Miracle-dz/UniFAR-FTUs huggingface dataset:
Visceral fat area to appendicular muscle mass ratio as a predictor for nonalcoholic fatty liver disease independent of obesity

Abstract Objective Obesity and sarcopenia are known to be closely related to nonalcoholic fatty liver disease (NAFLD). We attempted to explore the combined influence of fat and muscle tissue on NAFLD by using visceral fat area to appendicular muscle mass ratio (VAR) as a novel parameter. Material and methods In this cross-sectional study, a total of 3255 adults (1399 men and 1856 women) coming for a health examination were enrolled. NAFLD was diagnosed using ultrasound and VAR was measured by bioelectrical impedance analyzer. Results The prevalence of NAFLD was 46.5% in men and 26.6% in women. VAR differed significantly between subjects with and without NAFLD (4.27 vs. 3.26 in men, 7.89 vs. 5.01 in women, respectively, p < .001). Logistic regression analysis determined VAR as a risk factor for NAFLD, and the multivariable-adjusted odds ratios in the highest VAR quartile was 9.57 (95%CI: 5.98–15.30) for men and 12.37 (95%CI: 6.37–24.05) for women. From the receiver operating characteristic analysis, the area under the curve was 0.767 and 0.834, with the suitable cut-off VAR value of 3.469 and 6.357 for men and women, respectively. To control the influence of obesity, all subjects were stratified according to their BMI. For each BMI group, individuals with VAR above the cut-off value had significant higher prevalence and risk of NAFLD, with odds ratios ranging from 1.76 to 4.75. Conclusions Increased VAR is strongly associated with higher risk of NAFLD in both sexes independent of obesity and can serve as a screening reference for NAFLD.
Burden of caring for Alzheimer’s disease or dementia patients in Japan, the US, and EU: results from the National Health and Wellness Survey: a cross-sectional survey

Abstract Aims The growing prevalence of Alzheimer’s disease (AD) worldwide has sparked the implementation of national policies to support the growing burden among caregivers of AD/dementia patients. This study aims to quantify and compare the burden of AD/dementia caregivers and evaluate how different living arrangements might impact health outcomes among caregivers in Japan, five European countries (5EU), and the United States (US). Materials and methods This is a cross-sectional study based on existing data from the 2018 National Health and Wellness Survey. Health outcome measures included health-related quality of life (HRQoL), health state utilities, work productivity and activity impairment (WPAI), and measurement of depression and anxiety amongst AD/dementia caregivers and non-caregivers. Pairwise comparisons between AD/dementia caregivers in Japan, 5EU, and the US were conducted. Multivariate analysis was used to compare across groups within each region, with adjustment for potential confounding effects. Results A higher proportion of caregivers of AD/dementia patients in Japan were 65 years or older as compared to 5EU and US. On the contrary, female caregivers were significantly higher in the US than Japan and 5EU. The HRQoL and health state utilities index scores amongst AD/dementia caregivers were highest in Japan and lowest in the US. Caregivers in Japan incurred the lowest WPAI among the three regions. The proportion of AD/dementia patients reportedly living in an institution was highest in Japan as compared to the US and EU. Notably, US caregivers whose patients lived in an institution experienced significantly less caregiving burden as compared to caregivers whose patients lived in the community. Conclusions The caregiving burden among AD/dementia caregivers was substantial across the three regions, with similarities and differences between the West and Japan. The lower caregiving burden in Japan was potentially associated with national policies supporting long-term healthcare and institutionalized nursing care facilities for AD/dementia patients.
Focused Ultrasound-Enhanced Delivery of Intranasally Administered Anti-Programmed Cell Death-Ligand 1 Antibody to an Intracranial Murine Glioma Model

