Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time polymerase chain reaction (PCR) cycle threshold and Clostridioides difficile infection outcomes

Abstract Objective: Clostridioides difficile infection (CDI) causes significant morbidity and mortality; however, the diagnosis of CDI remains controversial. The primary aim of our study was to evaluate the association of polymerase chain reaction (PCR) cycle threshold (Ct) values with CDI disease severity, recurrence, and mortality among adult patients with CDI. Design: Retrospective cohort study. Setting: Single tertiary-care hospital. Patients: Adult patients diagnosed with hospital-onset, healthcare facility–associated CDI from June 2014 to September 2015. Methods: We performed a retrospective chart review of included patients. Univariate and multivariable logistic regression methods were used to evaluate the association between Ct values and CDI severity, 8-week recurrence, and 30-day mortality. Results: Among 318 included patients, 51% were male and the mean age was 62 years; ~32% of the patients developed severe CDI and 11% developed severe–complicated CDI. The 30-day all-cause mortality rate was 11% and the 8-week recurrence rate was 9.5%. The overall mean Ct value was 32.9 (range, 23–40). Multivariable analyses showed that lower values of PCR Ct were associated with increased odds of 30-day morality (odds ratio [OR] 0.83; 95% confidence interval [CI], 0.72–0.96) but were not independently associated with CDI severity (OR, 0.99; 95% CI, 0.90–1.09) or recurrence (OR, 0.88; 95% CI, 0.77–1.00). Conclusions: Our findings suggest that PCR Ct values at the time of diagnosis may have a limited predictive value and utility in clinical decision making for inpatients with CDI. Larger, prospective studies across different patient populations are needed to confirm our findings.
Off-topic verbosity: Relationships between verbal abilities and speech characteristics among young and older adults

Abstract Off-topic verbosity (OTV) refers to extended speech lacking in relevance and focus. Previous research has found that older adults have higher levels of OTV, and some contend that OTV is indicative of cognitive decline. The purpose of this study was to investigate relationships between verbal cognitive abilities and OTV speech characteristics among young adults (n = 62; age 18–28, M = 20.69) and older adults (n = 76; age 60–98, M = 76.46). Older adults had slower verbal speed and verbal set-shifting than young adults, and they displayed more tangentiality and egocentrism in their speech. Slower set-shifting was associated with increased tangentiality and decreased quantity of speech, particularly in older adults. These results provide some support for the age-related cognitive decline explanation of OTV, as posited by the inhibitory deficit hypothesis.
Quality of life and its associated factors among epileptic patients attending public hospitals in North Wollo Zone, Northeast Ethiopia: A cross-sectional study

