Miracle-dz/UniFAR-FTUs huggingface dataset:
Sense of belonging within the graduate community of a research-focused STEM department: Quantitative assessment using a visual narrative and item response theory

It is well-documented that the representation of women and racial/ethnic minorities diminishes at higher levels of academia, particularly in science, technology, engineering, and math (STEM). Sense of belonging—the extent to which an individual believes they are accepted, valued, and included in a community—is often emphasized as an important predictor of retention throughout academia. While literature addressing undergraduate sense of belonging is abundant, there has been little investigation of sense of belonging in graduate communities. Because graduate training is required to generate new scientific leaders, it is important to understand and address sense of belonging at the graduate level—paying explicit attention to devising strategies that can be used to increase representation at higher levels of academia. Here, a visual narrative survey and item response modeling are used to quantify sense of belonging among graduate students, postdoctoral researchers, and faculty within the Department of Chemistry at the University of California, Berkeley. Results suggest that graduate students, postdoctoral researchers, and faculty all experience impostor phenomenon. Respondents struggle most with maintaining positive self-perceptions of their productivity, capabilities as a scientist, and success—particularly in comparison to their peers. Communicating about science with peers, talking about teaching hurdles, and engaging in mentoring relationships also contribute significantly to sense of belonging. Faculty members have the highest sense of belonging, while senior graduate students and postdoctoral researchers are least likely to feel a sense of belonging. Additionally, graduate students and postdoctoral researchers who identify as underrepresented, as well as those who submit manuscripts for publication less than their peers, are less likely to feel a sense of belonging. This is the first study to generate a quantitative, nuanced understanding of sense of belonging within the entire graduate academic community of an R1 STEM department. We envision that these methods can be implemented within any research-focused academic unit to better understand the challenges facing community members and identify factors to address in promoting positive culture change. Furthermore, these methods and results should provide a foundation for devising interventions that academic stakeholders can use to directly improve graduate education.
Assessing Human Airway Epithelial Progenitor Cells for Cystic Fibrosis Cell Therapy.

Cystic fibrosis (CF) is caused by loss-of-function mutations in the CF transmembrane regulator (CFTR) gene. Pharmacologic therapies directed at CFTR have been developed but are not effective for mutations that result in little or no mRNA or protein expression. Cell therapy is a potential mutation-agnostic approach to treatment. One strategy is to harvest human bronchial epithelial cells (HBECs) for gene addition or genetic correction, followed by expansion and engraftment. This approach will require cells to grow extensively while retaining their ability to reconstitute CFTR activity. We hypothesized that conditionally reprogrammed cell (CRC) technology, namely growth in the presence of irradiated feeder cells and a Rho kinase inhibitor, would enable expansion while maintaining cell capacity to express functional CFTR. Our goal was to compare expression of the basal cell marker NGFR and 3D bronchosphere colony forming efficiency (CFE) in early and later passage HBECs grown using non-proprietary bronchial epithelial growth medium or the CRC method. Cell number and CFTR activity were determined in a competitive repopulation assay employing chimeric air-liquid interface (ALI) cultures. HBECs expanded using the CRC method expressed the highest NGFR levels, had the greatest 3D CFE at later passage, generated greater cell numbers in chimeric cultures, and most effectively reconstituted CFTR activity. In our study, the HBEC ALI model, an informative testing platform proven vital for the development of other CF therapies, illustrated that cells grown by CRC technology or equivalent methods may be useful for cell therapy of CF.
Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction

