Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Intracellular and Partitioning Asymmetries in Escherichia coli

Cell divisions in Escherichia coli are, in general, morphologically symmetric. However, in a few cases, significant asymmetries between sister cells exist. These asymmetries between sister cells result in functional differences between them. For example, cells inheriting the older pole, over generations, accumulate more unwanted protein aggregates than their sister and, consequently, have a reduced growth rate. The reduced ability of these cells to reproduce shows that even these unicellular organisms are susceptible to the effects of aging. To understand senescence in these organisms, it is critical to investigate the sources as well as the functional consequences of asymmetries in division. In this thesis, we characterize mechanisms responsible for functional and morphological asymmetries in division in E. coli cells, using live, single-cell, single-molecule imaging techniques and detailed stochastic models. First, to understand the functional asymmetries due to the heterogeneous spatial distribution of large, inert protein complexes, we study the kinetics of segregation and retention of such complexes by observing these events, one event at a time. For that, we track individual MS2-GFP tagged RNA complexes, as they move in the cell cytoplasm, and characterize the mechanisms responsible for their long-term spatial distribution and resulting partitioning. Next, to understand the morphological asymmetries, we study the difference in cell sizes between sister cells at division under different environmental conditions. Finally, we present the models and simulators developed to characterize and mimic these processes, as well as to explore their functional consequences. Our results suggest that functional and morphological asymmetries in division, in the growth conditions studied, appear to be mostly driven by the nucleoid. In particular, we find that the fluorescent complexes are retained at the poles due to nucleoid occlusion. Further, the positioning of the point of division is also regulated by the degree of proximity between the two replicated nucleoids in the cell at the moment preceding division. Finally, based on simulation results of the models in extreme conditions, we suggest that asymmetries in these processes in division can enhance the mean vitality of E. coli cell populations. Overall, the results suggest that nucleoid occlusion contributes, in different ways, to heterogeneities in E. coli cells that ultimately generate phenotypic differences between sister cells.
Determinants of infant carrying behavior in rural Papua New Guinea

The determinants of variability in infant carrying within and across societies is an understudied area within parental investment research. Carrying has positive and negative consequences as it may protect the infant from predators and pathogens but is energetically costly for caregivers. Moreover, carrying may delay independent locomotor development and exposure to antigens necessary for immunological competence. The purpose of this study is to compare infants' ages and developmental milestone attainment as predictors of carrying behavior and to identify other determinants of carrying behavior among traditional forager‐horticulturalists in Papua New Guinea.
Evaluation of a Machine Learning Model Based on Pretreatment Symptoms and Electroencephalographic Features to Predict Outcomes of Antidepressant Treatment in Adults With Depression

Key Points Question Can machine learning models predict improvement of various depressive symptoms with antidepressant treatment based on pretreatment symptom scores and electroencephalographic measures? Findings In this prognostic study, using the machine learning approach of gradient-boosted decision trees, the ElecTreeScore algorithm could reliably distinguish the patients who responded to treatment from those who did not based on various depressive symptoms using pretreatment symptom scores and electroencephalographic features (using the cross-validation approach on 518 patients). Meaning Machine learning approaches that include pretreatment symptom scores and electroencephalographic features may help predict which depressive symptoms will improve with antidepressants.
Revisiting the Business Life-Cycle

In this article, the authors offer a critique of 26 different models of the business life-cycle. They find that the models lack clarity in the specification of their stages, blur the distinction between the entrepreneur and the business, suffer from inconsistencies and biases, and suggest that movement through their stages is inevitable. The authors maintain that a new model is needed that unmistakably bounds these stages so that a company's position can clearly be assessed in order to facilitate efficient and effective business development. With this in mind, they propose an actionable six-stage constructivist model and discuss its implications for improved practice and research.
Health-related Quality of Life of Older Women Religious: Negative Influence of Frailty

The purpose of the current study was to describe the health-related quality of life (HRQOL) of older women religious (WR) and examine variables that may influence HRQOL. The sample consisted of WR, 65 years or older, living in the Cleveland Catholic Diocese. The participants completed a medical history, body-mass index (BMI) and blood pressure measurement, and self-report measures of HRQOL, frailty, social support, resilience, and depression. The study sample was composed of 108 older WR with a mean age of 75.6 (range 65–93 years). The women reported high levels of daily functioning, resilience, and social support, with low levels of depression. WR describe a relatively high level of HRQOL. Frailty was an independent negative predictor of HRQOL in all subscales except general health. Resilience and fear of falling had significant effects on several HRQOL subscales.
Assessment of Physical Activity in Adults: A Review of Validated Questionnaires From a Nutritionist’s Point of View

