Miracle-dz/UniFAR-FTUs huggingface dataset:
Design and performance of SIAT aPET: a uniform high-resolution small animal PET scanner using dual-ended readout detectors

In this work, a small animal PET scanner named SIAT aPET was developed using dual-ended readout depth encoding detectors to simultaneously achieve high spatial resolution and high sensitivity. The scanner consists of four detector rings with 12 detector modules per ring; the ring diameter is 111 mm and the axial field of view (FOV) is 105.6 mm. The images are reconstructed using an ordered subset expectation maximization (OSEM) algorithm. The spatial resolution of the scanner was measured by using a 22Na point source at the center axial FOV with different radial offsets. The sensitivity of the scanner was measured at center axis of the scanner with different axial positions. The count rate performance of the system was evaluated by scanning mouse-sized and rat-sized phantoms. An ultra-micro hot-rods phantom and two mice injected with 18F-NaF and 18F-FDG were scanned on the scanner. An average depth of interaction (DOI) resolution of 1.96 mm, energy resolution of 19.1% and timing resolution of 1.20 ns were obtained for the detector. Average spatial resolutions of 0.82 mm and 1.16 mm were obtained up to a distance of 30 mm radially from the center of the FOV when reconstructing a point source in 1% and 10% warm backgrounds, respectively, using OSEM reconstruction with 16 subsets and 10 iterations. Sensitivities of 16.0% and 11.9% were achieved at center of the scanner for energy windows of 250–750 keV and 350–750 keV respectively. Peak noise equivalent count rates (NECRs) of 324 kcps and 144 kcps were obtained at an activity of 26.4 MBq for the mouse-sized and rat-sized phantoms. Rods of 1.0 mm diameter can be visually resolved from the image of the ultra-micro hot-rods phantom. The capability of the scanner was demonstrated by high quality in-vivo mouse images.
Benefits of protected areas for nonbreeding waterbirds adjusting their distributions under climate warming

Climate warming is driving changes in species distributions and community composition. Many species have a so‐called climatic debt, that is, shifts in range lag behind shifts in temperature isoclines. Inside protected areas (PAs), community changes in response to climate warming can be facilitated by greater colonization rates by warm‐dwelling species, but also mitigated by lowering extirpation rates of cold‐dwelling species. An evaluation of the relative importance of colonization‐extirpation processes is important to inform conservation strategies that aim for both climate debt reduction and species conservation. We assessed the colonization‐extirpation dynamics involved in community changes in response to climate inside and outside PAs. To do so, we used 25 years of occurrence data of nonbreeding waterbirds in the western Palearctic (97 species, 7071 sites, 39 countries, 1993–2017). We used a community temperature index (CTI) framework based on species thermal affinities to investigate species turnover induced by temperature increase. We determined whether thermal community adjustment was associated with colonization by warm‐dwelling species or extirpation of cold‐dwelling species by modeling change in standard deviation of the CTI (CTISD). Using linear mixed‐effects models, we investigated whether communities in PAs had lower climatic debt and different patterns of community change than communities outside PAs. For CTI and CTISD combined, communities inside PAs had more species, higher colonization, lower extirpation, and lower climatic debt (16%) than communities outside PAs. Thus, our results suggest that PAs facilitate 2 independent processes that shape community dynamics and maintain biodiversity. The community adjustment was, however, not sufficiently fast to keep pace with the large temperature increases in the central and northeastern western Palearctic. Our results underline the potential of combining CTI and CTISD metrics to improve understanding of the colonization‐extirpation patterns driven by climate warming.
Observer Performance for Detection of Pulmonary Nodules at Chest CT over a Large Range of Radiation Dose Levels.