Background Epilepsy is thought to be caused by witchcraft, evil spirit, and God’s punishment for sins in many developing countries. As a result, people with epilepsy and their families usually suffer from stigma, discrimination, depression, and other psychiatric problems. Thus, this study aimed to assess the quality of life and its associated factors among epileptic patients attending public hospitals in North Wollo Zone, Northeast Ethiopia. Methods An institution-based cross-sectional study design was employed in this study. A simple random sampling technique was utilized. Health-related quality of life was measured based on the total score of the Quality of Life in Epilepsy Inventory (QOLIE-31) instrument. Data were entered into Epi-data 3.1 statistical package and exported to SPSS Version 20 for further analysis. Linear regression models were used to assess the relationship between quality of life and the independent variables. Statistically significant values were declared at a P-value of < 0.05. Results A total of 395 patients participated in the study making the response rate 98.5%. The mean age of the participants was 32.39 ±10.71 years. More than half, 199 (50.4%) of epileptic patients had an overall weighted average health related quality of life score of mean and above. Male sex (B = 4.34, 95%CI, 0.41, 8.27, P = 0.03), higher educational status (B = 7.18, 95%CI, 1.39, 13.00, P = 0.015) and age at onset of epilepsy (B = 0.237, 95%CI, 0.02, 0.45, P = 0.035) were associated with increased health related quality of life score. On the other hand, family history of epilepsy (B = -4.78, 95%CI,-9.24,-0.33, P = 0.035), uncontrolled seizure (B = -11.08, 95%CI,-15.11,-7.05, P < 0.001), more than 5 pre-treatment number of seizures (B = -4.86, 95%CI,-8.91,-0.81, P = 0.019), poor drug adherence (B = -11.65, 95%CI,-16.06,-7.23, P < 0.001), having moderate (B = -4.526, 95%CI,-8.59,-0.46, P = 0.029) to sever (B = -12.84, 95%CI,-18.30,-7.37, P < 0.001) anxiety and depression, believing that epilepsy is caused by evil spirit (B = -7.04, 95%CI,-11.46,-2.61, P = 0.002), drinking alcohol (B = -5.42, 95%CI,-10.72,-0.13, P = 0.045), and having other co-morbidities (B = -9.35, 95%CI,-14.35,-4.36, P < 0.001) were significantly negatively associated with the health related quality of life score among epileptic patients. Conclusions Only around half of the epileptic patients have a good health-related quality of life. In addition, multiple variables including family history, uncontrolled seizure, and poor drug adherence were associated with quality of life among epileptic patients. Hence, targeting these variables in epilepsy management is recommended.
Isolate-Based Surveillance of Bordetella pertussis, Austria, 2018–2020

Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018–2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.
Differences in resting-state functional connectivity according to the level of impulsiveness in patients with internet gaming disorder

Abstract Background and aims Impulsiveness is an important factor in the pathophysiology of Internet gaming disorder (IGD), and regional brain functions can be different depending on the level of impulsiveness. This study aimed to demonstrate that different brain mechanisms are involved depending on the level of impulsiveness among patients with IGD. Methods Resting-state functional MRI data were obtained from 23 IGD patients with high impulsivity, 27 IGD patients with low impulsivity, and 22 healthy controls, and seed-based functional connectivity was compared among the three groups. The seed regions were the ventromedial prefrontal cortex (vmPFC), dorsolateral prefrontal cortex, nucleus accumbens (NAcc), and amygdala. Results Connectivity of the vmPFC with the left temporo-parietal junction (TPJ) and NAcc-left insula connectivity were significantly decreased in the patients with high impulsivity, compared with the patients with low impulsivity and healthy controls. On the other hand, amygdala-based connectivity with the left inferior frontal gyrus showed decreases in both patient groups, compared with the healthy controls. Conclusion These findings may suggest a potential relationship between impulsivity and deficits in reward-related social cognition processes in patients with IGD. In particular, certain interventions targeted at vmPFC-TPJ connectivity, found to be impulsivity-specific brain connectivity, are likely to help with addiction recovery among impulsive patients with IGD.
Effects of increasing fire frequency on black carbon and organic matter in Podzols of Siberian Scots pine forests

Fires in boreal forests frequently convert organic matter in the organic layer to black carbon, but we know little of how changing fire frequency alters the amount, composition and distribution of black carbon and organic matter within soils, or affects podzolization. We compared black carbon and organic matter (organic carbon and nitrogen) in soils of three Siberian Scots pine forests with frequent, moderately frequent and infrequent fires.
Understanding parents’ decision-making on participation in clinical trials in children’s heart surgery: a qualitative study

