Miracle-dz/UniFAR-FTUs huggingface dataset:
Scuphr: A probabilistic framework for cell lineage tree reconstruction

Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method’s robustness is investigated using various synthetic datasets and a biological dataset of 18 cells. Author summary Cell lineage tree reconstruction carries a significant potential for studies of development and medicine. The lineage tree reconstruction task is especially challenging for cells taken from healthy tissue due to the scarcity of mutations. In addition, the single-cell whole-genome sequencing technology introduces artifacts such as amplification errors, allelic dropouts, and sequencing errors. We propose Scuphr, a probabilistic framework to reconstruct cell lineage trees. We designed Scuphr for single-cell DNA sequencing data; it accounts for technological artifacts in its graphical model and uses germline heterozygous sites to improve its accuracy. Scuphr is embarrassingly parallel; the speed of the computational analysis is inversely proportional to the number of available computational nodes. We demonstrated that Scuphr is fast, robust, and more accurate than the state-of-the-art method with the synthetic data experiments. Moreover, in the biological data experiment, we showed Scuphr successfully identifies different clones and further obtains more support on closely related cells within clones.
Children's automatic evaluation of self-generated actions is different from adults.

Performance monitoring (PM) is central to learning and decision-making. It allows individuals to swiftly detect deviations between actions and intentions, such as response errors, and adapt behavior accordingly. Previous research showed that in adult participants, error monitoring is associated with two distinct and robust behavioral effects. First, a systematic slowing down of reaction time speed is typically observed following error commission, which is known as post-error slowing (PES). Second, response errors have been reported to be automatically evaluated as negative events in adults. However, it remains unclear whether (i) children process response errors as adults do (PES), (ii) they also evaluate them as negative events, and (iii) their responses vary according to the pedagogy experienced. To address these questions, we adapted a simple decision-making task previously validated in adults to measure PES as well as the affective processing of response errors. We recruited 8-12 year old children enrolled in traditional (N = 56) or Montessori (N = 45) schools, and compared them to adults (N = 46) on the exact same task. Results showed that children processed correct actions as positive events, and that adults processed errors as negative events. By contrast, PES was similarly observed in all groups. Moreover, the former effect was observed in traditional schoolchildren, but not in Montessori schoolchildren. These findings suggest that unlike PES, which likely reflects an age-invariant attention orienting towards response errors, their affective processing depends on both age and pedagogy.
Sequencing of Historical Isolates, K-mer Mining and High Serological Cross-Reactivity with Ross River Virus Argue against the Presence of Getah Virus in Australia

Getah virus (GETV) is a mosquito-transmitted alphavirus primarily associated with disease in horses and pigs in Asia. GETV was also reported to have been isolated from mosquitoes in Australia in 1961; however, retrieval and sequencing of the original isolates (N544 and N554), illustrated that these viruses were virtually identical to the 1955 GETVMM2021 isolate from Malaysia. K-mer mining of the >40,000 terabases of sequence data in the Sequence Read Archive followed by BLASTn confirmation identified multiple GETV sequences in biosamples from Asia (often as contaminants), but not in biosamples from Australia. In contrast, sequence reads aligning to the Australian Ross River virus (RRV) were readily identified in Australian biosamples. To explore the serological relationship between GETV and other alphaviruses, an adult wild-type mouse model of GETV was established. High levels of cross-reactivity and cross-protection were evident for convalescent sera from mice infected with GETV or RRV, highlighting the difficulties associated with the interpretation of early serosurveys reporting GETV antibodies in Australian cattle and pigs. The evidence that GETV circulates in Australia is thus not compelling.
Association of Maternal Prepregnancy Diabetes and Gestational Diabetes Mellitus With Congenital Anomalies of the Newborn

OBJECTIVE To examine the association of maternal prepregnancy diabetes, gestational diabetes mellitus (GDM), and 12 subtypes of congenital anomalies of the newborn. RESEARCH DESIGN AND METHODS We included 29,211,974 live births with maternal age ranging from 18 to 49 years old documented in the National Vital Statistics System in the U.S. from 2011 to 2018. Information on prepregnancy diabetes, GDM, and congenital anomalies was retrieved from birth certificates. Log-binomial regression was used to estimate risk ratios (RRs) and 95% CIs for congenital anomalies overall and by subtypes. RESULTS Of the 29,211,974 live births, there were 90,061 infants who had congenital anomalies identified at birth. The adjusted RRs of congenital anomalies at birth were 2.44 (95% CI 2.33–2.55) for prepregnancy diabetes and 1.28 (95% CI 1.24–1.31) for GDM. The associations were generally consistent across subgroups by maternal age, race/ethnicity, prepregnancy obesity status, and infant sex. For specific subtypes of congenital anomalies, maternal prepregnancy diabetes or GDM was associated with an increased risk of most subtypes. For example, the adjusted RRs of cyanotic congenital heart disease were 4.61 (95% CI 4.28–4.96) for prepregnancy diabetes and 1.50 (95% CI 1.43–1.58) for GDM; the adjusted RRs of hypospadias were 1.88 (95% CI 1.67–2.12) for prepregnancy diabetes and 1.29 (95% CI 1.21–1.36) for GDM. CONCLUSIONS Prepregnancy diabetes and, to a lesser extent, GDM were associated with several subtypes of congenital anomalies of the newborn. These findings suggest potential benefits of preconception counseling in women with preexisting diabetes or at risk for GDM for the prevention of congenital anomalies.
Transport of a Peptide from Bovine αs1-Casein across Models of the Intestinal and Blood–Brain Barriers