Immune checkpoint inhibitors have great potential for the treatment of gliomas; however, their therapeutic efficacy has been partially limited by their inability to efficiently cross the blood–brain barrier (BBB). The objective of this study was to evaluate the capability of focused-ultrasound-mediated intranasal brain drug delivery (FUSIN) in achieving the locally enhanced delivery of anti-programmed cell death-ligand 1 antibody (aPD-L1) to the brain. Both non-tumor mice and mice transcranially implanted with GL261 glioma cells at the brainstem were used in this study. aPD-L1 was labeled with a near-infrared fluorescence dye (IRDye 800CW) and administered to mice through the nasal route to the brain, followed by focused ultrasound sonication in the presence of systemically injected microbubbles. FUSIN enhanced the accumulation of aPD-L1 at the FUS-targeted brainstem by an average of 4.03- and 3.74-fold compared with intranasal (IN) administration alone in the non-tumor mice and glioma mice, respectively. Immunohistochemistry staining found that aPD-L1 was mainly located within the perivascular spaces after IN delivery, while FUSIN further enhanced the penetration depth and delivery efficiency of aPD-L1 to the brain parenchyma. The delivered aPD-L1 was found to be colocalized with the tumor cells after FUSIN delivery to the brainstem glioma. These findings suggest that FUSIN is a promising technique to enhance the delivery of immune checkpoint inhibitors to gliomas.
Population-Level Effectiveness of HIV Pre-exposure Prophylaxis Among MSM and Transgender Persons With Bacterial Sexually Transmitted Infections

Background: Pre-exposure prophylaxis (PrEP) is highly efficacious, but its effectiveness may be limited by poor adherence or discontinuation. Our objective was to estimate the effectiveness of real-world PrEP use in a population at increased risk of HIV infection. Setting: King County, Washington. Methods: We conducted a retrospective cohort study using sexually transmitted infection (STI) partner services (PS) interview data collected January 2014–August 2018 in King County, Washington, USA. During PS interviews, men who have sex with men and transgender persons who have sex with men were asked if they were taking PrEP. We linked STI PS data to HIV surveillance data to estimate HIV incidence among self-reported PrEP users vs. nonusers using Cox proportional hazards regression, adjusting for age, race/ethnicity, and calendar year. Results: Among 4368 individuals, 1206 (28%) were taking PrEP at the time of the PS interview. The median observation time was 14 months (interquartile range 6–23 months). Five (0.4%) of 1206 PrEP users and 97 (3%) of 2162 PrEP nonusers were subsequently diagnosed with HIV (P < 0.001). HIV incidence was lower among PrEP users than nonusers [0.17 vs. 1.86 cases per 100 person-years, adjusted hazards ratio 0.21 (95% confidence interval: 0.08 to 0.58)]. Latinx ethnicity, Native Hawaiian/Pacific Islander ethnicity, gonorrhea, and syphilis were also independently associated with higher HIV risk. Conclusions: Self-reported PrEP use was associated with a 79% reduction in HIV incidence among men who have sex with men and transgender persons who have sex with men with STIs in King County.
Point-Counterpoint: Should Clinical Microbiology Laboratories Report Vancomycin MICs?

With numerous reported challenges to reporting MICs for vancomycin, clinical laboratories are attempting to identify accurate methods for MIC testing. However, the issues of poor reproducibility, accuracy, and clinical utility remain a challenge. In this Point-Counterpoint, Dr. Sara Revolinski discusses the pros of reporting MICs for vancomycin, while Dr. Christopher Doern argues for the use of caution. INTRODUCTION With numerous reported challenges to reporting MICs for vancomycin, clinical laboratories are attempting to identify accurate methods for MIC testing. However, the issues of poor reproducibility, accuracy, and clinical utility remain a challenge. In this Point-Counterpoint, Dr. Sara Revolinski discusses the pros of reporting MICs for vancomycin, while Dr. Christopher Doern argues for the use of caution.
Leptospiral Infection, Pathogenesis and Its Diagnosis—A Review

Leptospirosis is a perplexing conundrum for many. In the existing literature, the pathophysiological mechanisms pertaining to leptospirosis is still not understood in full. Considered as a neglected tropical zoonotic disease, leptospirosis is culminating as a serious problem worldwide, seemingly existing as co-infections with various other unrelated diseases, including dengue and malaria. Misdiagnosis is also common as non-specific symptoms are documented extensively in the literature. This can easily lead to death, as the severe form of leptospirosis (Weil’s disease) manifests as a complex of systemic complications, especially renal failure. The virulence of Leptospira sp. is usually attributed to the outer membrane proteins, including LipL32. With an armament of virulence factors at their disposal, their ability to easily adhere, invade and replicate within cells calls for a swift refinement in research progress to establish their exact pathophysiological framework. As an effort to reconstitute the current knowledge on leptospirosis, the basis of leptospiral infection, including its risk factors, classification, morphology, transmission, pathogenesis, co-infections and clinical manifestations are highlighted in this review. The various diagnostic techniques are also outlined with emphasis on their respective pros and cons.
Country-level determinants of the severity of the first global wave of the COVID-19 pandemic: an ecological study