Objectives Few children undergoing heart surgery are recruited to clinical trials and little is known about the views and attitudes of parents towards trials. This study explored parents’ perspectives on decision-making about their child’s participation in a clinical trial during their elective cardiac surgery. Design Qualitative interview study. Setting Single-centre substudy of a multicentre, double-blind, randomised controlled trial to investigate the effects of remote ischaemic preconditioning in children undergoing cardiac surgery. Participants Parents of children approached to participate in the trial, both consenters and decliners. Methods Semistructured interviews were conducted face-to-face or by telephone following discharge, digitally audio-recorded, transcribed and thematically analysed. Results Of 46 patients approached for the trial, 24 consenting and 2 declining parents agreed to participate in an interview (21 mothers, 5 fathers). Parental decision-making about research was influenced by (1) potential risks or additional procedures; (2) personal benefit and altruism for the ‘cardiac community’; (3) information, preparation, timing and approach; and (4) trust in the clinical team and collaboration with researchers. All of these were placed within the context of their understanding of the trial and knowledge of research. Conclusions Parents of children undergoing cardiac surgery attach value to clinical research and are supportive of clinical trials when there is no or minimal perceived additional risk. These findings enhance our understanding of the factors that influence parents’ decision-making and should be used to inform the design and conduct of future paediatric surgical trials. Trial registration number ISRCTN12923441; Pre-results.
Dysplasia of the fibrous sheath with axonemal and centriolar defects combined with lack of mitochondrial activity as associated factors of ICSI failure in primary ciliary dyskinesia syndrome

Primary ciliary dyskinesia (PCD) is a rare autosomal recessive disorder characterized by ciliary dysfunction and impaired mucociliary clearance, resulting in a range of clinical manifestations, including chronic bronchitis leading to bronchiectasis, chronic rhino-sinusitis and otitis media, situs inversus (in about 50% of cases) and severe male infertility (1). PCD was initially characterized in men with Kartagener syndrome in 1982 by ultrastructural analysis that demonstrated dyskinetic or immotile cilia, but not limited to this particular diagnosis (2). The incidence of PCD is estimated at 1/16.000 births based on the prevalence of situs inversus and bronchiectasis (3). In addition, the prevalence of PCD may be much higher in some communities and countries, particularly when inbreeding is present (4). Severe asthenozoospermia and up to complete immobility of the sperm are the main known causes of male infertility in patients with PCD, due to the inability of sperm to reach and fertilize the oocyte correctly. However, if this was the only reason, one would expect that with the use of assisted reproduction techniques (ARTs), particularly when the sperm is injected directly inside the oocyte, therefore without the physiological evolutionary ability to bypass the oocyte plasma membrane and cumulus cells, such as the invasive resourceful intracytoplasmic sperm injection (ICSI), in which one sperm is injected directly into the oocyte, the inability found in the PCD patient to conceive would be more commonly bypassed in the vast majority of cases. Surprisingly, exactly on the contrary, there are only a handful number of reports of successful pregnanies that resulted in childbirth among couples in which the male partner is affected by PCD syndrome and its variants (5). Even when the most advanced ARTs have been used, including alleged intracytoplasmic injection of morphologically selected sperm (IMSI), time lapse monitoring of IVF-produced embryos, preimplantation genetic diagnosis and screening, a high percentage of PCD male partners never get pregnant. The involuntary childlessness critically found in this group of individuals, suggests that in addition to the incapacity of sperm to reach the oocyte, there might be other unknown factors acting. This prompted us to use the arsenal of tests available in a high-complexity anDysplasia of the fibrous sheath with axonemal and centriolar defects combined with lack of mitochondrial activity as associated factors of ICSI failure in primary ciliary dyskinesia syndrome _______________________________________________
Association of SARS-CoV-2 Seropositive Antibody Test With Risk of Future Infection

Key Points Question Can observational clinical data from commercial laboratories be used to evaluate the comparative risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection for individuals who are antibody positive vs those who are antibody negative? Finding In this cohort study of more than 3.2 million US patients with a SARS-CoV-2 antibody test, 0.3% of those indexed with positive test results had evidence of a positive nucleic acid amplification test beyond 90 days after index, compared with 3.0% indexed with negative antibody test results. Meaning Individuals who are seropositive for SARS-CoV-2 based on commercial assays may be at decreased future risk of SARS-CoV-2 infection.
Coffee consumption and risk of renal cell carcinoma in the NIH-AARP Diet and Health Study.

