Miracle-dz/UniFAR-FTUs huggingface dataset:
Animal Health in Compost-Bedded Pack and Cubicle Dairy Barns in Six European Countries

Simple Summary Dairy barns with compost-bedded pack housing systems are relatively new in Europe. They have housing systems that are vastly different from traditional tie-stall or cubicle housing and provide possibilities for improved animal welfare. However, it is important to investigate how actual cow health is influenced. We used readily available data from 32 dairy herds throughout Europe, half of which had compost-bedded pack housing and half cubicle housing, to investigate differences in dairy cow health. We found that herds with compost-bedded packs had poorer udder health than did herds with cubicles, while they seemed to have fewer problems with reproductive disorders. Our conclusion was that there were few, relatively minor differences between the systems. This knowledge is valuable for farmers interested in applying new housing systems for dairy cows and for consumers who want to stay informed about production conditions in dairy herds. Abstract The purpose of this study was to compare animal health in compost-bedded pack (CBP) and cubicle housing (CH) systems using data from dairy herd improvement associations. Thirty-two commercial dairy farms located in Austria, Germany, Italy, The Netherlands, Slovenia, and Sweden were included in the study. A matching design (pairing CBP and CH within country) according to herd selection criteria was used. We explored the following health indicators: somatic cell counts (SCC), high SCC, new high SCC, ketosis risk, prolonged calving intervals, dystocia, and stillbirth. Traits for culling and culling-related issues, such as length of life and length of productive life, were also included. We used multivariable (mixed) linear and logistic regression models to evaluate differences between the systems. Udder health, as measured by SCC, was inferior in CBP, although the geometric means were low in both systems. The incidence of stillbirths was higher in CBP, while prolonged calving intervals were fewer, indicating that there were fewer reproductive disorders. There were no differences in longevity between the systems, although CBP had lower proportions of first calvers. Overall, we conclude that there were few and minor differences in health and longevity between the CBP and CH systems in the European context.
Prickle isoform participation in distinct polarization events in the Drosophila eye

Planar cell polarity (PCP) signaling regulates several polarization events during development of ommatidia in the Drosophila eye, including directing chirality by polarizing a cell fate choice and determining the direction and extent of ommatidial rotation. The pksple isoform of the PCP protein Prickle is known to participate in the R3/R4 cell fate decision, but the control of other polarization events and the potential contributions of the three Pk isoforms have not been clarified. Here, by characterizing expression and subcellular localization of individual isoforms together with re-analyzing isoform specific phenotypes, we show that the R3/R4 fate decision, its coordination with rotation direction, and completion of rotation to a final ±90° rotation angle are separable polarization decisions with distinct Pk isoform requirements and contributions. Both pksple and pkpk can enforce robust R3/R4 fate decisions, but only pksple can correctly orient them along the dorsal-ventral axis. In contrast, pksple and pkpk can fully and interchangeably sustain coordination of rotation direction and rotation to completion. We propose that expression dynamics and competitive interactions determine isoform participation in these processes. We propose that the selective requirement for pksple to orient the R3/R4 decision and their interchangeability for coordination and completion of rotation reflects their previously described differential interaction with the Fat/Dachsous system which is known to be required for orientation of R3/R4 decisions but not for coordination or completion of rotation.
Trajectory analyses in insurance medicine studies: Examples and key methodological aspects and pitfalls