Background There is a wide variation in radiation dose levels that can be used with chest CT in order to detect indeterminate pulmonary nodules. Purpose To compare the performance of lower-radiation-dose chest CT with that of routine dose in the detection of indeterminate pulmonary nodules 5 mm or greater. Materials and Methods In this retrospective study, CT projection data from 83 routine-dose chest CT examinations performed in 83 patients (120 kV, 70 quality reference mAs [QRM]) were collected between November 2013 and April 2014. Reference indeterminate pulmonary nodules were identified by two nonreader thoracic radiologists. By using validated noise insertion, five lower-dose data sets were reconstructed with filtered back projection (FBP) or iterative reconstruction (IR; 30 QRM with FBP, 10 QRM with IR, 5 QRM with FBP, 5 QRM with IR, and 2.5 QRM with IR). Three thoracic radiologists circled pulmonary nodules, rating confidence that the nodule was a 5-mm-or-greater indeterminate pulmonary nodule, and graded image quality. Analysis was performed on a per-nodule basis by using jackknife alternative free-response receiver operating characteristic figure of merit (FOM) and noninferiority limit of -0.10. Results There were 66 indeterminate pulmonary nodules (mean size, 8.6 mm ± 3.4 [standard deviation]; 21 part-solid nodules) in 42 patients (mean age, 51 years ± 17; 21 men and 21 women). Compared with the FOM for routine-dose CT (size-specific dose estimate, 6.5 mGy ± 1.8; FOM, 0.86 [95% confidence interval: 0.80, 0.91]), FOM was noninferior for all lower-dose configurations except for 2.5 QRM with IR. The sensitivity for subsolid nodules at 70 QRM was 60% (range, 48%-72%) and was significantly worse at a dose of 5 QRM and lower, whether or not IR was used (P < .05). Diagnostic image quality decreased with decreasing dose (P < .001) and was better with IR at 5 QRM (P < .05). Conclusion CT images reconstructed at dose levels down to 10 quality reference mAs (size-specific dose estimate, 0.9 mGy) had noninferior performance compared with routine dose in depicting pulmonary nodules. Iterative reconstruction improved subjective image quality but not performance at low dose levels. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by White and Kazerooni in this issue.
Seasonal variation of carbon dioxide and methane fluxes at single cropping paddy fields in central and western Japan

Based on the results of long-term flux measurement at two paddy flux sites, Mase (MSE) in central Japan and Hachihama (HCH) in western Japan, we present seasonal variation of carbon dioxide (CO 2 ) and methane (CH 4 ) exchanges between single rice cropping paddy fields and the atmosphere in 2003. CO 2 flux was measured by the eddy covariance method at the two sites, while CH 4 flux was measured at MSE site by the modified aerodynamic method. Net ecosystem CO 2 exchange (NEE) in the 2003 growing period showed a distinct seasonal variation with rice growth, and reached the maximum daily CO 2 uptake of 9.2-9.5 g C m -2 d -1 in the middle growing period. The total NEE in the growing period at HCH site was more negative than that at MSE site by 84 g C m -2 , 60% of which was caused by larger gross primary production (GPP) and the remainder by smaller ecosystem respiration (RE) at HCH site. The inter-site difference in GPP was principally caused by larger amount of incident photosynthetically active radiation at HCH site, which resulted from longer cultivation period at HCH site and shorter sunshine duration at MSE site in the mid-growing period. The inter-site difference in RE was attributed to that the rice growth at HCH site was out of phase with the seasonal variation of temperature. By including NEE in the non-growing period, we estimated the annual NEE at MSE site at a range between -192 and -284 g C m -2 . CH 4 emission flux at MSE site increased with days after flooding, and showed a flush of CH 4 after the pre-harvest drainage. The amount of CH4 emission during the 2003 growing period was 9.3 g C m -2 , which was negligible in the carbon budget of the paddy field when compared with the annual NEE, but it had significant influence on the greenhouse gas budget because of the large global warming potential of CH 4 .
A Call for Data-Driven Networks to Address Equity in the Context of Undergraduate Biology

