Miracle-dz/UniFAR-FTUs huggingface dataset:
A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking

Live cell time-lapse microscopy, a widely-used technique to study gene expression and protein dynamics in single cells, relies on segmentation and tracking of individual cells for data generation. The potential of the data that can be extracted from this technique is limited by the inability to accurately segment a large number of cells from such microscopy images and track them over long periods of time. Existing segmentation and tracking algorithms either require additional dyes or markers specific to segmentation or they are highly specific to one imaging condition and cell morphology and/or necessitate manual correction. Here we introduce a fully automated, fast and robust segmentation and tracking algorithm for budding yeast that overcomes these limitations. Full automatization is achieved through a novel automated seeding method, which first generates coarse seeds, then automatically fine-tunes cell boundaries using these seeds and automatically corrects segmentation mistakes. Our algorithm can accurately segment and track individual yeast cells without any specific dye or biomarker. Moreover, we show how existing channels devoted to a biological process of interest can be used to improve the segmentation. The algorithm is versatile in that it accurately segments not only cycling cells with smooth elliptical shapes, but also cells with arbitrary morphologies (e.g. sporulating and pheromone treated cells). In addition, the algorithm is largely independent of the specific imaging method (bright-field/phase) and objective used (40X/63X). We validate our algorithm’s performance on 9 cases each entailing a different imaging condition, objective magnification and/or cell morphology. Taken together, our algorithm presents a powerful segmentation and tracking tool that can be adapted to numerous budding yeast single-cell studies.
Co-existing of Neuromyelitis Optica and Fulminant Type 1 Diabetes

The patient was a 71-year-old woman with aquaporin-4-antibody positive neuromyelitis optica (NMO), with no history of diabetes. On admission, although she showed an extremely elevated plasma glucose level (1,080 mg/dL), her hemoglobin A1c level was low (7.1%), which indicated the rapid progression of diabetes. She also showed ketoacidosis and had a human leukocyte antigen haplotype, DRB1*09:01-DQB1*03:03 associated with Fulminant type 1 diabetes (FT1D). Based on these results, the patient was diagnosed with FT1D. We herein describe the first reported case of a patient with FT1D with NMO, which raises the possibility that T-cell-mediated autoimmunity is involved in the pathogenesis of both FT1D and NMO.
An Insight into the Roles of MicroRNAs and Exosomes in Sarcoma

Sarcomas are rare solid tumors, but at least one-third of patients with sarcoma die from tumor-related disease. MicroRNA (miRNA) is a noncoding RNA that regulates gene expression in all cells and plays a key role in the progression of cancers. Recently, it was identified that miRNAs are transferred between cells by enclosure in extracellular vesicles, especially exosomes. The exosome is a 100 nm-sized membraned vesicle that is secreted by many kinds of cells and contains miRNA, mRNA, DNA, and proteins. Cancer uses exosomes to influence not only the tumor microenvironment but also the distant organ to create a premetastatic niche. The progression of sarcoma is also regulated by miRNAs and exosomes. These miRNAs and exosomes can be targeted as biomarkers and treatments. In this review, we summarize the studies of miRNA and exosomes in sarcoma.
What you get is what you see: Decomposing Epistemic Planning using Functional STRIPS

Epistemic planning --- planning with knowledge and belief --- is essential in many multi-agent and human-agent interaction domains. Most state-of-the-art epistemic planners solve this problem by compiling to propositional classical planning, for example, generating all possible knowledge atoms, or compiling epistemic formula to normal forms. However, these methods become computationally infeasible as problems grow. In this paper, we decompose epistemic planning by delegating reasoning about epistemic formula to an external solver. We do this by modelling the problem using \emph{functional STRIPS}, which is more expressive than standard STRIPS and supports the use of external, black-box functions within action models. Exploiting recent work that demonstrates the relationship between what an agent `sees' and what it knows, we allow modellers to provide new implementations of externals functions. These define what agents see in their environment, allowing new epistemic logics to be defined without changing the planner. As a result, it increases the capability and flexibility of the epistemic model itself, and avoids the exponential pre-compilation step. We ran evaluations on well-known epistemic planning benchmarks to compare with an existing state-of-the-art planner, and on new scenarios based on different external functions. The results show that our planner scales significantly better than the state-of-the-art planner against which we compared, and can express problems more succinctly.
High-Energy Coherent X-Ray Diffraction Microscopy of Polycrystal Grains: Steps Toward a Multiscale Approach

