Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanochemical modelling of dorsal closure reveals emergent cell behaviour in tissue morphogenesis

Tissue morphogenesis integrates cell type-specific biochemistry and architecture, cellular force generation and mechanisms coordinating forces amongst neighbouring cells and tissues. We use finite element-based modelling to explore the interconnections at these multiple biological scales in embryonic dorsal closure, where pulsed actomyosin contractility in adjacent Amnioserosa (AS) cells powers the closure of an epidermis opening. Based on our in vivo observations, the model implements F-actin nucleation periodicity that is independent of MyoII activity. Our model reveals conditions, where depleting MyoII activity nevertheless indirectly affects oscillatory F-actin behaviour, without the need for biochemical feedback. In addition, it questions the previously proposed role of Dpp-mediated regulation of the patterned actomyosin dynamics in the AS tissue, suggesting them to be emergent. Tissue-specific Dpp interference supports the model’s prediction. The model further predicts that the mechanical properties of the surrounding epidermis tissue feed back on the shaping and patterning of the AS tissue. Finally, our model’s parameter space reproduces mutant phenotypes and provides predictions for their underlying cause. Our modelling approach thus reveals several unappreciated mechanistic properties of tissue morphogenesis.
Theory-Driven Analysis of Large Corpora: Semisupervised Topic Classification of the UN Speeches

There is a growing interest in quantitative analysis of large corpora among the international relations (IR) scholars, but many of them find it difficult to perform analysis consistently with existing theoretical frameworks using unsupervised machine learning models to further develop the field. To solve this problem, we created a set of techniques that utilize a semisupervised model that allows researchers to classify documents into predefined categories efficiently. We propose a dictionary making procedure to avoid inclusion of words that are likely to confuse the model and deteriorate the its classification performance classification accuracy using a new entropy-based diagnostic tool. In our experiments, we classify sentences of the United Nations General Assembly speeches into six predefined categories using the seeded Latent Dirichlet allocation and Newsmap, which were trained with a small “seed word dictionary” that we created following the procedure. The result shows that, while keyword dictionary can only classify 25% of sentences, Newsmap can classify over 60% of them accurately correctly and; its accuracy exceeds 70% when contextual information is taken into consideration by kernel smoothing of topic likelihoods. We argue that once seed word dictionaries are created by the international relations community, semisupervised models would become more useful than unsupervised models for theory-driven text analysis.
Optimizing high tunnel vegetable crop production through grafting, cultivar selection, and microclimate modification

Tomatoes and peppers are two of the most popular vegetable crops within the state of Iowa. Both solanaceous crops benefit from high tunnel production which allows for earlier planting and fruit production, improved yields and fruit quality, and an extended growing season. While tomatoes and peppers are two of the most economically beneficial crops to grow within high tunnels, growers struggle to optimize yields and manage the environment inside high tunnels, primarily heat and light. In the case of tomato, the use of vigorous, disease-resistant tomato rootstocks has become a sought-after production tool for increasing yields and productivity, although results are often tied to scion x rootstock x environment interactions. Additionally, adoption of tomato grafting is on the rise across the country, and growers are eager for information on how to successfully produce grafted plants. One of the main challenges that exist in grafting is the healing of plants immediately after grafting in order to optimize plant survival. Healing chambers can be either locally constructed or bought, but this input adds to the overall cost of producing a grafted plant. Growers are interested in learning about low-input alternative healing systems that are less expensive, yet efficient, in producing a successful graft union. While pepper production can also be improved through grafting, a more immediate concern for Iowa growers is the management of high temperatures and solar radiation within high tunnels which can contribute to increased flower abortion, decreased fruit set, and decreased yield due to losses from both abiotic and biotic disorders. High tunnels are an excellent resource for season extension in early spring and late fall, however, they can capture and hold excessive heat during peak summer months. The overarching goal of this research was to test and improve the use of grafting and shade cloth placement to improve tomato and pepper production in Midwest high tunnels. We
Morphologic, Immunohistochemical and Molecular Analyses of a Huge Clear Cell Papillary Renal Cell Carcinoma