The effect of food components on brain growth and development has attracted increasing attention. Milk has been shown to contain peptides that deliver important signals to the brains of neonates and infants. In order to reach the brain, milk peptides have to resist proteolytic degradation in the gastrointestinal tract, cross the gastrointestinal barrier and later cross the highly selective blood–brain barrier (BBB). To investigate this, we purified and characterized endogenous peptides from bovine milk and investigated their apical to basal transport by using human intestinal Caco-2 cells and primary porcine brain endothelial cell monolayer models. Among 192 characterized milk peptides, only the αS1-casein peptide 185PIGSENSEKTTMPLW199, and especially fragments of this peptide processed during the transport, could cross both the intestinal barrier and the BBB cell monolayer models. This peptide was also shown to resist simulated gastrointestinal digestion. This study demonstrates that a milk derived peptide can cross the major biological barriers in vitro and potentially reach the brain, where it may deliver physiological signals.
Implementing effective eLearning for scaling up global capacity building: findings from the malnutrition elearning course evaluation in Ghana

ABSTRACT Background Global demand for capacity building has increased interest for eLearning. As eLearning resources become more common, effective implementation is required to scale up utilization in Low- and Middle-Income Countries (LMICs). Objective This paper describes the process of implementing a malnutrition eLearning course, effectiveness of course delivery models devised, factors affecting course completion, and cost comparison between the models and face-to-face training at healthcare and academic institutions in Ghana. Methods Four delivery models: Mobile Training Centre (MTC), Online Delivery (OD), Institutional Computer Workstation (ICW) and Mixed Delivery (MD) – a combination of OD and ICW – were determined. Participants were enabled to access the course using one of the four models where contextually appropriate. Pre and post-assessments and questionnaires were administered to compare participants’ course completion status and knowledge gain between delivery models. The effect of access to computer and Internet at home and relevance of course to job and academic progression on course completion were further investigated. Comparison of delivery model costs against face-to-face training was also undertaken. Results Of 7 academic and 9 healthcare institutions involving 915 people, 9 used MTC (34.8%), 3 OD (18.8%), 3 ICW (34.2%) and 1 MD (12.2%). Course completion was higher among institutions where the course was relevant to job or implemented as part of required curriculum activities. Knowledge gain was significant among most participants, but higher among those who found the course relevant to job or academic progression. The implementation costs per participant for training with MTC were £51.0, OD £2.2, ICW £1.2 and MD £1.1, compared with a face-to-face training estimate of £105.0 (1 GHS = 0.14 GBP). Conclusion The malnutrition eLearning course makes global capacity building in malnutrition management achievable. Adopting contextually appropriate delivery models and ensuring training is relevant to job/academic progression can enhance eLearning effectiveness in LMICs.
Diagnostic Accuracy of the Biosynex CryptoPS Cryptococcal Antigen Semiquantitative Lateral Flow Assay in Patients with Advanced HIV Disease

