation Research. We will assess the quality of included studies using the Mixed Methods Appraisal Tool. Ethics and dissemination Ethical approval is not required as this systematic review involves only previously published literature. The results will be published in a peer-reviewed journal, presented at scientific conferences and disseminated to relevant consumer groups. PROSPERO registration number CRD42022338299.
Arabidopsis FIBRILLIN6 influences carotenoid biosynthesis by directly promoting phytoene synthase activity

Abstract Carotenoids are health-promoting plastidial isoprenoids with essential functions in plants as photoprotectants and photosynthetic pigments in chloroplasts. They also accumulate in specialized plastids named chromoplasts, providing color to non-photosynthetic tissues such as flower petals and ripe fruit. Carotenoid accumulation in chromoplasts requires specialized structures and proteins such as fibrillins (FBNs). The FBN family includes structural components of carotenoid sequestering structures in chromoplasts and members with metabolic roles in chloroplasts and other plastid types. However, the association of FBNs with carotenoids in plastids other than chromoplasts has remained unexplored. Here, we show that Arabidopsis (Arabidopsis thaliana) FBN6 interacts with phytoene synthase (PSY), the first enzyme of the carotenoid pathway. FBN6, but not FBN4 (a FBN that does not interact with PSY), enhances the activity of plant PSY (but not of the bacterial PSY crtB) in Escherichia coli cells. Overexpression of FBN6 in Nicotiana benthamiana leaves results in a higher production of phytoene, the product of PSY activity, whereas loss of FBN6 activity in Arabidopsis mutants dramatically reduces the production of carotenoids during seedling de-etiolation and after exposure to high light. Our work hence demonstrates that FBNs promote not only the accumulation of carotenoids in chromoplasts but also their biosynthesis in chloroplasts.
Streptomyces rare codon UUA: from features associated with 2 adpA related locations to candidate phage regulatory translational bypassing

ABSTRACT In Streptomyces species, the cell cycle involves a switch from an early and vegetative state to a later phase where secondary products including antibiotics are synthesized, aerial hyphae form and sporulation occurs. AdpA, which has two domains, activates the expression of numerous genes involved in the switch from the vegetative growth phase. The adpA mRNA of many Streptomyces species has a UUA codon in a linker region between 5’ sequence encoding one domain and 3’ sequence encoding its other and C-terminal domain. UUA codons are exceptionally rare in Streptomyces, and its functional cognate tRNA is not present in a fully modified and acylated form, in the early and vegetative phase of the cell cycle though it is aminoacylated later. Here, we report candidate recoding signals that may influence decoding of the linker region UUA. Additionally, a short ORF 5’ of the main ORF has been identified with a GUG at, or near, its 5’ end and an in-frame UUA near its 3’ end. The latter is commonly 5 nucleotides 5’ of the main ORF start. Ribosome profiling data show translation of that 5’ region. Ten years ago, UUA-mediated translational bypassing was proposed as a sensor by a Streptomyces phage of its host’s cell cycle stage and an effector of its lytic/lysogeny switch. We provide the first experimental evidence supportive of this proposal.
Natural Resource Stocks, Flows, and Regional Economic Change: Seeing the Forest and the Trees

In this article we examine and critique issues affecting natural resource-dependent regions and focus on the increased importance of nonmarket uses of natural resources. We suggest that because most of our regional science tools are market-based, nonmarket uses of these resources are overlooked in policy analysis. We also outline a method that captures the nonmarket aspects of natural resources within a regional economic model.
Circulating monocytes expressing senescence‐associated features are enriched in COVID‐19 patients with severe disease