Physical activity (PA) is a component of total energy expenditure. PA and PA energy expenditure (PAEE) can be estimated by objective techniques (OTs). However, the use of questionnaires is frequent in clinical settings and epidemiological studies. We conducted a search on PubMed, Scopus, and Google Scholar databases to perform a review of studies reporting the reliability and validity of PA questionnaires validated against OTs—doubly labeled water (DLW) or accelerometers—in free-living adults. We selected original articles published between 2009 and 2019 that reported validation studies of PA questionnaires. We identified 53 studies that fulfilled the eligibility criteria. Four PA questionnaires were validated against DLW and the remaining against accelerometers. Three questionnaires were compared with both DLW and accelerometer results. The correlation between questionnaire-estimated PAEE and DLW results ranged from r = . 22 to r = . 46, while that between questionnaire-estimated total PA (TPA) and accelerometer results ranged from r = . 11 to r = . 54 The intraclass correlation coefficients were between . 56 and . 84. Despite having good reliability, most of the questionnaires included in this review have shown limited validity for estimating TPA in adults. OTs should be considered as a first option, when possible. Further research is warranted on techniques to obtain more accurate PA and PAEE estimates.
Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects.

Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5-3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.
A partial revision of the genus Periclimenes Costa, 1884 (Crustacea: Decapoda: Palaemonidae)

A partial revision of the pontoniine shrimp genus Periclimenes Costa, 1844, is proposed, with the resurrection of the genus Harpilius Dana, 1852, and the designation of a new genus Kemponia. Three species are now placed in the genus Harpilius. Kemponia is designated to include 24 species of an expanded Periclimenes grandis species group . Both genera are primarily coral reef species, with Harpilius species obligatory associates of scleractinian corals. The species of Kemponia are predominantly free-living, some as micro-predators. A few species are associates of scleractinian corals.
Bioprocess considerations for T‐cell therapy: Investigating the impact of agitation, dissolved oxygen, and pH on T‐cell expansion and differentiation

Adoptive T‐cell therapy (ACT) has emerged as a promising new way to treat systemic cancers such as acute lymphoblastic leukemia. However, the robustness and reproducibility of the manufacturing process remains a challenge. Here, a single‐use 24‐well microbioreactor (micro‐Matrix) was assessed for its use as a high‐throughput screening tool to investigate the effect and the interaction of different shaking speeds, dissolved oxygen (DO), and pH levels on the growth and differentiation of primary T cells in a perfusion‐mimic process. The full factorial design allowed for the generation of predictive models, which were used to find optimal culture conditions. Agitation was shown to play a fundamental role in the proliferation of T cells. A shaking speed of 200 rpm drastically improved the final viable cell concentration (VCC), while the viability was maintained above 90% throughout the cultivation. VCCs reached a maximum of 9.22 × 106 cells/ml. The distribution of CD8+ central memory T cells (TCM), was found to be largely unaffected by the shaking speed. A clear interaction between pH and DO (p < .001) was established for the cell growth and the optimal culture conditions were identified for a combination of 200 rpm, 25% DO, and pH of 7.4. The combination of microbioreactor technology and Design of Experiment methodology provides a powerful tool to rapidly gain an understanding of the design space of the T‐cell manufacturing process.
Individualistic response to past climate changes: niche differentiation promotes diverging Quaternary range dynamics in the subspecies of Testudo graeca

Understanding how species have responded to past climate changes might inform how current climate change may affect species. However, current perspectives on species’ response to Quaternary cycles mainly stem from studies on mid and high latitudes and limited information is available at lower latitudes. In these systems a greater variation in individual species’ responses to glacial cycles has been suggested, but we lack of clear case studies of such variations. Here, by means of ecological niche modelling, we characterized the niche differentiation of the five subspecies of the tortoise Testudo graeca in north Africa and described the range dynamics suffered by each of the subspecies since the Last Glacial Maxima. Molecular data was employed to infer past population dynamics. The five subspecies present a clear niche differentiation, particularly in relation to rainfall, covering a range from semiarid to humid species. The ecological differentiation among subspecies promotes very different, even opposite, post-glacial range dynamics. Since the Last Glacial Maxima, the ranges have either expanded (T. g. graeca), contracted (T. g. marokkensis), shifted northwards (T. g. soussensis) or remained stable (T. g. cyrenaica and T. g. nabeulensis). Molecular data supported the majority of these range dynamics. Our work exemplifies how, in a climate change scenario, phylogenetically very close taxa (i.e. at the subspecies level) might experience strikingly different biogeographical dynamics due to former niche differentiation. Our work supports an individualistic response to glacial cycles, which can be particularly strong in lower latitudes. In these areas precipitation changes during glacial periods may have strongly affected distribution ranges in idiosyncratic ways. We hypothesize that in those species limited by precipitation the response to glacial cycles (and climate changes) is more unpredictable than in those limited by temperature.
Molecular typing and genomic characteristic of human adenoviruses in Datong, Northern China