Objective We aimed to identify the country-level determinants of the severity of the first wave of the COVID-19 pandemic. Design Ecological study of publicly available data. Countries reporting >25 COVID-19 related deaths until 8 June 2020 were included. The outcome was log mean mortality rate from COVID-19, an estimate of the country-level daily increase in reported deaths during the ascending phase of the epidemic curve. Potential determinants assessed were most recently published demographic parameters (population and population density, percentage population living in urban areas, population >65 years, average body mass index and smoking prevalence); economic parameters (gross domestic product per capita); environmental parameters (pollution levels and mean temperature (January–May); comorbidities (prevalence of diabetes, hypertension and cancer); health system parameters (WHO Health Index and hospital beds per 10 000 population); international arrivals; the stringency index, as a measure of country-level response to COVID-19; BCG vaccination coverage; UV radiation exposure; and testing capacity. Multivariable linear regression was used to analyse the data. Primary outcome Country-level mean mortality rate: the mean slope of the COVID-19 mortality curve during its ascending phase. Participants Thirty-seven countries were included: Algeria, Argentina, Austria, Belgium, Brazil, Canada, Chile, Colombia, the Dominican Republic, Ecuador, Egypt, Finland, France, Germany, Hungary, India, Indonesia, Ireland, Italy, Japan, Mexico, the Netherlands, Peru, the Philippines, Poland, Portugal, Romania, the Russian Federation, Saudi Arabia, South Africa, Spain, Sweden, Switzerland, Turkey, Ukraine, the UK and the USA. Results Of all country-level determinants included in the multivariable model, total number of international arrivals (beta 0.033 (95% CI 0.012 to 0.054)) and BCG vaccination coverage (−0.018 (95% CI −0.034 to –0.002)), were significantly associated with the natural logarithm of the mean death rate. Conclusions International travel was directly associated with the mortality slope and thus potentially the spread of COVID-19. Very early restrictions on international travel should be considered to control COVID-19 outbreaks and prevent related deaths.
Design and Synthesis of Luminescent Lanthanide-Based Bimodal Nanoprobes for Dual Magnetic Resonance (MR) and Optical Imaging

Current biomedical imaging techniques are crucial for the diagnosis of various diseases. Each imaging technique uses specific probes that, although each one has its own merits, do not encompass all the functionalities required for comprehensive imaging (sensitivity, non-invasiveness, etc.). Bimodal imaging methods are therefore rapidly becoming an important topic in advanced healthcare. This bimodality can be achieved by successive image acquisitions involving different and independent probes, one for each mode, with the risk of artifacts. It can be also achieved simultaneously by using a single probe combining a complete set of physical and chemical characteristics, in order to record complementary views of the same biological object at the same time. In this scenario, and focusing on bimodal magnetic resonance imaging (MRI) and optical imaging (OI), probes can be engineered by the attachment, more or less covalently, of a contrast agent (CA) to an organic or inorganic dye, or by designing single objects containing both the optical emitter and MRI-active dipole. If in the first type of system, there is frequent concern that at some point the dye may dissociate from the magnetic dipole, it may not in the second type. This review aims to present a summary of current activity relating to this kind of dual probes, with a special emphasis on lanthanide-based luminescent nano-objects.
Continuous biocatalytic recovery of neodymium and europium