Background Trajectory analyses are being increasingly used in efforts to increase understanding about the heterogeneity in the development of different longitudinal outcomes such as sickness absence, use of medication, income, or other time varying outcomes. However, several methodological and interpretational challenges are related to using trajectory analyses. This methodological study aimed to compare results using two different types of software to identify trajectories and to discuss methodological aspects related to them and the interpretation of the results. Methods Group-based trajectory models (GBTM) and latent class growth models (LCGM) were fitted, using SAS and Mplus, respectively. The data for the examples were derived from a representative sample of Spanish workers in Catalonia, covered by the social security system (n = 166,192). Repeatedly measured sickness absence spells per trimester (n = 96,453) were from the Catalan Institute of Medical Evaluations. The analyses were stratified by sex and two birth cohorts (1949–1969 and 1970–1990). Results Neither of the software were superior to the other. Four groups were the optimal number of groups in both software, however, we detected differences in the starting values and shapes of the trajectories between the two software used, which allow for different conclusions when they are applied. We cover questions related to model fit, selecting the optimal number of trajectory groups, investigating covariates, how to interpret the results, and what are the key pitfalls and strengths of using these person-oriented methods. Conclusions Future studies could address further methodological aspects around these statistical techniques, to facilitate epidemiological and other research dealing with longitudinal study designs.
Statistical optimization of arachidonic acid synthesis by Mortierella alpina CBS 754.68 in a solid‐state fermenter

Abstract Arachidonic acid (ARA) is an omega‐6 fatty acid that plays a major role in human health. The present study optimizes the production of ARA by the soil fungus Mortierella alpina CBS 754.68 on oil cakes. In the first step, the best substrate was chosen from four oil cakes, namely soybean, sunflower, olive, and colza oil cakes, of which sunflower oil cake showed the highest yield. In the next step, screening tests were performed using the Plackett‐Burman design. Seven variables (substrate particle size, moisture content, time, temperature, yeast extract, glucose, and glutamate) were investigated (each taking values of +1 and −1). Among these variables, time, temperature, and substrate particle size significantly affected ARA production (p < .05), so they were further investigated in the optimization step. The optimal fermentation time, temperature, and substrate particle size calculated by response surface methodology were 8.75 days, 18.5°C, and 1.3 mm–1.7 mm, respectively. Under these conditions, M. alpina was predicted to produce 4.19 mg of ARA/g dry weight of substrate (DWS). The actual yield, determined in evaluation tests, was 4.48 ± 0.16 mg ARA/g DWS, which shows the accuracy of the model. In the final step, the effect of the aeration rate on producing ARA was investigated in a packed‐bed solid‐state fermenter under the determined optimal conditions. In this stage, the highest ARA yield was 10.13 ± 0.26 mg/g DWS, approximately double that of the optimization step, and this confirms that aeration increases ARA production by M. alpina.
Where to Retire? Experiences of Older African Immigrants in the United States

Doubling in size since the 1970s, the aging needs of the African immigrant population are not fully understood. This qualitative study examined experiences of aging and retirement planning for African immigrant older adults in the United States (U.S.). Specifically, it explored the factors, processes, and ultimate decision of where these older adults planned to retire. Secondary analysis of semi-structured interviews with 15 older African immigrants in the Baltimore–Washington Metropolitan area was conducted. Data was analyzed using thematic analyses in NVivo. The majority of participants were women, with a mean age of 64. Three overarching themes with ten sub-themes were identified. The themes included: (1) cultural identity, which indicated the participant’s comfort with the U.S. society and culture; (2) decision making, meaning factors that impact participants’ choice of retirement location; and (3) decision made, meaning the final choice of where participants would like to retire. Age-friendliness for immigrant older adults in the U.S. is complex and it includes traditional domains such as physical and sociocultural environment (e.g., housing, transportation, and income). However, immigrant age-friendliness also needs to include wider contextual aspects such as political climate of their country of origin, immigrant status, family responsibilities, and acculturation in the U.S. More research is needed to better understand and facilitate age-friendly environments and transnational aging of immigrant older adults.
Treatment of Graves' Disease Associated With Severe Neutropenia