The molecular prevalence of human adenoviruses (HAdVs) in Datong city and molecular evolution of HAdV‐C species is still obscure. Here, we explored the molecular prevalence of HAdVs by simultaneous sequencing of hexon and fiber. Then, the penton gene fragments of HAdV‐C species were determined by sequencing. Finally, genomic and proteotyping analysis were performed for exploration of molecular evolution of unique HAdV‐6. Our results showed that dominant molecular types of HAdVs were HAdV‐3, HAdV‐2, and HAdV‐1 based on the hexon and fiber genotype. Among H2F2 isolates, P1H2F2 was most common, followed by P2H2F2 and HAdV‐89. The clinical symptoms of HAdV‐1 or HAdV‐2 infected patients were more severe than HAdV‐3 infected patients, the prognosis of HAdV‐1, HAdV‐2, and HAdV‐3 infected patients was indifference. Genomic and proteotyping analysis demonstrated that DT15 was different from HAdV‐6 prototype, with high‐discrepant sequences localized in the E3 region. In conclusion, HAdV‐1 and HAdV‐2 have a high affinity to infect younger children and cause more severe symptoms than HAdV‐3. The E3 gene of HAdV‐C species was considered as highly recombination and mutation region.
Loss of NF-kB1 and c-Rel accelerates oral carcinogenesis in mice.

Oral squamous cell carcinoma (OSCC) is a major subcategory of head and neck squamous cell carcinomas (HNSCC) and is currently the 6th highest cause of cancer mortality world-wide (Bray et al., 2018; Siegel, Miller, & Jemal, 2019). Despite current treatments such as surgery with adjunctive radiation and chemotherapy, the 5-year survival has remained at 50% for decades (Kumar, Nanavati, Modi, & Dobariya, 2016; Rivera, 2015). Most human solid cancers are believed to be driven by chronic inflammation that instigates nascent tumour proliferation (dysplasia), transformation and metastasis while conversely suppressing anti-tumour immune responses (Taniguchi & Karin, 2018). Inflammation promoted by dysregulated NF-κB (nuclear factor of kappa B) is also a hallmark of early OSCC (Cancer Genome Atlas, 2015; Tang et al., 2015). Lack of knowledge of this molecular driver is a key feature limiting curative outcomes.
Recurrent de novo WFS1 pathogenic variants in Chinese sporadic patients with nonsyndromic sensorineural hearing loss

Hereditary hearing loss (HL) is heterogeneous in terms of their phenotypic features, modes of inheritance, and causative gene mutations. The contribution of genetic variants to sporadic HL remains largely expanding. Either recessive or de novo dominant variants could result in an apparently sporadic occurrence of HL. In an attempt to find such variants we recruited 128 Chinese patients with sporadic nonsyndromic sensorineural HL (NSHL) and performed targeted deafness multigene sequencing in these unrelated trios‐families to elucidate the molecular basis.
Low Health Literacy Is Associated With Frailty and Reduced Likelihood of Liver Transplant Listing: A Prospective Cohort Study

The effect of low health literacy (HL) on outcomes in end‐stage liver disease (ESLD) is largely unknown. The association of low HL on clinical outcomes was investigated in a prospective cohort of outpatients with ESLD undergoing liver transplantation (LT) evaluation. From 2014 to 2017, 276 patients underwent LT evaluation with assessments of liver disease severity, medical and psychosocial comorbidities, physical frailty, and malnutrition. Literacy was measured with the Newest Vital Sign, a brief validated assessment. Multivariate models assessed relationships between HL and clinical outcomes adjusting for clinical and psychosocial variables. The median Model for End‐Stage Liver Disease–sodium score of the study sample was 15 (interquartile range, 11‐19), 71 (25.7%) of candidates were frail, 117 (42.4%) had malnutrition, 151 (54.7%) had hepatic encephalopathy, 104 (37.7%) had low HL, and 85 (39.2%) had marginal or poor social support. Adjusting for education level, socioeconomic factors, and severity of illness, low HL was independently associated with physical frailty (adjusted odds ratio [aOR], 3.59; 95% confidence interval [CI], 1.50‐8.59; P = 0.004) and not being wait‐listed (aOR 1.96; 95% CI, 1.03‐3.75; P = 0.04). Strong social support attenuated the relationship between low HL and not being wait‐listed (aOR, 1.58; 95% CI, 0.74‐3.36; P = 0.24). Low HL is common and a largely unrecognized risk factor for poor health outcomes among patients with ESLD. Patient‐oriented infrastructure and support are needed at the health system level to ensure all patients can successfully navigate the complex process of LT evaluation and wait‐listing.
Nepali private schools and tolerated illegality: A Foucauldian analysis of privatisation of education in Nepal