Among the tumors of the kidney, the clear cell papillary renal cell carcinoma (CCPRCC) is a recently described entity. This tumor is well circumscribed, with a fibrous capsule, showing mostly a prominent cystic component and a diameter less than 4 cm. Necrosis is not a feature. Tumor cells are clear with low grade nuclei with a predominantly tubule-papillary architecture and immunohistochemical staining strongly positive for CK7, and for CA IX and negative for RACEMASE, features which differentiate this tumor from clear cell renal cell carcinoma (CCRCC) and papillary renal cell carcinoma (papillary RCC). In these latter tumors, it has been reported, unlike the other two, no loss or gain of chromosomes 7 and Y, no chromosome 3p deletion, and no KRAS mutation. In this report, a huge clear cell papillary renal cell carcinoma case, 9 cm diameter, in a 42-year-old male is described. Pathologic diagnosis of the tumor was confirmed by immunohistochemical analysis including CD10, CA IX, CK7, RACEMASE, and 34 beta E12 stainings. Molecular detection of KRAS, BRAF, NRAS, PIK3CA, ALK, ERBB2, DDR2, MAP2K1, RET, and EGFR gene mutational analysis has also been performed. Molecular findings are in accordance with the speculation that the CCRCC is an indolent tumor which may be defined as low malignant potential. In fact, in the molecular analysis, none out of all genes evaluated showed mutation.
Stochastic Parameterizations and the Climate Response to External Forcing: An Experiment With EC‐Earth

The impacts of including stochastic physics schemes (SPS) in the atmospheric component of the EC‐Earth climate model is studied by analyzing coupled simulations from 1850 to 2160. Sea ice in the Arctic retreats more slowly when SPS are included. An abrupt loss of winter sea ice is simulated 10 years later if the SPS are activated. However, this abrupt collapse is associated with a global surface air temperature (GSAT) of 17.4 ± 0.35 °C in all the cases. While the transient climate sensitivity is smaller if SPS are included up to the end of the 21st century, the opposite occurs in a warmer climate and in the absence of Arctic sea ice all the year‐round. These results are explained by the skewed interaction between stochastic perturbations and the process of condensation. Under a warmer climate, tropical convection is enhanced with SPS leading to the formation of high‐level clouds, which further increases GSAT.
Role of Sub-constructs of Psychological Capital and Transformational Leadership in Engaging Employees in Service Sector

Abstract The purpose of this study is to examine the relationship between transformational leadership (TL) and employee engagement through the mediating role of the sub constructs of psychological capital. The article has used a single cross-sectional descriptive design. The sample consisted of 450 full-time employees working in the service sector in India. The data were mainly analyzed through structural and measurement model. The result of the study revealed that TL has an influence on employee engagement. The relationship between TL and employee engagement is mediated by sub-construct hope of psychological capital. Implication of this study is of high importance for organizations continuously working to increase the level of employee engagement to further enhance competitiveness. Prior research has examined the antecedents of employee work engagement, but little is known about the role of TL and a positive psychological state, in shaping employee work engagement. Imparting TL training and style can help to generate psychological capital which will positively drive employee engagement. Organizations with transformational leaders will be able to make employees feel valued and happy by igniting feeling of hope. The engaged workforce will result in the positive social outcome. This study is original as earlier studies have not explored the important role of hope and also optimism as dimensions of psychological capital. The article supports the critical role of leadership and psychological capital in creating highly engaged employees which have not been studied in an Indian context with specific focus to the service sector.
Analogical and Metaphorical Thinking, Storytelling, and Entrepreneurial Identity and Narrative Development: A Visual Art-Based Learning Innovation

This article describes a novel visual art-based exercise (VAE) that was developed and conducted as part of an introductory-level, project-based entrepreneurial leadership course. The VAE engages students in reflective explorations of paintings and analogical and metaphorical thinking and analysis in support of two learning outcomes. The first outcome is for students to gain greater awareness of their emergent entrepreneurial identities. The second outcome is for students to enhance their capacities to effectively integrate analogies and metaphors with entrepreneurial narratives. Participatory inquiry guides the structure and delivery of the VAE with its application being focused on opportunity identification and conceptualization, solution development, and entrepreneurial narrative development and delivery. The three stages of the exercise (i.e., Staging, Transfer, and Integration) are described in detail, and its effectiveness is qualitatively assessed specific to the intended outcomes in order to facilitate and support adoption.
Anxiety among people living with HIV/AIDS on antiretroviral treatment attending tertiary care hospitals in Lucknow, Uttar Pradesh, India