The enzymatic reactions leading to the deamination of β-lysine, lysine, or 2-aminoadipic acid are of great interest for the metabolic conversion of lysine to adipic acid. Enzymes able to carry out these reactions are not known, however ammonia lyases (EC 4.3.1.-) perform deamination on a wide range of substrates. We have studied 3-methylaspartate ammonia lyase (MAL, EC 4.3.1.2) as a potential candidate for protein engineering to enable deamination towards β-lysine, that we have shown to be a competitive inhibitor of MAL. We have characterized MAL activity, binding and inhibition properties on six different compounds that would allow to define the molecular determinants necessary for MAL to deaminate our substrate of interest. Docking calculations showed that β-lysine as well as the other compounds investigated could fit spatially into MAL catalytic pocket, although they probably are weak or very transient binders and we identified molecular determinants involved in the binding of the substrate. The hydrophobic interactions formed by the methyl group of 3-methylaspartic acid, together with the presence of the amino group on carbon 2, play an essential role in the appropriate binding of the substrate. The results showed that β-lysine is able to fit and bind in MAL catalytic pocket and can be potentially converted from inhibitor to substrate of MAL upon enzyme engineering. The characterization of the binding and inhibition properties of the substrates tested here provide the foundation for future and more extensive studies on engineering MAL that could lead to a MAL variant able to catalyse this challenging deamination reaction.
Status Variation in Anticipatory Stressors and Their Associations with Depressive Symptoms

Members of structurally disadvantaged social groups report more frequent exposure to a variety of negative life events and chronic strains, yet little research has examined whether similar patterns exist for anticipatory stressors, or challenging circumstances that loom as potential threats in the future. This study uses data collected as part of a national survey of college seniors (N = 995) to examine how anticipatory stress regarding economic and residential security, exposure to traumatic events, and experiences of discrimination vary by gender identity, race-ethnicity, sexual orientation, and first-generation college student status. Consistent with stress theory, anticipatory stressors are more commonly reported by members of disadvantaged groups. Notably, variation in anticipatory stressors explains a nontrivial proportion of differences in depressive symptoms found across gender identity and sexual orientation categories. Findings signal the necessity of incorporating anticipatory stressors into research in the stress paradigm to further disentangle the contributions of social stressors to health disparities.
Silicon Alters Leaf Surface Morphology and Suppresses Insect Herbivory in a Model Grass Species

Grasses accumulate large amounts of silicon (Si) which is deposited in trichomes, specialised silica cells and cell walls. This may increase leaf toughness and reduce cell rupture, palatability and digestion. Few studies have measured leaf mechanical traits in response to Si, thus the effect of Si on herbivores can be difficult to disentangle from Si-induced changes in leaf surface morphology. We assessed the effects of Si on Brachypodium distachyon mechanical traits (specific leaf area (SLA), thickness, leaf dry matter content (LDMC), relative electrolyte leakage (REL)) and leaf surface morphology (macrohairs, prickle, silica and epidermal cells) and determined the effects of Si on the growth of two generalist insect herbivores (Helicoverpa armigera and Acheta domesticus). Si had no effect on leaf mechanical traits; however, Si changed leaf surface morphology: silica and prickle cells were on average 127% and 36% larger in Si supplemented plants, respectively. Prickle cell density was significantly reduced by Si, while macrohair density remained unchanged. Caterpillars were more negatively affected by Si compared to crickets, possibly due to the latter having a thicker and thus more protective gut lining. Our data show that Si acts as a direct defence against leaf-chewing insects by changing the morphology of specialised defence structures without altering leaf mechanical traits.
Fully Automated Segmentation of Globes for Volume Quantification in CT Images of Orbits using Deep Learning

BACKGROUND AND PURPOSE: Fast and accurate quantification of globe volumes in the event of an ocular trauma can provide clinicians with valuable diagnostic information. In this work, an automated workflow using a deep learning-based convolutional neural network is proposed for prediction of globe contours and their subsequent volume quantification in CT images of the orbits. MATERIALS AND METHODS: An automated workflow using a deep learning -based convolutional neural network is proposed for prediction of globe contours in CT images of the orbits. The network, 2D Modified Residual UNET (MRes-UNET2D), was trained on axial CT images from 80 subjects with no imaging or clinical findings of globe injuries. The predicted globe contours and volume estimates were compared with manual annotations by experienced observers on 2 different test cohorts. RESULTS: On the first test cohort (n = 18), the average Dice, precision, and recall scores were 0.95, 96%, and 95%, respectively. The average 95% Hausdorff distance was only 1.5 mm, with a 5.3% error in globe volume estimates. No statistically significant differences (P = .72) were observed in the median globe volume estimates from our model and the ground truth. On the second test cohort (n = 9) in which a neuroradiologist and 2 residents independently marked the globe contours, MRes-UNET2D (Dice = 0.95) approached human interobserver variability (Dice = 0.94). We also demonstrated the utility of inter-globe volume difference as a quantitative marker for trauma in 3 subjects with known globe injuries. CONCLUSIONS: We showed that with fast prediction times, we can reliably detect and quantify globe volumes in CT images of the orbits across a variety of acquisition parameters.
Calanolides E1 and E2, two related coumarins from Calophyllum brasiliense Cambess. (Clusiaceae), displayed in vitro activity against amastigote forms of Trypanosoma cruzi and Leishmania infantum