Severe neutropenia in newly diagnosed hyperthyroidism is a diagnostic and therapeutic dilemma since antithyroid drugs (ATDs) cannot be started if the absolute neutrophil count (ANC) is <1 x 109/L. We report the case of a patient followed for hyperthyroidism associated with severe neutropenia treated with dexamethasone and ATD. The patient was 51 years old and was hospitalized for hyperthyroidism with a thyroid stimulating hormone (TSH) level <0.005 (0.4-4) mUI/L, T4 at 415 (9.3-17.1) ng/L and T3 at 148 (2-4.4) pg/mL on Graves' disease (GD) confirmed by the TSH receptor antibodies at 38 IU/mL and scintigraphy, associated with neutropenia, with ANC at 0.4 x 109/L. He was put on prednisolone 60 mg/day and propranolol 60 mg/day for three weeks without improvement. Faced with the association of hyperthyroidism and severe neutropenia, we could not start the ATD for fear of agranulocytosis; we put the patient on propranolol 60 mg and dexamethasone 6 mg with progressive degression resulting in a spectacular increase of ANC from 0.4 x 109/L to 7.1 x 109/L, which allowed us to start the ATD (carbimazole) at a dose of 30 mg, and then 50 mg, with monitoring of ANC and transaminases every 48 hours. Euthyroidism was achieved after 15 days. A curative treatment with radioactive iodine ablation was administered. Our patient did not respond to prednisolone but responded dramatically to dexamethasone; this leads us to consider using dexamethasone for the rapid preparation for radical treatment of patients with GD.
Role of Betatrophin and Inflammation Markers in Type 2 Diabetes Mellitus, Prediabetes and Metabolic Syndrome.

OBJECTIVE To determine the association of betatrophin and inflammation factors in metabolic diseases such as diabetes, impaired fasting glucose, impaired glucose tolerance and metabolic syndrome. STUDY DESIGN A cross-sectional, analytical study. PLACE AND DURATION OF STUDY Fırat University Medical School between April 2017 and December 2020. METHODOLOGY The study included 20 patients with type 2 diabetes mellitus, 20 patients with impaired fasting glucose (IFG), 20 patients with impaired glucose tolerance (IGT), 20 patients with metabolic syndrome (MetS), and a control group consisting of 20 healthy individuals. Anthropometric, fasting serum biochemical data were collected. Circulating betatrophin, and inflammation markers were measured by enzyme-linked immunosorbent assay (ELISA). The association of betatrophin, TNF-alpha, and IL-6 levels between groups were performed with One-way ANOVA and post-hoc Tukey HSD test. RESULTS Significantly higher levels of circulating betatrophin were observed in IFG, IGT, And MetS groups compared to healthy controls (p=0.017). There were significantly difference TNF-α levels in IFG, IGT, and MetS groups compared to healthy controls (p<0.001). The levels of IL-6 were significantly higher in MetS group than healthy controls (p=0.007). CONCLUSION The circulating betatrophin and TNF-α levels were increased in MetS, IFG and IGT. IL-6 was decreased in MetS compared to the healty controls. Further studies are needed to elucidate the role of betatrophin and inflammatory parameters in the development of T2DM and prediabetic syndromes, whether betatrophin could have clinical applications in the development of new antidiabetic agents. Key Words: Betatrophin, IL-6, TNF-alpha, Metabolic syndrome, Insulin resistance, Diabetes mellitus type 2.
Special Section on Pharmacokinetics and ADME of Biological Therapeutics — Minireview Characterizing the Pharmacokinetics and Biodistribution of Therapeutic Proteins: An Industry White Paper

Characterization of the pharmacokinetics and biodistribution of therapeutic proteins (TPs) is a hot topic within the pharmaceutical industry, particularly with an ever-increasing catalog of novel modality TPs. Here, we review the current practices, and provide a summary of extensive cross-company discussions as well as a survey completed by International Consortium for Innovation and Quality members on this theme. A wide variety of in vitro, in vivo and in silico techniques are currently used to assess pharmacokinetics and biodistribution of TPs, and we discuss the relevance of these from an industry perspective, focusing on pharmacokinetic/ pharmacodynamic understanding at the preclinical stage of development, and translation to human. We consider that the ‘ traditional in vivo biodistribution study
Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All