Background: One of the major health challenges faced by India is the rapid growth of HIV/AIDS and its impact upon human life. Co-morbidities like anxiety are often overlooked while providing ART services to HIV/AIDS patients. Therefore the present study was conducted to assess the anxiety and associated factors among PLHA (People Living with HIV/AIDS) on antiretroviral treatment attending tertiary care hospitals in Lucknow. Methods: Hospital‑based cross-sectional study was conducted from November 2013 to March 2014 among 170 patients on treatment attending antiretroviral therapy (ART) centre of two tertiary care hospitals of Lucknow. Systematic random sampling was used to recruit patients. The anxiety level of all included patients was scored as per Hamilton anxiety rating scale. Results: The mean HAM-A score of 179 patients was 10.74±6.04. Majority (92.1%) of the patients had HAM-A score less than 17 indicating mild severity, 5.0% of the patient had mild to moderate severity while only 2.7% had moderate to severe level of anxiety symptoms. None of the patient had very severe level of anxiety. Significant association was found between level of anxiety symptoms with educational status (0.03), perception of side-effects during last one month (0.03) and duration of treatment (0.04). Conclusions: People living with HIV/AIDS need to be periodically educated and informed about various issues associated with the disease severity and antiretroviral treatment along with its side-effects so that they could better cope with disease and its treatment outcomes over time and be able to seek early treatment accordingly.
Single-cell resolution characterization of circulating tumor cell clusters

Metastatic dissemination is responsible for more than 90% of cancer-related deaths. However, the molecular features underlying the metastatic process are largely uncharacterized. Cancer cells that leave a primary tumor and enter the bloodstream are referred to as circulating tumor cells (CTCs). While extraordinarily rare compared to normal blood cells, their isolation and characterization offers a unique opportunity to study how metastasis occurs. Recent breakthrough developments in microfluidics technology have enabled a more detailed examination of blood samples, highlighting that tumor cells in circulation are organized as single and clustered CTCs, with the latter being associated with greater metastatic potential. Moreover, an additional subtype of CTCs was observed and characterized as white blood cells (WBCs) – associated CTCs with unknown prevalence and function. The goal of my Ph.D. Thesis was to investigate CTCs in depth by implementing a novel approach in cancer metastasis research. For the first time, a single cell-resolution, parallel genome and transcriptome sequencing of single, clustered and WBC-associated CTCs of cancer patients and metastatic mouse models have been applied. This technique provided a mean for multiple observations including a breakthrough discovery – WBCs circulating in association with tumor cells have a crucial impact on their metastatic potential and these cell aggregates were described as the most metastatic CTC subtype. Moreover, single-cell RNA sequencing revealed a specific pattern of these WBCs, with neutrophils representing the majority of the cases. Additionally, cell-cell junction and cytokine-receptor pairs that define CTC-neutrophil clusters were described and proposed as key vulnerabilities of the metastatic process. Thus, the association between neutrophils and CTCs fuels cell cycle progression within the bloodstream and expands the metastatic potential of CTCs, providing a rationale for targeting this interaction in breast cancer. Over the course of three and a half years, more than 160 patients with diverse cancer types agreed to donate blood for the ‘CTC Study’. The association between crucial clinical parameters and CTC characteristics have been evaluated in a selected group of 73 consecutive patients characterized by progressive invasive breast cancer, high tumor load, and treatment discontinuation. Among these patients, a correlation between treatment with the monoclonal antibody denosumab and the absence of CTCs were observed. Additionally, low red blood cell count was associated with the presence of CTCs, whereas high CA 15-3 tumor marker, high mean corpuscular volume, high white blood cell count and high mean platelet volume associated specifically with CTC clusters. These findings carry clinical applications, however further studies will be needed to validate the involvement of denosumab in the prevention of CTC generation.
Health, wellness, and workplace experiences of lesbian, gay, and bisexual social workers