Batch-grown cells and a continuously-grown biofilm of a Serratia sp. were utilized to recover the rare earth elements (REEs) lanthanum and neodymium from solution. Selectivity was obtained for La(III) over Th(IV) using columns of polyacrylamide gel-immobilized cells challenged at a rapid flow rate, exploiting the different solution chemistries and behaviors of REEs(III) and Th(IV). Biofilm-grown cells had a ten-fold higher activity of mediating phosphatase, which promotes metal deposition as the corresponding metal phosphate, reflected as a correspondingly enhanced level of removal of Nd(III) (as NdPO4) in flow-through columns utilizing the biofilm on reticulated foam. The biofilms retained activity in the removal of Nd(III) for >1 year, losing activity exponentially with a half life of 3 months. The flow rate giving 50% removal (FA1/2) of Nd(III) by 3 month old biofilms at pH 5.5 was 272 and 275 mL h−1 using two independent biofilm preparations, equivalent to a FA1/2 of 34 column volumes per h for fresh biofilms. The removal of Nd(III) was sustained at pH values down to 3.5 with approx. 20% of the column activity lost upon return to pH 5.5. A similar result occurred in the presence of the common REE leaching agent ammonium sulfate (100 mM), but this did not affect the ability of Serratia sp. to recover REEs. With a view to the potential for future biomanufacturing of Nd(III)-catalysts, the deposited material was identified as NdPO4 by X-ray powder diffraction with a nanoparticle size of 14.5 nm, irrespective of the biofilm age.
Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

Population genomics is a fast‐developing discipline with promising applications in a growing number of life sciences fields. Advances in sequencing technologies and bioinformatics tools allow population genomics to exploit genome‐wide information to identify the molecular variants underlying traits of interest and the evolutionary forces that modulate these variants through space and time. However, the cost of genomic analyses of multiple populations is still too high to address them through individual genome sequencing. Pooling individuals for sequencing can be a more effective strategy in Single Nucleotide Polymorphism (SNP) detection and allele frequency estimation because of a higher total coverage. However, compared to individual sequencing, SNP calling from pools has the additional difficulty of distinguishing rare variants from sequencing errors, which is often avoided by establishing a minimum threshold allele frequency for the analysis. Finding an optimal balance between minimizing information loss and reducing sequencing costs is essential to ensure the success of population genomics studies. Here, we have benchmarked the performance of SNP callers for Pool‐seq data, based on different approaches, under different conditions, and using computer simulations and real data. We found that SNP callers performance varied for allele frequencies up to 0.35. We also found that SNP callers based on Bayesian (SNAPE‐pooled) or maximum likelihood (MAPGD) approaches outperform the two heuristic callers tested (VarScan and PoolSNP), in terms of the balance between sensitivity and FDR both in simulated and sequencing data. Our results will help inform the selection of the most appropriate SNP caller not only for large‐scale population studies but also in cases where the Pool‐seq strategy is the only option, such as in metagenomic or polyploid studies.
Computed Tomography–Based Measurements of the Cochlear Duct: Implications for Cochlear Implant Pitch Tuning

Supplemental Digital Content is available in the text. Objectives: To determine the sources of variability for cochlear duct length (CDL) measurements for the purposes of fine-tuning cochlear implants (CI) and to propose a set of standardized landmarks for computed tomography (CT) pitch mapping. Design: This was a retrospective cohort study involving 21 CI users at a tertiary referral center. The intervention involved flat-panel CT image acquisition and secondary reconstructions of CIs in vivo. The main outcome measures were CDL measurements, CI electrode localization measurements, and frequency calculations. Results: Direct CT-based measurements of CI and intracochlear landmarks are methodologically valid, with a percentage of error of 1.0% ± 0.9%. Round window (RW) position markers (anterior edge, center, or posterior edge) and bony canal wall localization markers (medial edge, duct center, or lateral edge) significantly impact CDL calculations [F(2, 78) = 9.9, p < 0.001 and F(2, 78) = 1806, p < 0.001, respectively]. These pitch distortions could be as large as 11 semitones. When using predefined anatomical landmarks, there was still a difference between researchers [F(2, 78) = 12.5; p < 0.001], but the average variability of electrode location was reduced to differences of 1.6 semitones (from 11 semitones. Conclusions: A lack of standardization regarding RW and bony canal wall landmarks results in great CDL measurement variability and distorted pitch map calculations. We propose using the posterior edge of the RW and lateral bony wall as standardized anatomical parameters for CDL calculations in CI users to improve pitch map calculations. More accurate and precise pitch maps may improve CI-associated pitch outcomes.
The epidemiology of patients treated at a private hospital as a consequence of the September 19th 2017 earthquake in Mexico City.