Abstract In the present work, the MeOH extract from stem barks of Calophyllum brasiliense Cambess. (Clusiaceae) displayed activity against amastigote forms of Trypanosoma cruzi and Leishmania infantum and was subjected to a bioactivity-guided fractionation to give two related coumarins - calanolides E1 (1) and E2 (2). Compounds 1 and 2 were actives to T. cruzi with EC50 values of 12.1 and 8.2 μM, respectively. When tested against L. infantum, the EC50 values were 37.1 and 29.1 μM, respectively. Compound 2, corresponding to anti isomer, showed the best selectivity index (SI) with values >24.4 to T. cruzi and >6.9 to L. infantum in comparison to the syn isomer 1. Furthermore, using an in silico multi-parametric prediction, both compounds did not contain any PAINS sub-structures. Therefore, these data suggest that coumarins 1 and 2 may contribute as scaffolds for the design of novel drug candidates for leishmaniasis and Chagas disease. Graphical Abstract
2'-O-methoxyethyl splice-switching oligos correct splicing from IVS2-745 β-thalassemia patient cells restoring hemoglobin A production and chain rebalance

β-thalassemia is a disorder caused by altered hemoglobin protein synthesis which affects individuals worldwide. Severe forms of the disease, left untreated, can result in death before the age of 3 years.1 The standard of care consists of chronic and costly palliative treatment by blood transfusion combined with iron chelation. This dual approach suppresses anemia and reduces iron-related toxicities in patients. Allogeneic bone marrow transplant is an option, but limited by the availability of a highly compatible hematopoietic stem cell donor. While gene therapy is being explored in several trials, its use is highly limited to developed regions with centers of excellence and well-established healthcare systems. 2 Hence, there remains a tremendous unmet medical need to develop alternative treatment strategies for b-thalassemia.3 Occurrence of aberrant splicing is one of the processes that affects b-globin synthesis in b-thalassemia. The (C>G) IVS2-745 is a splicing mutation within intron 2 of the b-globin (HBB) gene. It leads to an aberrantly spliced mRNA that incorporates an intron fragment. This results in an in-frame premature termination codon that inhibits b-globin production. Here, we propose the use of uniform 2'-O-methoxyethyl (2'-MOE) splice switching oligos (SSO) to reverse this aberrant splicing in the pre-mRNA. With these SSO we show aberrant to wild-type splice switching. This switching leads to an increase of adult hemoglobin up to 80% in erythroid cells from patients with the IVS2-745 HBB mutation. Furthermore, we demonstrate a restoration of the balance between b-like- and α-globin chains, and up to an 87% reduction in toxic heme aggregates. While examining the potential benefit of 2'-MOE-SSO in a mixed sickle-thalassemic phenotypic setting, we found reduced sickle hemoglobin synthesis and sickle cell formation due to HbA induction. In summary, 2'-MOE-SSO are a promising therapy for forms of b-thalassemia caused by mutations leading to aberrant splicing.
Metabolites, Nutrients, and Lifestyle Factors in Relation to Coffee Consumption: An Environment-Wide Association Study