Abstract Inflammatory bowel disease [IBD] has a multifactorial origin and originates from a complex interplay of environmental factors with the innate immune system at the intestinal epithelial interface in a genetically susceptible individual. All these factors make its aetiology intricate and largely unknown. Multi-omic datasets obtained from IBD patients are required to gain further insights into IBD biology. We here review the landscape of multi-omic data availability in IBD and identify barriers and gaps for future research. We also outline the various technical and non-technical factors that influence the utility and interpretability of multi-omic datasets and thereby the study design of any research project generating such datasets. Coordinated generation of multi-omic datasets and their systemic integration with clinical phenotypes and environmental exposures will not only enhance understanding of the fundamental mechanisms of IBD but also improve therapeutic strategies. Finally, we provide recommendations to enable and facilitate generation of multi-omic datasets.
Correlation of metabolic characteristics with maternal, fetal and placental asprosin in human pregnancy

Objective Asprosin is a recently discovered hormone associated with obesity and diabetes mellitus. Little is known about asprosin’s role during pregnancy, but a contribution of asprosin to pregnancy complications resulting from maternal obesity and gestational diabetes mellitus (GDM) is conceivable. We assessed the potential effects of obesity, GDM and other clinical parameters on maternal and fetal umbilical plasma asprosin concentrations and placental asprosin expression. Design The Cologne-Placenta Cohort Study comprises 247 female patients, from whom blood and placentas were collected at the University Hospital Cologne. Methods We studied the maternal and fetal umbilical plasma and placentas of pregnant women with an elective, primary section. Sandwich ELISA measurements of maternal and fetal umbilical plasma and immunohistochemical stainings of placental tissue were performed to determine the asprosin levels. Also, the relation between asprosin levels and clinical blood parameters was studied. Results There was a strong correlation between the maternal and fetal plasma asprosin levels and both increased with GDM in normal-weight and obese women. Asprosin immunoreactivity was measured in cultivated placental cells and placental tissue. BMI and GDM were not but pre-pregnancy exercise and smoking were correlated with maternal and/or fetal asprosin levels. Placental asprosin levels were associated with maternal but not with fetal plasma asprosin levels and with BMI but not with GDM. Placental asprosin was related to maternal insulin levels and increased upon insulin treatment in GDM patients. Conclusions Asprosin could potentially act as a biomarker and contribute to the clinical manifestation of pregnancy complications associated with maternal obesity.
A Prostate Specific Membrane Antigen-Targeted Near-Infrared Conjugate for Identifying Pulmonary Squamous Cell Carcinoma During Resection.

Pulmonary squamous cell carcinoma is the second-most common lung cancer subtype and has a low 5-year survival rate at 17.6%. Complete resection with negative margins can be curative, but a high number of patients suffer early postoperative recurrence due to inadequate disease clearance at the index operation. Intraoperative molecular imaging (IMI) with tumor-targeted optical contrast agents is effective in improving resection completeness for other tumor types, but there are no IMI tracers targeted to pulmonary squamous cell carcinoma. In this report, we describe the use of a novel prostate specific membrane antigen (PSMA)-targeted near-infrared conjugate (OTL78) to identify pulmonary squamous cell carcinoma. We identified PSMA as a viable target by examining its expression in human lung tumor specimens from a surgical cohort. 94% of tumors expressed PSMA in either the pulmonary squamous cells or in the tumor neovasculature. Using in vitro and in vivo models, we found that OTL78 reliably localized pulmonary squamous cell carcinoma in a PSMA-dependent manner. Lastly, we found that IMI with OTL78 markedly improved surgeons' ability to identify residual disease after surgery in a preclinical model. Ultimately, this novel optical tracer may aid surgical resection of pulmonary squamous cell carcinoma and potentially improve long-term outcomes.
Growth factor dependence of the proliferation and survival of cultured lacrimal gland epithelial cells isolated from late‐embryonic mice