Abstract Using data from an online survey of 6,112 licensed social workers in 13 U.S. states, rates of reported behavioral health problems and service utilization, physical health problems, adverse childhood experiences, workplace stress, and compassion satisfaction were compared between heterosexual male, heterosexual female, gay/bisexual male, and lesbian/bisexual female respondents. Sexual minority workers reported far higher rates of mental health problems and service utilization, higher rates of physical problems, more frequent reporting of adverse childhood experiences, with no differences found between groups regarding workplace stress and compassion satisfaction. Minority stress theory and historical trauma are used as frameworks to conceptualize the findings.
Nutritional surveillance in Tuscany. Relationship between 8-9 y-old school children BMI and parents’ BMI and educational level.

Introduction. Parents are responsible not only for the genetic structure of their children, but also for passing on their behaviours and attitudes toward life. It is, therefore, interesting to study if there is any connection between school-age children's obesity and that of their parents as well as between children's obesity and parents' educational level, as a partial indicator of the socio-economic status (SES) of the family in Tuscany. Methods. We gathered a statistical sample of 3,076 (1,583 males and 1,493 females) 8- to 9-year-old school children; their weight and height were measured by standardized personnel and instruments. We calculated the Body Mass Index (BMI) classes using Cole et al. cut-off for children and adolescents. A self-administered questionnaire revealed the patents' weight, height and educational level. The educational levels were classified as high, medium and low. Results. The prevalence of obese children rose with increases in the parents' BMI class: from 1.6% for underweight mothers to 22.8% for obese mothers and from 7.1% for under-normal-weight fathers to 18.7% for obese fathers (P < 0.001). An inverse relationship was observed for the parents' educational level, the lowest educational level corresponding to the highest prevalence of obese children: 19.7% for mothers with a low educational level compared to 2.7% for mothers with a high educational level (P < 0.001); similarly, the corresponding prevalence for fathers was 13.0% compared to 3.8% (P < 0.05). Conclusion. The parents' obesity and the cultural resources of the family, particularly the mother's, seem to influence the prevalence of overweight and obesity in pre-pubertal children in Tuscany.
Prevalência de diabetes mellitus e adesão medicamentosa em idosos da Estratégia Saúde da Família de Porto Alegre/RS

Introducao Com o envelhecimento populacional, ha o aparecimento de doencas cronicas incapacitantes, entre as quais se destaca a diabetes mellitus (DM). O objetivo do estudo e descrever a prevalencia de DM em idosos da Estrategia Saude da Familia (ESF) de Porto Alegre, no Estado do Rio Grande do Sul, de acordo com o tratamento, a adesao medicamentosa e variaveis sociodemograficas e de saude. Metodos Estudo transversal, realizado em individuos acima de 60 anos. Os dados foram coletados por instrumento (dados sociodemograficos, condicoes de saude, habitos de vida e informacoes de medicamentos). A adesao medicamentosa foi avaliada pela escala de Morisky. Resultados Foram analisados 763 idosos, com idade media de 69,1±7,5 anos, dos quais 63,7% eram do sexo feminino. A prevalencia de DM foi de 23,5%, principalmente nas mulheres (27,2%), na faixa etaria de 60 a 79 anos (24,6%), nos viuvos (28,4%) e nos que relataram ter cuidador (27,6%). Nas variaveis de saude, idosos com maior indice de massa corporal (IMC) e aqueles com doenca cardiaca apresentaram maior prevalencia de DM. A metformina foi o hipoglicemiante que apresentou maior frequencia de uso (76,5%). Conclusao A atencao ao idoso diabetico vem crescendo nas ESF, por isso este estudo contribuira para o desenvolvimento de estrategias para melhor atencao a essa populacao.
The Euler characteristic and topological phase transitions in complex systems