National efforts to improve equitable teaching practices in biology education have led to an increase in research on the barriers to student participation and performance, as well as solutions for overcoming these barriers. Fewer studies have examined the extent to which the resulting data trends and effective strategies are generalizable across multiple contexts or are specific to individual classrooms, institutions, or geographic regions. To address gaps in our understanding, as well as to establish baseline information about students across contexts, a working group associated with a research coordination network (Equity and Diversity in Undergraduate STEM, EDU-STEM) convened in Las Vegas, Nevada, in November of 2019. We addressed the following objectives: 1) characterize the present state of equity and diversity in undergraduate biology education research; 2) address the value of a network of educators focused on science, technology, engineering, and mathematics equity; 3) summarize the status of data collection and results; 4) identify and prioritize questions and interventions for future collaboration; and 5) construct a recruitment plan that will further the efforts of the EDU-STEM research coordination network. The report that follows is a summary of the conclusions and future directions from our discussion.
A replication and extension of the interpersonal process model of demand/withdraw behavior: Incorporating subjective emotional experience.

The demand/withdraw (D/W) interaction pattern is a maladaptive cycle of behavior that is associated with a wide range of deleterious individual and relational outcomes. Partners' emotional responding during couple conflict has long been theorized to play a central role in the occurrence of D/W. The interpersonal process model of D/W behavior suggests that each partner's emotional responses are associated with their own as well as the other partner's behavior in the D/W cycle and that the nature of these associations varies across partners. A prior test of the interpersonal process model provided support for sex- and role-specific associations between vocal emotional expression and demanding and withdrawing behaviors. The current study expands the conceptual frame of the interpersonal process model by incorporating subjective emotional experience. Hypothesized associations between subjective emotional experience, emotional expression, and role-specific demanding and withdrawing behaviors were tested in a sample of 59 couples using an actor-partner interdependence model. Results reveal that spouses experience and express nonsignificantly different levels of negative affect but strongly differ in how the experience and expression of those emotions are related to demanding and withdrawing behaviors. High levels of women's demanding behavior were associated with the combination of experiencing and expressing high levels of negative affect, while high levels of men's withdrawing behavior were associated with experiencing high levels of negative affect but expressing low levels of negative affect. Implications of results for understanding emotional processes in maladaptive cycles and for clinical practice are discussed. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
The Effects of 6-Month Vitamin D Supplementation during the Non-Surgical Treatment of Periodontitis in Vitamin-D-Deficient Patients: A Randomized Double-Blind Placebo-Controlled Study

Background: This study assessed the effects of weekly vitamin D (VD) supplementation on clinical and biological parameters after scaling and root planning (SRP) in the treatment of periodontitis and served to validate the VD dosage regimen. Methods: It was a monocentric, randomized, double-blind, placebo-controlled clinical trial with 6 months follow-up. Healthy Caucasian periodontitis patients presenting serum 25(OH) vitamin D3 below 30 ng/mL were randomly allocated to test group (SRP + VD 25,000 international units (IU)/week) or the control group (SRP + placebo). Results: A total of 59 patients were screened, 27 were included and 26 completed 3 months (M) and 21 completed 6M control. Test (n = 13) and control groups (n = 14) had similar 25(OH) vitamin D3 levels at baseline (17.6 ± 7.4 vs. 14.4 ± 5.2, respectively). After one month, there was a significant difference between groups (32.9 ± 5.2 vs. 16.1 ± 4.7), also seen at M3 and M6 (t-test, p < 0.001). Periodontal treatment was successful in both groups, since it resulted in a reduction of all measured clinical parameters at M3 and M6 (probing pocket depth (PPD), full mouth bleeding and plaque). However, the reduction in PPD was greater in the test group. Conclusions: In this short-term pilot study, no significant differences were observed between two groups. However, supplementation with VD tended to improve the treatment of periodontitis in patients with initial 25(OH) vitamin D3 < 30 ng/mL and proved safe and efficacious. NCT03162406.
Non-deep simple morphophysiological dormancy in seeds of the rare Alpinia galanga: a first report for Zingiberaceae