We present proof-of-concept imaging measurements of a polycrystalline material that integrate the elements of conventional high-energy X-ray diffraction microscopy with coherent diffraction imaging techniques, and that can enable in-situ strain-sensitive imaging of lattice structure in ensembles of deeply embedded crystals over five decades of length scale upon full realization. Such multi-scale imaging capabilities are critical to addressing important questions in a variety of research areas such as materials science and engineering, chemistry, and solid state physics. Towards this eventual goal, the following key aspects are demonstrated: 1) high-energy Bragg coherent diffraction imaging (HE-BCDI) of sub-micron-scale crystallites at 52 keV at current third-generation synchrotron light sources, 2) HE-BCDI performed in conjunction with far-field high-energy diffraction microscopy (ff-HEDM) on the grains of a polycrystalline sample in an smoothly integrated manner, and 3) the orientation information of an ensemble of grains obtained via ff-HEDM used to perform complementary HE-BCDI on multiple Bragg reflections of a single targeted grain. These steps lay the foundation for integration of HE-BCDI, which typically provides a spatial resolution tens of nanometers, into a broad suite of well-established HEDM methods, extending HEDM beyond the few-micrometer resolution bound and into the nanoscale, and positioning the approach to take full advantage of the orders-of-magnitude improvement of X-ray coherence expected at fourth generation light sources presently being built and commissioned worldwide.
Output Feedback Controller Synthesis for Negative Imaginary Systems

This paper presents necessary and sufficient conditions for deriving a strictly proper dynamic controller which satisfies the negative imaginary output feedback control problem. Our synthesis method divides the output feedback control problem into a state feedback problem and a dual output injection problem. Thus, a controller is formed using the solutions to a pair of dual algebraic Riccati equations. Finally, an illustrative example is offered to show how this method may be applied.
Health-related quality of life of people living with HIV infection in Spain: a gender perspective

ABSTRACT Studies exploring gender differences in health-related quality of life (HRQOL) of people living with HIV/AIDS (PLWHA) are scarce and contradictory. This study evaluated gender differences in HRQOL of 744 PLWHA with median (IQR) age 44 (37–48) years and HIV infection diagnosed 12 (5–20) years earlier. Results showed important differences between genders (p < .05). Better male physical health was related to being employed, not having economic worries, not receiving psychological support, not having injected drugs in past, low negative mood HIV-related, low HIV illness representation and internalized stigma, and high body image satisfaction and health behavior. For women, variables were fewer years since HIV diagnosis and low enacted stigma-personal experience of rejection. Mentally, variables in men were being employed, not having injected drugs, having a stable partner, high health behavior, use of problem-solving coping, personal autonomy and personal meaning. In women, better mental health was related to high CD4 cells, self-esteem and body image satisfaction, and negative mood HIV-related. Men and women coincided in absence of past opportunistic infections being related to better physical and mental health, and absence of side effects for physical health and low HIV-related stress and HIV illness representation for mental health. Our results highlight the need for detailed study of gender differences that identify the bio-psycho-socio inequalities that affect HRQOL.
Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus

Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
Analysis of 50 Neurodegenerative Genes in Clinically Diagnosed Early-Onset Alzheimer’s Disease

Alzheimer’s disease (AD), Parkinson’s disease (PD), frontotemporal dementia (FTD), amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), and prion diseases have a certain degree of clinical, pathological, and molecular overlapping. Previous studies revealed that many causative mutations in AD, PD, and FTD/ALS genes could be found in clinical familial and sporadic AD. To further elucidate the missing heritability in early-onset Alzheimer’s disease (EOAD), we genetically characterized a Thai EOAD cohort by Next-Generation Sequencing (NGS) with a high depth of coverage, capturing variants in 50 previously recognized AD and other related disorders’ genes. A novel mutation, APP p.V604M, and the known causative variant, PSEN1 p.E184G, were found in two of the familiar cases. Remarkably, among 61 missense variants were additionally discovered from 21 genes out of 50 genes, six potential mutations including MAPT P513A, LRRK2 p.R1628P, TREM2 p.L211P, and CSF1R (p.P54Q and pL536V) may be considered to be probably/possibly pathogenic and risk factors for other dementia leading to neuronal degeneration. All allele frequencies of the identified missense mutations were compared to 622 control individuals. Our study provides initial evidence that AD and other neurodegenerative diseases may represent shades of the same disease spectrum, and consideration should be given to offer exactly embracing genetic testing to patients diagnosed with EOAD. Our results need to be further confirmed with a larger cohort from this area.
Development of a fluorescent loop-mediated isothermal amplification assay for rapid and simple diagnosis of bovine leukemia virus infection

Bovine leukemia virus (BLV) causes enzootic bovine leukosis (EBL), a condition that threatens the sustainability of the livestock industry. A fluorescent loop-mediated isothermal amplification (fLAMP) assay targeting BLV env sequences was developed and used to evaluate 100 bovine blood samples. Compared with a conventional real-time PCR (rPCR) assay, the fLAMP assay achieved 87.3% (62/71) sensitivity and 100% (29/29) specificity. The rPCR assay took 65 min, while the fLAMP assay took 8 min to 30 min from the beginning of DNA amplification to final judgement with a comparable limit of detection. The fLAMP is a potential tool for the rapid and simple diagnosis of BLV infection to supplement ELISA testing and can be used by local laboratories and slaughterhouses without special equipment.
The Administration of Pro re nata Medication by Mental Health Nurses: A Thematic Analysis