Coffee consumption has been inversely associated with various diseases; however, the underlying mechanisms are not entirely clear. We used data of 17,752 Third National Health and Nutrition Examination Survey participants to investigate the association of 245 metabolites, nutrients, and lifestyle factors with coffee consumption. We used data from the first phase (n = 8825) to identify factors with a false discovery rate of <5%. We then replicated our results using data from the second phase (n = 8927). Regular coffee consumption was positively associated with active and passive smoking, serum lead and urinary cadmium concentrations, dietary intake of potassium and magnesium, and aspirin intake. In contrast, regular coffee consumption was inversely associated with serum folate and red blood cell folate levels, serum vitamin E and C, and beta-cryptoxanthin concentrations, Healthy Eating Index score, and total serum bilirubin. Most of the aforementioned associations were also observed for caffeinated beverage intake. In our assessment of the association between coffee consumption and selected metabolites, nutrients, and lifestyle factors, we observed that regular coffee and caffeinated beverage consumption was strongly associated with smoking, serum lead levels, and poorer dietary habits.
The Effects of Combretum zeyheri Leaf Extract on Ergosterol Synthesis in Candida albicans

The in vitro effects of Combretum zeyheri leaf ethanol extract (CZLE) on ergosterol biosynthesis of Candida albicans were investigated by quantifying the ergosterol in C. albicans in the presence and absence of the extract using UV-visible spectrophotometric analyses. Miconazole was used as the positive control. CZLE showed ergosterol biosynthesis inhibition at sub-inhibitory concentration for growth of C. albicans and also at the MIC (0.08 mg.mL−1). The decrease in ergosterol in C. albicans cells was dose-dependant with 67%, 79%, and 100% after growing in 20, 40, and 80 μg. mL−1 of CZLE, respectively. CZLE exerted its fungicidal effects by targeting the ergosterol biosynthesis in C. albicans and disrupting the membrane integrity.
Zoonotic Vectorborne Pathogens and Ectoparasites of Dogs and Cats in Eastern and Southeast Asia

To provide data that can be used to inform treatment and prevention strategies for zoonotic pathogens in animal and human populations, we assessed the occurrence of zoonotic pathogens and their vectors on 2,381 client-owned dogs and cats living in metropolitan areas of 8 countries in eastern and Southeast Asia during 2017–2018. Overall exposure to ectoparasites was 42.4% in dogs and 31.3% in cats. Our data cover a wide geographic distribution of several pathogens, including Leishmania infantum and zoonotic species of filariae, and of animals infested with arthropods known to be vectors of zoonotic pathogens. Because dogs and cats share a common environment with humans, they are likely to be key reservoirs of pathogens that infect persons in the same environment. These results will help epidemiologists and policy makers provide tailored recommendations for future surveillance and prevention strategies.
Effect of dietary protein levels on reproductive development and distribution of amino acids in the body tissues of female Pangasianodon hypophthalmus (Sauvage, 1878) broodstock in captivity

The present study investigated the optimum dietary protein level for the maturation of adult Pangasianodon hypophthalmus broodstock. Four isocaloric diets containing 250, 300, 350 and 400 g kg−1 of protein levels were prepared and presented to triplicate groups of fish. The fish (mean weight 770 ± 17.23 g and 712 ± 23.42 g for females and males respectively) were stocked in outdoor canvas tanks (4 m × 1 m × 1 m) at a stocking density of 20 fish/tank with a male: female ratio of 1:4. The fish were fed the test diets to satiation twice daily for 6 months. Gonadosomatic index (GSI) and fecundity were similar among fish fed dietary protein levels, higher than those fed on the 250 g kg−1. Final weight, weight gain, oocyte weight were significantly highest (P < 0.05) for the fish fed 350 and 400 g kg−1 dietary protein treatments. Only the 350 g kg−1 dietary protein treatment resulted in significantly best ovipositor diameter and % ripe egg. Amino acid levels were highest in the muscle followed by the oocyte and liver of fish fed 350 and 400 g kg−1 dietary protein levels. The present results suggested that a dietary protein level of 350 g kg−1 can be recommended for the development of P. hypophthalmus broodstock.
Validation of the Phenology Model for the Codling Moth, Cydia pomonella (Lepidoptera: Tortricidae), in South African Pome Fruit Orchards