Accurate biomarkers for predicting COVID‐19 severity have remained an unmet need due to an incomplete understanding of virus pathogenesis and heterogeneity among patients. Cellular senescence and its pro‐inflammatory phenotype are suggested to be a consequence of SARS‐CoV‐2 infection and potentially drive infection‐dependent pathological sequelae. Senescence‐associated markers in infected individuals have been identified primarily in the lower respiratory tract, while little is known about their presence in more easily accessible bio‐specimens. Here, we measured the abundance of senescence‐associated signatures in whole blood, plasma and peripheral blood mononuclear cells (PBMCs) of COVID‐19 patients and patients without an infection. Bulk transcriptomic and targeted proteomic assays revealed that the level of senescence‐associated markers, including the senescence‐associated secretory phenotype (SASP), is predictive of SARS‐CoV‐2 infection. Single‐cell RNA‐sequencing data demonstrated that a senescence signature is particularly enriched in monocytes of COVID‐19 patients, partially correlating with disease severity. Our findings suggest that monocytes are prematurely induced to senescence by SARS‐CoV‐2 infection, might contribute to exacerbating a SASP‐like inflammatory response and can serve as markers and predictors for COVID‐19 and its sequelae.
The size of wind‐driven coastal polynyas

The sizes of wind-generated coastal polynyas have been observed to be nearly constant for steady atmospheric conditions owing to the balance between the advection of sea ice away from the coast and the area-averaged production rate of new ice. A simple model is used to explore the relationship of several environmental parameters to the maximum size attained by the polynya and the speed at which the maximum is reached for a given atmospheric event. The model results suggest that size is strongly a function of air temperature, such that colder air produces a smaller polynya for a given offshore wind velocity. However, size is only moderately a function of wind speed, especially for winds greater than 10 m s−1, since increasing the speed increases both the advection rate and the ice production rate. The model results are compared to observations made around a coastal polynya during February 1982 and 1983 along the southern coast of St. Lawrence Island in the northern Bering Sea and during February 1985 along the southern coast of the Seward Peninsula. The model correctly predicts the general maximum dimensions of these winter polynyas, although the atmospheric stationarity assumptions limit the usefulness of the predictions of the speed at which the maximum is reached. The results of this study suggest that the contribution of heat from the coastal ocean to the high-latitude winter atmosphere is a self-limiting process proportional to the amount of time the wind-driven ice drift has a component normal to the coast. This has important implications for the interpretation of satellite imagery for ice-covered oceans and for understanding high-latitude climate dynamics.
Eradicating Atherosclerotic Events by Targeting Early Subclinical Disease: It Is Time to Retire the Therapeutic Paradigm of Too Much, Too Late

Recent decades have seen spectacular advances in understanding and managing atherosclerotic cardiovascular disease, but paradoxically, clinical progress has stalled. Residual risk of atherosclerotic cardiovascular disease events is particularly vexing, given recognized lifestyle interventions and powerful modern medications. Why? Atherosclerosis begins early in life, yet clinical trials and mechanistic studies often emphasize terminal, end-stage plaques, meaning on the verge of causing heart attacks and strokes. Thus, current clinical evidence drives us to emphasize aggressive treatments that are delayed until patients already have advanced arterial disease. I call this paradigm “too much, too late. ” This brief review covers exciting efforts that focus on preventing, or finding and treating, arterial disease before its end-stage. Also included are specific proposals to establish a new evidence base that could justify intensive short-term interventions (induction-phase therapy) to treat subclinical plaques that are early enough perhaps to heal. If we can establish that such plaques are actionable, then broad screening to find them in early midlife individuals would become imperative—and achievable. You have a lump in your coronaries! can motivate patients and clinicians. We must stop thinking of a heart attack as a disease. The real disease is atherosclerosis. In my opinion, an atherosclerotic heart attack is a medical failure. It is a manifestation of longstanding arterial disease that we had allowed to progress to its end-stage, despite knowing that atherosclerosis begins early in life and despite the availability of remarkably safe and highly effective therapies. The field needs a transformational advance to shift the paradigm out of end-stage management and into early interventions that hold the possibility of eradicating the clinical burden of atherosclerotic cardiovascular disease, currently the biggest killer in the world. We urgently need a new evidence base to redirect our main focus from terminal, end-stage atherosclerosis to earlier, and likely reversible, human arterial disease.