In this work, we use methods and concepts of applied algebraic topology to comprehensively explore the recent idea of topological phase transitions (TPTs) in complex systems. TPTs are characterized by the emergence of nontrivial homology groups as a function of a threshold parameter. Under certain conditions, one can identify TPTs via the zeros of the Euler characteristic or by singularities of the Euler entropy. Recent works provide strong evidence that TPTs can be interpreted as the intrinsic fingerprint of a complex network. This work illustrates this possibility by investigating various networks from a topological perspective. We first review the concept of TPTs in brain networks and discuss it in the context of high-order interactions in complex systems. We then investigate TPTs in protein–protein interaction networks using methods of topological data analysis for two variants of the duplication–divergence model. We compare our theoretical and computational results to experimental data freely available for gene co-expression networks of S. cerevisiae, also known as baker’s yeast, as well as of the nematode C. elegans. Supporting our theoretical expectations, we can detect TPTs in both networks obtained according to different similarity measures. We then perform numerical simulations of TPTs in four classical network models: the Erdős–Rényi, the Watts–Strogatz, the random geometric, and the Barabasi–Albert models. Finally, we discuss the relevance of these insights for network science. Given the universality and wide use of those network models across disciplines, our work indicates that TPTs permeate a wide range of theoretical and empirical networks, offering promising avenues for further research.
Pharmacogenomics of CYP3A5 Polymorphism: Predicting Dose-adjustedTrough Levels of Tacrolimus in South Indian Renal Transplant Patients

Tacrolimus is a potent immunosuppressant clinically used for the long term treatment of antirejection of transplanted organs in liver and kidney transplant recipients although dose optimization is often poorly managed. So far, no study has been carried out in the South Indian kidney transplant patients. The objective of this study was to evaluate the potential influence of a functional polymorphism in CYP3A5*3 gene on tacrolimus physiological availability/dose ratio in South Indian renal transplant patients. Twenty five renal transplant recipients receiving tacrolimus were enrolled in this study. Their body weight, drug dosage, and therapeutic concentration of tacrolimus were observed. All patients were on a standard immunosuppressive regime of tacrolimus-mycophenolate mofetil (Immunosuppressant) along with steroids at a starting dose of 0.1 mg/kg/day tacrolimus. CYP3A5 genotyping was performed by PCR followed with RFLP. Confirmation of RFLP analysis and variation in the nucleotide sequence of CYP3A5*3 gene were determined by direct sequencing using a validated automated genetic analyzer. A significant association was found between tacrolimus dose/kg/d and CYP3A5 gene (A6986G) polymorphism in the study population. The CYP3A5 *1/*1,*1/*3 and *3/*3 genotypes were detected in 5 (20%), 5 (20%) and 15 (60%) of the 25 graft recipients, respectively. CYP3A5*3 genotypes were found to be a good predictor of tacrolimus Level/Dose (L/D) ratio in kidney transplant recipients. Significantly higher L/D ratios were observed among non-expressors 9.483 ng/mL (range 4.5-14.1 ng/mL) as compared with the expressors 5.154 ng/mL (range 4.42-6.5 ng/mL) of CYP3A5. Biopsy Proven Acute Rejection (BPAR) episodes were significantly higher in CYP3A5*1 homozygotes compared to patients with CYP3A5*1/*3 and CYP3A5*3/*3 genotypes (40% vs. 20% and 13%, respectively). The dosenormalized tacrolimus concentration (ng/mL/mg/Kg) was significantly lower in patients having CYP3A5*1/*3 polymorphism. This is the first study to extensively determine the effect of CYP3A5*3 genetic polymorphism on tacrolimus pharmacokinetics in South Indian renal transplant recipients, and this study also showed that the majority of our patients carry mutant allele A6986G in the CYP3A5*3 gene. Identification of CYP3A5 polymorphism prior to transplantation is important for selecting the appropriate initial dosage of tacrolimus for each patient.
Relaxation methods for optimal control problems

We consider a nonlinear optimal control problem with dynamics described by a differential inclusion involving a maximal monotone map [Formula: see text]. We do not assume that [Formula: see text], incorporating in this way systems with unilateral constraints in our framework. We present two relaxation methods. The first one is an outgrowth of the reduction method from the existence theory, while the second method uses Young measures. We show that the two relaxation methods are equivalent and admissible.