Abstract Pro re nata (PRN) medication is medication administered by nurses as required commonly in response to a patient’s symptoms or behaviour including insomnia, agitation or anxiety. There is a paucity of research around the process of PRN administration in mental health settings in Ireland and international evidence suggests inconsistencies in practices. This study aimed to explore the process of PRN medication administration by mental health nurses. Using a qualitative descriptive design, semi-structured interviews were undertaken with 19 mental health nurses in three acute inpatient units in one mental health service in Ireland. Most participants reported undertaking an assessment of the patient before administering PRN medication; however, many also reported having observed incidents of poor practice. There was evidence of some interdisciplinary sensitivities around instructions regarding the use of PRN medications between doctors who prescribed them and nurses who dispensed them. A need for service improvements were also identified including the use of alternative strategies to PRN use such as de-escalation techniques and education around psychopharmacology. PRN medication is commonly used in mental health settings; however, this study suggests that there is potential for improvement in relation to how it is prescribed and administered. Overuse of PRN medication has been associated with increased morbidity. Mental health nurses are required to carefully consider whether PRN medication is warranted in the first instance and how its use might impact on patients.
Awareness of Age-Related Macular Degeneration in Community-Dwelling Elderly Persons in Germany

ABSTRACT Background: Due to current demographic trends age-related macular degeneration (AMD) is becoming more prevalent. When disease progresses to late-stage neovascular AMD, rapid initiation of treatment is required to achieve optimal outcomes. However, many affected individuals may be unaware of their disease impeding and delaying care seeking. Therefore, in an exploratory study we assessed whether elderly persons living independently in the community were aware of their AMD. Methods: Participants were recruited in eleven seniors’ community centers. Participants underwent a standardized interview followed by non-mydriatic fundus photography of the macula and the optic disc in both eyes (Canon CR-2AF, Canon, New York, USA). The images were graded by an ophthalmologist and the data were analyzed descriptively. Results: A total of 281 participants (73.9 ± 8.1 years; 71.9% women) underwent bilateral fundus photography. The fundus photographs of 208 participants (74%; 73.6 ± 7.0 years; 73.1% women) could be graded. In a third (32.2%, n = 67) no pathological changes were detected. AMD was present in 24.5% of the examined subjects (n = 51). Half of the cases had early (47.1%), followed by intermediate (41.2%) and late (11.7%) AMD. Only one third (n = 16, 31.4%) were aware of their disease. Conclusions: A quarter of community dwelling elderly had AMD but only a third of these were aware of being affected with AMD. This confirms previous studies demonstrating low awareness for age-related eye diseases in the community. Considering the increase in population aging, awareness campaigns for AMD are needed.
A case of nivolumab-associated colitis, which relapsed after mucosal healing and was then successfully treated with mesalazine

Abstract Currently, the number of patients treated with immune-checkpoint inhibitor involving nivolumab is increasing. Nevertheless, it causes various immune-related adverse events (irAEs). Here, we report the case of a patient who underwent long-term follow-up after suffering from nivolumab-associated colitis. The patient was a 57-year-old man who underwent resection of a bladder tumor. Following surgery, lymph node metastasis was detected, and he was treated by nivolumab. Two months after treatment with nivolumab, the patient complained of bloody diarrhea. Colonoscopy revealed pancolitis with erosions, loss of vascular pattern and erythema. Pathological findings indicated a disease state of pan-ulcerative colitis. As an irAE by nivolumab, the patient was started with 30 mg of prednisolone. Prednisolone treatment successfully induced clinical remission and mucosal healing. Nevertheless, eight months after stopping the steroid treatment, the colitis relapsed with diarrhea following elevation of fecal immunochemical test (FIT) and fecal calprotectin (CPT). The relapsed colitis was treated by mesalazine, and then diarrhea was improved. Nivolumab-associated colitis relapsed following mucosal healing suggesting that it is necessary to consider maintenance therapy as well as remission induction for long-term survivor. The present case also demonstrates that the FIT and CPT would be effective biomarker to assess the disease activity of nivolumab-associated colitis.
Effector and Activated T Cells Induce Preterm Labor and Birth That Is Prevented by Treatment with Progesterone