High cryptococcal antigen (CrAg) titers in blood are associated with subclinical meningitis and mortality in CrAg-positive individuals with advanced HIV disease (AHD). We evaluated a novel semiquantitative lateral flow assay (LFA), CryptoPS, that may be able to identify individuals with high CrAg titers in a cohort of AHD patients undergoing CrAg screening. In a prospective cohort of patients with AHD (CD4 cell count, ≤200/μl) receiving CD4 count testing, whole blood was tested for CrAg by CryptoPS and the IMMY LFA; the two assays were conducted by two different operators, each blind to the results of the other assay. ABSTRACT High cryptococcal antigen (CrAg) titers in blood are associated with subclinical meningitis and mortality in CrAg-positive individuals with advanced HIV disease (AHD). We evaluated a novel semiquantitative lateral flow assay (LFA), CryptoPS, that may be able to identify individuals with high CrAg titers in a cohort of AHD patients undergoing CrAg screening. In a prospective cohort of patients with AHD (CD4 cell count, ≤200/μl) receiving CD4 count testing, whole blood was tested for CrAg by CryptoPS and the IMMY LFA; the two assays were conducted by two different operators, each blind to the results of the other assay. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of CryptoPS were assessed against the IMMY LFA as a reference. CryptoPS low-titer (T1 band) and high-titer (T2 band) results were compared with IMMY LFA titers obtained through serial dilution. A total of 916 specimens were tested. The sensitivity of the CryptoPS assay was 61.0% (25/41) (95% confidence interval [95% CI], 44.5 to 75.8%), its specificity was 96.6% (845/875) (95% CI, 95.1 to 97.7%), its PPV was 45.5% (95% CI, 32.0 to 59.4%), and its NPV was 98.1% (95% CI, 97.0 to 98.9%). All (16/16) CryptoPS false-negative results were obtained for samples with IMMY titers of ≤1:160. Of 29 patients (30 specimens) who tested positive by CryptoPS but negative by the IMMY LFA, none developed cryptococcal meningitis over 3 months of follow-up without fluconazole. Median CrAg titers were 1:20 (interquartile range [IQR], 0 to 1:160) in CryptoPS T1-positive samples and 1:2,560 (IQR, 1:1,280 to 1:10,240) in T2-positive samples. We conclude that the diagnostic accuracy of the CryptoPS assay was suboptimal in the context of CrAg screening, with poor sensitivity at low CrAg titers. However, the CryptoPS assay reliably detected individuals with high titers, which are associated with poor outcomes.
Integrated telehealth-assisted home-based specialist palliative care in rural Australia: A feasibility study

Introduction This study assessed the feasibility of integrating telehealth-assisted home-based specialist palliative care (TH-SPC) into a rural community setting. Methods This was a prospective mixed-methods pilot study conducted in rural Victoria, Australia. Newly engaged adult patients and their caregivers of a community palliative-care service received video consultations with metropolitan-located specialist palliative-care physicians, alongside standard care. Those eligible patients who failed to receive TH-SPC were treated as a control group upon analysis. Data were collected over three months and at 30 days prior to death. Feasibility outcomes included efficiency of process, user satisfaction, clinical outcome and health-care metrics. Results A total of 21 patients completed the study, with an average age of 70.4 years and an average survival of 5.8 months. Fourteen patients received TH-SPC, and seven received standard care alone. Patient–caregiver feedback for TH-SPC showed a high level of overall satisfaction. Compared to standard care, the TH-SPC group demonstrated less functional decline from baseline at two weeks (Australia-modified Karnofsky Performance Status: –1.35 vs. –12.30, p = 0.067) and three months (8.48 vs. –10.79, p = 0.04) after the intervention. At 30 days prior to death, functional status remained better in the TH-SPC group, with fewer per capita community palliative-care nursing visits (5.46 vs. 9.32, effect size = 0.7), general practitioner visits (0.13 vs. 3.88, effect size = 1.34) and hospital admissions (0.02 vs. 0.2, effect size = 0.65). Discussion TH-SPC was successfully integrated into rural community-based palliative care, with potential benefits in performance status preservation and health-care resource utilisation.
Role of Probiotics in Stimulating the Immune System in Viral Respiratory Tract Infections: A Narrative Review

Viral respiratory tract infection (RTI) is the most frequent cause of infectious illnesses including the common cold. Pharmacological solutions for treating or preventing viral RTIs are so far limited and thus several self-care products are available in the market. Some dietary supplements such as probiotics have been shown to modulate immune system function and their role in reducing the risk and the course of RTIs has been investigated extensively within the past decade. However, the mechanism of action and the efficacy of probiotics against viral RTIs remains unclear. We searched PubMed, Google Scholar, and Web of Knowledge for pre-clinical and clinical studies investigating the effect of probiotics on respiratory virus infections, immune response, and the course of upper and lower respiratory tract illness. The literature summarized in this narrative review points out that specific probiotic strains seem effective in pre-clinical models, through stimulating the immune system and inhibiting viral replication. Clinical studies indicate variable efficacy on upper respiratory illnesses and lack proof of diagnosed viral infections. However, meta-analyses of clinical studies indicate that probiotics could be beneficial in upper respiratory illnesses without specific etiology. Further studies aiming at discovering the mechanisms of action of probiotics and clinical efficacy are warranted.
Time-lapse photography reveals the occurrence of unexpected bee-pollination in Calanthe izuinsularis, an endangered orchid endemic to the Izu archipelago