BACKGROUND Coffee consumption has been associated with a reduced risk of some cancers, but the evidence for renal cell carcinoma (RCC) is inconclusive. We investigated the relationship between coffee and RCC within a large cohort. METHODS Coffee intake was assessed at baseline in the National Institutes of Health-American Association of Retired Persons Diet and Health Study. Among 420 118 participants eligible for analysis, 2674 incident cases were identified. We fitted Cox-regression models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for coffee consumption vs non-drinkers. RESULTS We observed HRs of 0.94 (95% CI 0.81, 1.09), 0.94 (0.81, 1.09), 0.80 (0.70, 0.92) and 0.77 (0.66, 0.90) for usual coffee intake of <1, 1, 2-3 and ≥4 cups/day, respectively (Ptrend = 0.00003). This relationship was observed among never-smokers (≥4 cups/day: HR 0.62, 95% CI 0.46, 0.83; Ptrend = 0.000003) but not ever-smokers (HR 0.85, 95% CI 0.70, 1.05; Ptrend = 0.35; Pinteraction = 0.0009) and remained in analyses restricted to cases diagnosed >10 years after baseline (HR 0.65, 95% CI 0.51, 0.82; Ptrend = 0.0005). Associations were similar between subgroups who drank predominately caffeinated or decaffeinated coffee (Pinteraction = 0.74). CONCLUSION In this investigation of coffee and RCC, to our knowledge the largest to date, we observed a 20% reduced risk for intake of ≥2 cups/day vs not drinking. Our findings add RCC to the growing list of cancers for which coffee consumption may be protective.
Comparison of Speech Recognition With an Organ of Corti Versus Spiral Ganglion Frequency-to-Place Function in Place-Based Mapping of Cochlear Implant and Electric-Acoustic Stimulation Devices

Supplemental Digital Content is available in the text Objective: To compare acute speech recognition with a cochlear implant (CI) alone or electric-acoustic stimulation (EAS) device for place-based maps calculated with an organ of Corti (OC) versus a spiral ganglion (SG) frequency-to-place function. Patients: Eleven adult CI recipients of a lateral wall electrode array. Intervention: Postoperative imaging was used to derive place-based maps calculated with an OC versus SG function. Main Outcome Measure: Phoneme recognition was evaluated at initial activation with consonant-nucleus-consonant (CNC) words presented using an OC versus a SG place-based map. Results: For the 9 CI-alone users, there was a nonsignificant trend for better acute phoneme recognition with the SG map (mean 18 RAUs) than the OC map (mean 9 RAUs; p = 0.071, 95% CI [≤−1.2]). When including the 2 EAS users in the analysis, performance was significantly better with the SG map (mean 21 RAUs) than the OC map (mean 7 RAUs; p = 0.019, 95% CI [≤−6.2]). Conclusions: Better phoneme recognition with the SG frequency-to-place function could indicate more natural tonotopic alignment of information compared with the OC place-based map. A prospective, randomized investigation is currently underway to assess longitudinal outcomes with place-based mapping in CI-alone and EAS devices using the SG frequency-to-place function.
Exploring the use of residual variance for uniformity of body weight in meat quail lines using Bayesian inference

ABSTRACT 1. Uniformity in animal products is an important aspect of the production system. Several studies have reported estimates of genetics on residual variance in different species, indicating that it could be exploited to improve uniformity by selection. Nevertheless, there are no reports about the possibilities of such a selection strategy in meat quail. 2. Records of hatching weight (HW) and body weight at 42 days (W42) of female and male birds from two meat quail lines (UFV1 and UFV2) were analysed. A three-step genetic evaluation was used to investigate the effect of genetic variation on residual variance of HW and W42 in both lines. In Step 1, a single-trait model was fitted to the data. In Step 2, log-transformed squared estimated residuals (ln(ê2)) were evaluated for these traits. In Step 3, a multi-trait analysis was performed to estimate the genetic correlation between the additive genetic effects for HW, W42, and their respective ln(ê2). 3. The heritability estimates ranged from 0.12 to 0.23 for HW and from 0.22 to 0.35 for W42. The estimated heritabilities for the residual part were low and ranged from 0.0003 to 0.02 for both traits, and the genetic coefficient of variation residual variance estimates ranged from 0.31 to 0.42 for HW and from 0.09 to 0.25 for W42. Genetic correlations between the means (HW and W42) and ln(ê2) values were both positive and did not differ from zero, indicating no association between mean and ln(ê2). 4. In conclusion, the uniformity of HW and W42 could be improved by selecting for lower residual variance in both meat quail lines, but the accuracy of selection may be low due to low heritability for uniformity, mainly for W42.
A Comparison of Monomeric Phenols Produced from Lignin by Fast Pyrolysis and Hydrothermal Conversions