Epidermal growth factor (EGF) and hepatocyte growth factor (HGF) regulate the growth and morphogenesis of various exocrine glands with branched morphologies. Their roles in lacrimal gland (LG) development remain unknown, but fibroblast growth factor (FGF) 10 is crucial for early LG organogenesis. To clarify the roles of EGF, HGF, and FGF10 in LG development, LG epithelial cells were isolated from late‐embryonic and neonatal mice; cultured; and treated with EGF, HGF, or FGF10 and their respective receptor tyrosine kinase (RTK) inhibitors AG1478, PHA665752, or SU5402. EGF and HGF increased the number of viable cells by enhancing DNA synthesis, FGF10 and SU5402 showed no such effect, and RTK inhibitors exhibited the opposite effect. EGF and HGF receptors were immunostained in cultured late‐embryonic LG epithelial cells and terminal LG acini from late embryos and adult mice. HGF was detected in neonatal LG epithelial cell culture supernatants by western blotting. In the absence of EGF and HGF RTK inhibitors, growth factor addition increased the number of viable cells and suppressed cell death. However, when one RTK was inhibited and a growth factor targeting an intact RTK was added, the number of dead cells increased as the number of viable cells increased. No cells survived when both RTKs were inhibited. In explant cultures of LGs from embryos, AG1478 or PHA665752 decreased the number of Ki67‐positive proliferating epithelial cells in terminal acini. Thus, EGF and HGF may function in a cooperative autocrine manner, supporting cell proliferation and survival during LG development in late‐embryonic and neonatal mice.
Effects of Transparency on Perceived Humanness: Implications for Rendering Skin Tones Using Optical See-Through Displays

Current optical see-through displays in the field of augmented reality are limited in their ability to display colors with low <italic>lightness</italic> in the hue, saturation, lightness (HSL) color space, causing such colors to appear transparent. This hardware limitation may add unintended bias into scenarios with virtual humans. Humans have varying skin tones including HSL colors with low lightness. When virtual humans are displayed with optical see-through devices, people with low lightness skin tones may be displayed semi-transparently while those with high lightness skin tones will be displayed more opaquely. For example, a Black avatar may appear semi-transparent in the same scene as a White avatar who will appear more opaque. We present an exploratory user study (<inline-formula><tex-math notation="LaTeX">$\mathrm{N}=160$</tex-math><alternatives><graphic position="float" orientation="portrait" xlink:href="28tvcg05-peck-3150521-eqinline-1-small.tif"/></alternatives></inline-formula>) investigating whether differing opacity levels result in dehumanizing avatar and human faces. Results support that dehumanization occurs as opacity decreases. This suggests that in similar lighting, low lightness skin tones (e.g., Black faces) will be viewed as less human than high lightness skin tones (e.g., White faces). Additionally, the perceived emotionality of virtual human faces also predicts perceived humanness. Angry faces were seen overall as less human, and at lower opacity levels happy faces were seen as more human. Our results suggest that additional research is needed to understand the effects and interactions of emotionality and opacity on dehumanization. Further, we provide evidence that unintentional racial bias may be added when developing for optical see-through devices using virtual humans. We highlight the potential bias and discuss implications and directions for future research.
Environmental DNA captures native and non-native fish community variations across the lentic and lotic systems of a megacity

Globally, urbanization poses a major threat to terrestrial biodiversity, yet its impact on fish diversity is poorly understood, mainly because of surveying difficulties. In this study, environmental DNA metabarcoding was used to survey fish communities at 109 lentic and lotic sites across Beijing, and how environmental variables affect fish biodiversity at fine urban spatial scales was investigated. We identified 52 native and 23 non-native taxa, with lentic and lotic waters harboring both common and habitat-specific species. Water quality strongly affected native fish diversity, especially in lentic systems, but had little influence on non-native diversity. Fish diversity showed little response to urban land cover variation, but the relative sequence abundance of non-natives in lotic waters increased linearly with distance from the city center. Our findings illustrate the complex effects of urbanization on native versus non-native fishes in different aquatic habitats and highlight the distinctive considerations needed to conserve urban aquatic biodiversity.