Abstract Little information is available on seed dormancy of members of the Zingiberales and especially the Zingiberaceae. Our aim was to investigate the dormancy breaking and germination requirements of Alpinia galanga in vitro with a minimum number of seeds, using the move-along experiment. The mass of imbibed seeds increased by 17.5% in 1 d, showing that seeds were water permeable. The best germination in the move-along experiment (86.7%) was obtained when seeds were exposed to the sequence of temperature regimes that began with winter (20/10°C), and seeds began to germinate after 6 weeks at this temperature regime. Seeds dry stored for 4 months and then incubated at the sequence of temperature regimes that began with summer (30/20°C) started germinating in the sixth week at this temperature regime and had germinated to 93.3% after 18 weeks. Seeds kept dry for 4 months and then treated with 50 mg l−1 gibberellic acid (GA3) began to germinate at 30/20°C after 2 weeks. Control seeds incubated continuously at 20/10, 25/15 or 30/20°C germinated to 80.6, 77.8 and 60.0%, respectively. When incubated at 15, 20, 25 or 30°C, the ideal temperature for embryo growth was 20°C. Since GA3 and dry storage can break non-deep physiological dormancy and embryos grew during warm stratification, seeds of A. galanga have non-deep simple morphophysiological dormancy (MPD). This is the first report of non-deep simple MPD in the Zingiberaceae.
UFMylation is Associated with LPS-induced Inflammatory Response in Goat Endometrial Epithelial Cells.

The endometrium plays an important role in the defense against invading pathogens, although the mechanisms are not clear. UFMylation is a recently discovered novel ubiquitination-like modification system that plays a pivotal role in inflammation and the immune response. The purpose of this study was to investigate the effects of UFMylation on lipopolysaccharide (LPS)-induced inflammatory responses in immortalized goat endometrial epithelial cells (gEECs). Ubiquitin-fold modifier conjugating enzyme 1 (UFM1) and DDRGK domain containing 1 (DDRGK1) were mainly localized in the luminal epithelium and glandular epithelium of mouse and goat endometrial tissues. The expression levels of UFM1, Ubiquitin like modifier activating enzyme 5 (UBA5), UFM1 specific ligase 1 (UFL1) and DDRGK1, as key components of the UFMylation system, were significantly activated by 5 μg/mL LPS-induced inflammatory response in gEECs for 6 h. Meanwhile, the expression levels of interleukin-6 (IL-6) was significantly upregulated and tumor necrosis factor-α (TNF-α) was significantly down-regulated after overexpression of UFM1 in gEECs. Additionally, we observed UFM1 and DDRGK1 were markedly increased on LPS-stimulated mouse endometritis in vivo. In conclusion, the current study demonstrated that UFMylation was significantly activated by LPS and might be involved in regulating inflammatory response in in gEECs.
Meaning-Making of War Experiences: Stories From Kosova

The research evidence shows that war had many detrimental effects on the mental health, wellbeing, and social functioning of the people of Kosova, which is similar to the findings in many other postconflict societies. However, there are few studies focusing on the process of meaning-making of war experiences and their impacts on resilience and growth. This phenomenological study aimed to explore the lived war experiences of citizens of Kosova from the perspectives of three generations (grandparents, parents and children) through semistructured interviews, which were conducted with 37 participants. Thematic analysis revealed that the journey of the meaning-making of war experiences in Kosova is rather dynamic and reflects the context in which each generational cohort lived and grew. The findings provide a deeper understanding of the strategies used by each generation for meaning-making and how these strategies contributed to resilience and growth. The implications for mental health counselors, social workers, and policymakers are discussed.
Gut microbiota degrades toxic isothiocyanates in a flea beetle pest

Microbial symbionts of herbivorous insects have been suggested to aid in the detoxification of plant defense compounds; however, quantitative studies on microbial contribution to plant toxin degradation remain scarce. Here, we demonstrate microbiome‐mediated degradation of plant‐derived toxic isothiocyanates in the cabbage stem flea beetle Psylliodes chrysocephala, a major pest of oilseed rape. Suppression of microbiota in antibiotic‐fed beetles resulted in up to 11.3‐fold higher levels of unmetabolized isothiocyanates compared to control beetles but did not affect other known detoxification pathways in P. chrysocephala. We characterized the microbiome of laboratory‐reared and field‐collected insects using 16S rRNA amplicon sequencing and isolated bacteria belonging to the three core genera Pantoea, Acinetobacter and Pseudomonas. Only Pantoea isolates rapidly degraded isothiocyanates in vitro, and restored isothiocyanate degradation in vivo when reintroduced in antibiotic‐fed beetles. Pantoea was consistently present across beetle life stages and in field and lab populations. In addition, Pantoea was detected in undamaged tissues of the host plant Brassica rapa, indicating that P. chrysocephala could possibly acquire an isothiocyanate detoxifying bacterium through their diet. Our results demonstrate that both insect endogenous mechanisms and the microbiota can contribute to the detoxification of plant defense compounds and together they can better account for the fate of ingested plant metabolites.
Reduced Water Negatively Impacts Social Bee Survival and Productivity Via Shifts in Floral Nutrition