The codling moth, Cydia pomonella (Linnaeus) (Lepidoptera: Tortricidae), is a key pest of pome fruits in the Western Cape, South Africa. Up to 1993, the industry recommendation for commencement of the codling moth spray programme was at 75 % petal fall in order to avoid the negative impact of organophosphate sprays on bees during bloom. However, codling moth can emerge, mate and oviposit before and during full bloom in pome fruit orchards. Consequently, petal-fall does not necessarily correspond with the commencement of egg-laying or first egg hatch. The availability of insecticides with a softer environmental profile made it possible to apply sprays earlier than 75 % petal-fall. The development of phenology models provided a means of accurately predicting biological events such as the initiation of egg-laying and first egg hatch. Using lower and upper development thresholds of 10 °C and 32 °C, respectively, and hourly temperature recordings, phenology models were evaluated by comparing the number of degree-days (°D) accumulated using a selection of three biofixes, and date of first egg hatch. The number of °D accumulated from the selection of biofixes to first observed egg hatch varied from 130.7 to 179. The least variation in the number of °D between biofix and first egg hatch occurred when the second trap catch was used as the biofix. A biofix based on the first evening when the temperature reached or exceeded 17 °C at 18:00 after first trap catch also showed less variation than when the biofix was based on first trap catch. The mean number of °D at which 50 % of the moths of the first flight emerged was 166.6 °D, while the mean number of °D at which 50 % oviposition occurred was 290 °D following biofix. The number of °D between the second and third flight biofixes varied between 488.7 and 531.2 °D, with a mean of 508.1 °D. The results are of significance in improving the timing and reducing the number of insecticide sprays for codling moth control.
New Chromosome Number Reports in Cousinia Species (Compositae)

The cytological study of several populations in 4 species of Cousinia tenuifolia, C. tabrisiana, C. urumiensis and C. microcephala showed the occurrence of 2n=2x=26 chromosome number in all the species studied, information which is new to science. The species formed mainly bivalents and univalents in the metaphase of meiosis I, but in some populations quadrivalents were also formed due to heterozygote translocations. A wide range of meiotic abnormalities were observed including laggard chromosome formation, chromosomes stickiness and tripolar cell formation, leading to the formation of unreduced pollen grains. The occurrence of 0-2 B-chromosomes was observed in most of the species and populations studied. Karyotype analysis showed that the chromosomes are metacentric (m) and submetacentric (sm), varying in size from 0.55 to 1.79 μm. The ANOVA test showed significant difference in total chromosome length, size of the long arm and short arm of the chromosomes as well as arm ratio of the chromosome pair numbers 1–4 and 8, indicating the role of both quantitative and structural changes of chromosome in cytological diversity of Cousinia species.
The histology of normal llama skin.

Skin biopsy specimens of normal llama skin were examined histologically. Adnexal structures similar to those of most other domestic mammals included epitrichial sweat glands, sebaceous glands and arrector pili muscles. Unique features of normal llama skin included a very thick dermis with marked differences between superficial and deep dermis, prominent cutaneous vascular plexuses, unidentified cells with eosinophilic granules within the adventitia of the vascular plexuses, both simple and compound hair follicles, 'metatarsal glands', 'interdigital glands', footpad glands and the absence of eyelid tarsal glands.
Recovery of atypical Aeromonas salmonicida from ulcerated fish from the Baltic Sea

Ulcerated fish of six different species were collected during the BMB/ICES Sea-going Workshop “Fish Diseases and Parasites in the Baltic Sea”, 25 November to 8 December 1994, and examined for bacteriological infections. Atypical Aeromonas salmonicida strains were isolated from the majority of the ulcers of dab Limanda limanda, flounder Platichthys flesus, and turbot Scophthalmus maximus. A fast-growing strain was isolated in pure cultures from both ulcers and visceral organs of viviparous blenny Zoarces viviparus. Available data suggest that atypical A. salmonicida is generally involved in the development of ulceration’s in Baltic flounder and probably also in other fish species. The strains isolated from ulcerated flounders were indistinguishable from those previously reported from this species from the Baltic Sea and the North Sea, and the ulcer disease is considered to be associated with one, well-defined biotype of A. salmonicida.