Abstract Lignin, a by-product in biorefining industries such as lignocellulose-to-ethanol and paper-making processes, is a promising renewable source for value-added phenolic chemicals. Hydrothermal conversion and fast pyrolysis are two main thermo-chemical approaches for depolymerization of lignin. Hydrothermal conversion is a low temperature (250–500°C) and high pressure (5–30 MPa) process particularly suited for high moisture materials, whereas fast pyrolysis takes place at atmospheric pressure and moderate temperatures in the absence of oxygen and requires drying of the feedstock. In this paper, we present experimental results that provide a comparison of distributions of monomeric phenols produced by fast pyrolysis and hydrothermal conversion of lignin. Hydrothermal conversion experiments were performed in a 150 ml autoclave at 300°C for 30 minutes with different alkaline concentrations. Pyrolysis was carried out in a spouted bed reactor at 500°C. Hydrothermal conversion of lignin under 1 M alkaline solutions resulted in lower char yields (12.1%) compared to fast pyrolysis, which resulted in 54.5% solid yields. Monomer phenols obtained from hydrothermal conversion of lignin were found to have a narrower distribution dominated by catechol and its methyl derivative. In contrast, fast pyrolysis produced a wider distribution of monomeric phenols dominated by guaiacol and its derivatives with various chains substituted para to the hydroxyl group. Mechanisms of lignin fast pyrolysis and the methoxy group conversion under hydrothermal conditions were proposed respectively. In conclusion, hydrothermal technology is better suited for production of value added monomer phenols from lignin.
Discrepancies Between Community-Dwelling Individuals with Dementia and Their Proxies in Completing the Cornell Scale for Depression in Dementia: A Secondary Data Analysis

Background Depressive symptoms are common in people with dementia. Purpose This study examined the discrepancies in the ratings of depressive symptoms between people with dementia and their family caregivers, and the extent to which these discrepancies varied according to the functional status of people with dementia. Participants and Methods This study is a cross-sectional secondary analysis. Twenty-five people living with dementia (“participants”) and their family caregivers (“proxies”) participated as pairs in the study (participant mean age = 71.36, SD = 8.63; proxy mean age = 67.54, SD = 11.46). Data were collected in Victoria, Australia between May 2018 and May 2019. Participants were administered a semi-structured interview comprising the Cornell Scale for Depression in Dementia (CSDD). Proxies independently completed the CSDD and the Functional Activities Questionnaire (FAQ). A paired sample t-test was used to investigate differences in CSDD scores between participants and proxies. Kendall’s tau-b correlation was used to examine the relationship between FAQ scores and discrepancy scores of CSDD. Participants were then classified into either low or high functional impairment. Mann–Whitney U-test was used to examine whether the discrepancy scores of CSDD were similar between these two groups. Intraclass correlation coefficients were calculated to indicate the level of agreement between participants and proxies in each group. Results The CSDD scores of participants were significantly lower than proxies. The size of the discrepancy in CSDD scores was positively correlated with FAQ scores. The “high functional impairment” group had larger discrepancy scores and a lower level of agreement than the “low functional impairment” group. Conclusion The findings highlighted that relying on proxy CSDD scores may not reflect estimates of depressive symptoms by people with dementia. Hence, both perspectives need to be taken into account, particularly when the level of functional impairment in dementia is advanced.