Preterm labor commonly precedes preterm birth, the leading cause of perinatal morbidity and mortality worldwide. Most research has focused on establishing a causal link between innate immune activation and pathological inflammation leading to preterm labor and birth. However, the role of maternal effector/activated T cells in the pathogenesis of preterm labor/birth is poorly understood. In this study, we first demonstrated that effector memory and activated maternal T cells expressing granzyme B and perforin are enriched at the maternal-fetal interface (decidua) of women with spontaneous preterm labor. Next, using a murine model, we reported that prior to inducing preterm birth, in vivo T cell activation caused maternal hypothermia, bradycardia, systemic inflammation, cervical dilation, intra-amniotic inflammation, and fetal growth restriction, all of which are clinical signs associated with preterm labor. In vivo T cell activation also induced B cell cytokine responses, a proinflammatory macrophage polarization, and other inflammatory responses at the maternal-fetal interface and myometrium in the absence of an increased influx of neutrophils. Finally, we showed that treatment with progesterone can serve as a strategy to prevent preterm labor/birth and adverse neonatal outcomes by attenuating the proinflammatory responses at the maternal-fetal interface and cervix induced by T cell activation. Collectively, these findings provide mechanistic evidence showing that effector and activated T cells cause pathological inflammation at the maternal-fetal interface, in the mother, and in the fetus, inducing preterm labor and birth and adverse neonatal outcomes. Such adverse effects can be prevented by treatment with progesterone, a clinically approved strategy.
Response to Questions Posed by the Food Safety and Inspection Service Regarding Salmonella Control Strategies in Poultry †.

The U.S. Department of Agriculture’s (USDA) Food Safety and Inspection Service (FSIS) considers reducing human foodborne salmonellosis as one of its top priorities. The Agency estimates approximately 360,000 salmonellosis cases are associated with FSIS-regulated products. Consequently, the FSIS released its Salmonella Action Plan to protect consumers by making meat, poultry, and egg products safer. Furthermore, the Agency has set new performance standards for poultry products. Despite these efforts, the Agency believes that the incidence of salmonellosis and prevalence of Salmonella contamination on poultry products warrant further action on the part of food safety agencies, industry, and consumers. Moreover, the FSIS realizes that the focus must be throughout the farm-to-table continuum, and they charged the National Advisory Committee on the Microbiological Criteria for Foods (NACMCF) to address the issue. The NACMCF sought data from literature, subject matter experts, and the industry. Its findings to the specific questions posed by the Agency are as follows:
Workload and Fatigue Assessment on Air Traffic Controller

Workload experienced during certain work periods may cause fatigue. In Air Traffic Control work, a high air traffic rate may increase the workload and fatigue, especially during rush hour and may lead to risky situations. This study intended to estimate the value of the mental workload and fatigue of an Air Traffic Controller (ATCo) in airport X during their work period. The NASA-TLX and Samn Perelli Scale were used to quantify mental workload and fatigue. The questionnaires were distributed to ATCo and 257 questionnaires were obtained. Results showed the value of the mental load at airport X tended to be higher than other airports (average 66.53), especially for mental demand, time pressure, and effort. The value of fatigue before and after work also increased (average 1, 749 to 3, 506) included in the safe category. However, there was no convincing evidence that differences in mental load values affect the value of fatigue. These results indicated that although the workload of ATCO was relatively high, the ATCo in Airport X still can handle it and did not cause excessive fatigue.
Psychosocial Stress and Overweight and Obesity: Findings From the Chicago Community Adult Health Study.

BACKGROUND Psychosocial stress has been implicated as a risk factor for overweight and obesity. However, research on psychosocial stressors and overweight and obesity has typically focused on single stressors in isolation, which may overestimate the impact of a specific stressor and fail to describe the role of cumulative stress on overweight and obesity risk. PURPOSE This study explores the association between overweight/obesity and cumulative exposure to a wide range of psychosocial stressors, among a multiracial/ethnic sample of adults. METHODS Using secondary data from the Chicago Community Adult Health Study (n = 2,983), we conducted multinomial logistic regression analyses to quantify associations between eight psychosocial stressors, individually and in combination, and measured overweight and obesity, adjusted for sociodemographic factors, alcohol use and smoking. RESULTS In separated covariate-adjusted models, childhood adversities (odds ratio [OR] = 1.16; confidence interval [CI] = [1.03, 1.30]), acute life events (OR = 1.18; CI = [1.04, 1.34]), financial strain (OR = 1.30; CI = [1.15, 1.47]), and relationship stressors (OR = 1.18; CI = [1.04, 1.35]) were associated with increased odds of obesity. In a model adjusted for all stressors simultaneously, financial strain was the only stressor independently associated with overweight (OR = 1.17; CI = [1.00, 1.36]) and obesity (OR = 1.21; CI = [1.05, 1.39]). Participants with stress exposure in the highest quintile across 2, 3, or ≥4 (compared to no) types of stressors had significantly higher odds of obesity. CONCLUSIONS Multiple types of stressors may be risk factors for obesity, and cumulative exposure to these stressors may increase the odds of obesity. Reducing exposure to stressors at the population level may have the potential to contribute to reducing the burden of obesity.