ABSTRACT Calanthe izuinsularis is a rare, beautiful and fragrant orchid endemic to the Izu archipelago. Although it is known that mainland populations of closely related Calanthe species are pollinated by medium- to large-sized bees, it is likely that C. izuinsularis has been forced to alter its floral biology to attract alternative pollinators, as large-sized bees are rarely found on the Izu Islands. Indeed, the unusual floral characteristics of C. izuinsularis, which produces pale flowers that emit a strong and fragrant scent during the night, are considered the adaptation to a moth-pollinator syndrome. As expected, our time-lapse photography using a digital camera revealed that the inflorescences of C. izuinsularis were most frequently visited by nocturnal moths such as Noctuidae, Geometridae and Crambidae, which accounted for 50% of all insect visits (in terms of both the number of frames with captured visitors and the number of times visited). However, our study could not provide evidence of a pollinator shift towards moths because none of the moth species was observed with pollinaria. On the other hand, our study found that the pollinaria of C. izuinsularis could become attached to the mesothorax of the small-sized sweat bee Lasioglossum occidens. Therefore, our study suggests that C. izuinsularis is still somewhat dependent on bee pollination, while the orchid has changed its floral colouration and scent. The occurrence of bee-pollination in C. izuinsularis would provide an explanation for how the natural hybridisation between C. aristulifera, C. discolor and C. izuinsularis can occur.
Older Black Americans During COVID-19: Race and Age Double Jeopardy

The concept of “double jeopardy”—being both older and Black—describes how racism and ageism together shape higher risks for coronavirus exposure, COVID-19 disease, and poor health outcomes for older Black adults. Black people and older adults are the two groups most affected by COVID-19 morbidity and mortality. Double jeopardy, as a race- and age-informed analysis, demonstrates how Black race and older age are associated with practices and policies that shape key life circumstances (e.g., racial residential segregation, family and household composition) and resources in ways that embody elevated risk for COVID-19. The concept of double jeopardy underscores long-standing race- and age-based inequities and social vulnerabilities that produce devastating COVID-19 related deaths and injuries for older Black adults. Developing policies and actions that address race- and age-based inequities and social vulnerabilities can lower risks and enhance protective factors to ensure the health of older Black Americans during the COVID-19 pandemic.
Preventing Occupational Tuberculosis in Health Workers: An Analysis of State Responsibilities and Worker Rights in Mozambique

Given the very high incidence of tuberculosis (TB) among health workers in Mozambique, a low-income country in Southern Africa, implementation of measures to protect health workers from occupational TB remains a major challenge. This study explores how Mozambique’s legal framework and health system governance facilitate—or hinder—implementation of protective measures in its public (state-provided) healthcare sector. Using a mixed-methods approach, we examined international, constitutional, regulatory, and policy frameworks. We also recorded and analysed the content of a workshop and policy discussion group on the topic to elicit the perspectives of health workers and of officials responsible for implementing workplace TB policies. We found that despite a well-developed legal framework and national infection prevention and control policy, a number of implementation barrier persisted: lack of legal codification of TB as an occupational disease; absence of regulations assigning specific responsibilities to employers; failure to deal with privacy and stigma fears among health workers; and limited awareness among health workers of their legal rights, including that of collective action. While all these elements require attention to protect health workers from occupational TB, a stronger emphasis on their human and labour rights is needed alongside their perceived responsibilities as caregivers.
“I Hate the Word ‘Liver’”: A Photovoice Study of Burmese and Bhutanese Adolescent Health Care Brokers in Northeast Ohio

Introduction: Adolescents health care brokers interpret for family and community members lacking English language proficiency in health care settings. The purpose of this study was to explore personal experiences of Burmese and Bhutanese teenagers who served as health care brokers in resettled refugee families in Northeast Ohio. Method: A mixed methods design using photovoice guided this study. Participants completed the Adolescent Language Brokering Survey, took photos, wrote in journals, and attended focus groups. Results: Eight Burmese and Bhutanese teenagers participated. Three themes became apparent: health care brokering within sociocultural contexts, mediation during health care encounters, and representations of childhood. Discussion: The adolescents were proud to be health care brokers yet found it disrupted their lives because they were living in both their traditional culture and the American culture. Photovoice empowered them through dissemination of findings during a photo exposition, community meeting, and health literacy class. Health care professionals must recognize benefits and prohibitions when working with adolescent health care brokers.
Role of therapeutic plasma exchanges in refractory severe warm autoimmune hemolytic anemia: Presentation of two case reports

Warm autoimmune hemolytic anemia (WAIHA) is a disorder with a usually good response to corticosteroid treatment, whereas in some cases first‐line treatment's response is poor and other therapies such as intravenous immunoglobulins (IVIGs), rituximab, or splenectomy must be applied.