Abstract Pollinators provide a key ecosystem service vital for the survival and stability of the biosphere. Identifying factors influencing the plant–pollinator mutualism and pollinator management is necessary for maintaining a healthy ecosystem. Since healthy beehives require substantial amounts of carbohydrates (nectar) and protein (pollen) from forage plants such as clover, we must assess how resources offered by plants change under limited water conditions in order to fully understand how drought modifies the pollination mutualism. Here we document how reduced water availability leads to decreased nectar quality and quantity and decreased protein quality of pollen. Furthermore, we provide conclusive evidence that these lower quality resources lead to decreased survival and productivity in both developing honey bees (Hymenoptera: Apidae) and bumble bees (Hymenoptera: Apidae). The results emphasize the importance of the nutritional effects of reduced water on bees when predicting shifts of pollination mutualisms under climate change.
TGF-β and Eomes control the homeostasis of CD8+ regulatory T cells

In contrast to well-studied CD4+ T reg cells, the molecular mechanisms controlling CD8+ T reg cells remain largely elusive. Here, the authors find that TGF-β signal and transcription factor Eomes cooperate to promote the function, location, and homeostasis of CD8+ T reg cells.
Mechanisms of Photoreceptor Death in Retinitis Pigmentosa

Retinitis pigmentosa (RP) is the most common cause of inherited blindness and is characterised by the progressive loss of retinal photoreceptors. However, RP is a highly heterogeneous disease and, while much progress has been made in developing gene replacement and gene editing treatments for RP, it is also necessary to develop treatments that are applicable to all causative mutations. Further understanding of the mechanisms leading to photoreceptor death is essential for the development of these treatments. Recent work has therefore focused on the role of apoptotic and non-apoptotic cell death pathways in RP and the various mechanisms that trigger these pathways in degenerating photoreceptors. In particular, several recent studies have begun to elucidate the role of microglia and innate immune response in the progression of RP. Here, we discuss some of the recent progress in understanding mechanisms of rod and cone photoreceptor death in RP and summarise recent clinical trials targeting these pathways.
Curcumin Loaded Nanoliposomes Localization by Nanoscale Characterization

Curcumin is a hydrophobic drug gaining growing attention because of its high availability, its innocuity, and its anticancer, antitumoral, and antioxidative activity. However, its poor ‎‎bioavailability in the human body, caused by its low aqueous solubility and fast degradation, ‎‎presents a big hurdle for its oral administration. Here, we used nano-vesicles made of ‎‎phospholipids to carry and protect curcumin in its membrane. Various curcumin amounts were ‎‎encapsulated in the produced phospholipid system to form drug-loaded liposomes. ‎Curcumin’s ‎concentration was evaluated using UV-visible measurements. The maximal ‎amount of curcumin ‎that could be added to liposomes was assessed. Nuclear magnetic ‎resonance (NMR) analyses ‎were used to determine curcumin’s interactions and localization ‎within the phospholipid ‎membrane of the liposomes. X-ray scattering (SAXS) and atomic ‎force microscopy (AFM) ‎experiments were performed to characterize the membrane structure ‎and organization, as well as its ‎mechanical properties at the nanoscale. Conservation of the membrane’s properties is found with ‎the addition of curcumin in various ‎amounts before saturation, allowing the preparation of a ‎defined nanocarrier with desired ‎amounts of the drug.