The Education Act 1971 is the main policy document under which schools in Nepal are operated. With the change in political regime, this policy has been amended as per the ideology of the incoming regime. Although private schools started to show their influence in Nepal in the late 1980s, excessive growth of private schools began with the neoliberal policy adopted by the incoming political parties soon after Nepal became a multiparty democratic country in the early 1990s. However, with the Maoists becoming a dominant political force in the country in the late 1990s, several challenges in the operation of private schools began. Issues such as closing down or monitoring of private schools are now common mass media headlines. This paper analyses such a situation in the operation of private schools in Nepal. It uses primary sources of data collected via semi-structured interviews with teachers, administrators and principals of two private schools located in the capital city of Nepal, Kathmandu. It also uses secondary sources that include mass media output and other documentary sources such as documents from private schools’ associations and government policy related to private schools. This study found that operation of private schools in Nepal is comparable to what Michel Foucault calls tolerated illegality.
Bioprocess development for scalable production of cultivated meat

Traditional farm‐based products based on livestock are one of the main contributors to greenhouse gas emissions. Cultivated meat is an alternative that mimics animal meat, being produced in a bioreactor under controlled conditions rather than through the slaughtering of animals. The first step in the production of cultivated meat is the generation of sufficient reserves of starting cells. In this study, bovine adipose‐derived stem cells (bASCs) were used as starting cells due to their ability to differentiate towards both fat and muscle, two cell types found in meat. A bioprocess for the expansion of these cells on microcarriers in spinner flasks was developed. Different cell seeding densities (1,500, 3,000, and 6,000 cells/cm2) and feeding strategies (80%, 65%, 50%, and combined 80%/50% medium exchanges) were investigated. Cell characterization was assessed pre‐ and postbioprocessing to ensure that bioprocessing did not negatively affect bASC quality. The best growth was obtained with the lowest cell seeding density (1,500 cells/cm2) with an 80% medium exchange performed (p < .0001) which yielded a 28‐fold expansion. The ability to differentiate towards adipogenic, osteogenic, and chondrogenic lineages was retained postbioprocessing and no significant difference (p > .5) was found in clonogenicity pre‐ or postbioprocessing in any of the feeding regimes tested.
The Gender Gap in Reaching “Old Age” in the Russian Federation: A Regional Approach

ABSTRACT Reaching older age and longevity in later life is determined by health and mortality across the life course. In the case of Russia, the history of high male mortality skews the interaction between population aging and gender. These differentials can be viewed through a spatial lens in order to both understand their causes, and to better determine policy responses, especially in a federal political system. Using alternative conceptualizations of the “boundary to old age”, we produce the first estimates of the gender gap in reaching “old age” for all Russian Federal Subjects using 2017 data. We identify some regional differentiations, but uncertainties around the consistency of registration as well as overall heterogeneity mean that clear-cut regional patterns are hard to ascribe. Our analysis shows the highly significant gender gap at the age of “becoming old” in Russia when disaggregated by region. When looking at the regional level and comparing to other countries, the range of male “boundaries to old age” is almost as great as the global range. We argue that when applying alternative “old-age thresholds”, this gap represents a more accurate representation of interaction between space, gender, and mortality in Russia. We conclude with policy and research priorities to better understand and ameliorate the drivers of these spatial and gendered inequalities.
Expression of GUS and GFP reporter genes in transgenic hairy roots of tomato and potato plants via Agrobacterium rhizogenes mediated transformation.

In response to the threats caused by phytopathogens and plant disease, this investigation looks at the potential of genetic modification technology as a strategy to protect plant crops globally. Specifically, it will explore the usefulness of GUS (β-Glucuronidase) and GFP (Green fluorescent protein) as reporter genes in Agrobacterium-mediated transformation of tomato (Lycopersicum esculentum L.) and potato (Solanum tuberosum L.) hairy roots. Transformation of Agrobacterium with GUS and GFP will be analysed using PCR to evaluate the efficacy of this vector. Compiling knowledge of genetic markers and transformation techniques will allow for high yield and efficient crop plant transformations.