INTRODUCTION Natural disasters can happen anytime. There is no gold standard for emergency department triaging and setup during these kind of emergencies. On September 19th 2017, at 13:14:40, a 7.1 magnitude on the Richter scale earthquake hit Mexico City. Buildings, including hospitals, collapsed. Our hospital offered free medical attention to those affected by the earthquake. MATERIAL AND METHODS We reviewed the patient database for all patients who had been treated between September 19th and September 24th as a consequence of earthquake related injuries in both campuses. Age, gender, diagnosis, injured part, transportation method to hospital, triage color assigned in the emergency room, campus where attention was received, attention type, time spent in hospital, attention type. We calculated frequencies, medians, and standard deviation of lesions, triage code, and treatment in the emergency room. RESULTS After the September 19th 2017 earthquake in Mexico City, our hospital treated 184 patients, most were female, most patients were between 21 and 60 years of age, the most common diagnosis were lower extremity trauma (no fractures), lower limb fractures, psychiatric disorders, craneoencephalic trauma and other upper extremity trauma. Most patients received a green triage and were discharged from the emergency department. CONCLUSION Epidemiology of patients treated at our hospital is consistent with epidemiology reported in the literature for earthquake casualties. There was an adequate adaption of the emergency department for the reception and treatment of massive casualties. Patient records were mostly complete. We believe a standardized format designed specifically for these kinds of situations could be of great help in order to keep accurate patient records.
Genetics of Parkinson's disease in the Polish population.

INTRODUCTION Genetic forms of Parkinson's disease (PD) often cluster in different ethnic groups and may present with recognisable unique clinical manifestations. Our aim was to summarise the current state of knowledge regarding the genetic causes of PD and describe the first Polish patient with SNCA duplication. METHODOLOGY We searched the electronic database, PubMed, for studies between January 1995 and June 2020 that evaluated genetics in Polish patients with PD, using the search terms 'Parkinson's disease, 'Polish', 'genetics', 'mutations', and 'variants'. RESULTS In total, 73 publications were included in the review; 11 genes responsible for monogenic forms and 19 risk factor genes have been analysed in the Polish population. Pathogenic variants were reported in four monogenic genes (LRRK2, PRKN, PINK1, and SNCA). Eight genes were associated with PD risk in the Polish population (GBA, TFAM, NFE2L2, MMP12, HLA-DRA, COMT, MAOB, and DBH). Multiplex ligation-dependent probe amplification and Sanger sequencing in PRKN, PINK1, DJ1, LRRK2, and SNCA revealed SNCA duplication in a 43-year-old Polish patient with PD examined by movement disorder specialists. CONCLUSION Only a limited number of positive results have been reported in genes previously associated with PD in the Polish population. In the era of personalised medicine, it is important to report on genetic findings in specific populations.
Long‐term effectiveness of an online decision aid for female cancer patients regarding fertility preservation: Knowledge, attitude, and decisional regret

The decision, whether to undergo fertility preservation or not is highly demanding for cancer patients. Decision aids may act as an additional source of support. So far, only a limited number of decision aids regarding fertility preservation for female cancer patients exist and have been evaluated systematically. This paper presents the results of secondary analyses of the first randomized controlled trial evaluating an online decision aid for female cancer patients affected by different types of cancer. It focuses on fertility‐related knowledge, attitude toward fertility preservation, and long‐term effectiveness regarding decisional regret.
Commuter Students’ Readiness to Help in Incidents of Campus Sexual Violence

The present study examines commuter students’ readiness to help in incidents of sexual violence. Participants included 1,366 students, the majority of whom (79%) were commuters. Structural equation modeling was used to examine commuter status on readiness to help in incidents of sexual violence and the effect of awareness of sexual violence resources and sense of community on readiness to help. The results demonstrate that commuter students are less ready to help in incidents of sexual violence compared with non-commuters. These results suggest that those looking to engage students in sexual assault prevention efforts need to increase efforts to engage commuters.