Miracle-dz/UniFAR-FTUs huggingface dataset:
Monitoring frequency of intra‐fraction patient motion using the ExacTrac system for LINAC‐based SRS treatments

Abstract Purpose The aim of this study was to investigate the intra‐fractional patient motion using the ExacTrac system in LINAC‐based stereotactic radiosurgery (SRS). Method A retrospective analysis of 104 SRS patients with kilovoltage image‐guided setup (Brainlab ExacTrac) data was performed. Each patient was imaged pre‐treatment, and at two time points during treatment (1st and 2nd mid‐treatment), and bony anatomy of the skull was used to establish setup error at each time point. The datasets included the translational and rotational setup error, as well as the time period between image acquisitions. After each image acquisition, the patient was repositioned using the calculated shift to correct the setup error. Only translational errors were corrected due to the absence of a 6D treatment table. Setup time and directional shift values were analyzed to determine correlation between shift magnitudes as well as time between acquisitions. Results The average magnitude translation was 0.64 ± 0.59 mm, 0.79 ± 0.45 mm, and 0.65 ± 0.35 mm for the pre‐treatment, 1st mid‐treatment, and 2nd mid‐treatment imaging time points. The average time from pre‐treatment image acquisition to 1st mid‐treatment image acquisition was 7.98 ± 0.45 min, from 1st to 2nd mid‐treatment image was 4.87 ± 1.96 min. The greatest translation was 3.64 mm, occurring in the pre‐treatment image. No patient had a 1st or 2nd mid‐treatment image with greater than 2 mm magnitude shifts. Conclusion There was no correlation between patient motion over time, in direction or magnitude, and duration of treatment. The imaging frequency could be reduced to decrease imaging dose and treatment time without significant changes in patient position.
Using an interlaboratory study to revise methods for conducting 10‐d to 42‐d water or sediment toxicity tests with Hyalella azteca

Studies have been conducted to refine US Environmental Protection Agency, ASTM International, and Environment Canada standard methods for conducting 42‐d reproduction tests with Hyalella azteca in water or in sediment. Modifications to the H. azteca method include better‐defined ionic composition requirements for exposure water (i.e., >15 mg/L of chloride and >0.02 mg/L of bromide) and improved survival, growth, and reproduction with alternate diets provided as increased rations over time in water‐only or whole‐sediment toxicity tests. A total of 24 laboratories volunteered to participate in the present interlaboratory study evaluating the performance of H. azteca in 42‐d studies in control sand or control sediment using the refined methods. Improved growth and reproduction of H. azteca was observed with 2 alternate diets of 1) ramped diatoms (Thalassiosira weissflogii) + ramped Tetramin or 2) yeast–cerophyll–trout chow (YCT) + ramped Tetramin, especially when compared with results from the traditional diet of 1.8 mg YCT/d. Laboratories were able to meet proposed test acceptability criteria and in most cases had lower variation in growth or reproduction compared with previous interlaboratory studies using the traditional YCT diet. Laboratory success in conducting 42‐d H. azteca exposures benefited from adherence to several key requirements of the detailed testing, culturing, and handling methods. Results from the present interlaboratory study are being used to help revise standard methods for conducting 10‐d to 42‐d water or sediment toxicity exposures with H. azteca. Environ Toxicol Chem 2016;35:2439–2447. © 2016 SETAC
Domestic cattle (Bos taurus taurus) are motivated to obtain forage and demonstrate contrafreeloading

Domestic cattle (Bos taurus taurus) are adapted to digest high-roughage diets, but in confinement they are commonly fed low-roughage, high-energy diets. This practice may leave cattle with an unfulfilled need to consume forage. A way to quantify motivation is to require animals to work to access a resource. Using this method, we evaluated cattle motivation to obtain forage when fed high- or low-roughage diets during and 30 d before the study. Individual heifers were fed Sudan grass (Sorghum × drummondii) hay (high roughage, n = 6) or a diet with 12% forage (as fed, low roughage, n = 6) in an open feed trough. In a second trough, 200 g/d of Sudan grass hay were fed behind a push gate, to which additional weight was added daily until heifers no longer pushed. We predicted heifers would push heavier weights, show a shorter latency, and spend more time pushing the gate when fed a low- vs. high-roughage diet. Indeed, heifers fed a low-roughage diet pushed the gate immediately after hay delivery (1.7 min) and much sooner than those fed a high-roughage diet (75.7 min). On the day before they no longer pushed the gate, latency for heifers in the low-roughage treatment remained only 3.2 min after hay delivery. The suddenness with which they ceased pushing the next day suggests they were unable to move heavier weights to express their motivation. This may explain why maximum weight pushed and time spent pushing the gate did not differ between treatments. The gate pushing by heifers with unrestricted hay access is the first demonstration by cattle of contrafreeloading: performing work to obtain a resource that is simultaneously available for free. In conclusion, consuming forage is important to cattle and is affected by both their primary diet and an internal motivation to work to obtain feed.
Gender Confirming Medical Interventions and Eating Disorder Symptoms Among Transgender Individuals

Objective: Studies indicate that transgender individuals may be at risk of developing eating disorder symptoms (EDS). Elevated risk may be attributed to body dissatisfaction and/or societal reactions to nonconforming gender expression, such as nonaffirmation of a person’s gender identity (e.g., using incorrect pronouns). Limited research suggests that gender-confirming medical interventions (GCMIs) may prevent or reduce EDS among transgender people. Method: Participants included 154 transfeminine spectrum (TFS) and 288 transmasculine spectrum (TMS) individuals who completed the Trans Health Survey. Serial multiple mediation analyses controlling for age, education, and income were used to examine whether body satisfaction and nonaffirmation mediate any found relationships between various GCMIs (genital surgery, chest surgery, hormone use, hysterectomy, and hair removal) and EDS. Results: For TFS individuals, the nonaffirmation to body satisfaction path mediated relationships between all GCMIs and EDS, although body satisfaction alone accounted for more of the indirect effects than this path for chest surgery. For TMS individuals, relationships between all GCMIs and EDS were mediated by the nonaffirmation to body satisfaction path. Conclusion: Findings support the hypothesis that GCMIs reduce experiences of nonaffirmation, which increases body satisfaction and thus decreases EDS. Among TFS participants, the relationship between chest surgery and lower levels of EDS was mediated most strongly by body satisfaction alone, suggesting that satisfaction with one’s body may result in lower EDS even if affirmation from the external world is unchanged. Implications of these findings for intervention, policy, and legal efforts are discussed, and future research recommendations are provided.
Keyframe-based Video Summarization with Human in the Loop

: In this work, we focus on the popular keyframe-based approach for video summarization. Keyframes represent important and diverse content of an input video and a summary is generated by temporally expanding the keyframes to key shots which are merged to a continuous dynamic video summary. In our approach, keyframes are selected from scenes that represent semantically similar content. For scene detection, we propose a simple yet effective dynamic extension of a video Bag-of-Words (BoW) method which provides over segmentation (high recall) for keyframe selection. For keyframe selection, we investigate two effective approaches: local region descriptors (visual content) and optical ﬂow descriptors (motion content). We provide several interesting ﬁndings. 1) While scenes (visually similar content) can be effectively detected by region descriptors, optical ﬂow (motion changes) provides better keyframes. 2) However, the suitable parameters of the motion descriptor based keyframe selection vary from one video to another and average performances remain low. To avoid more complex processing, we introduce a human-in-the-loop step where user selects keyframes pro-duced by the three best methods. 3) Our human assisted and learning-free method achieves superior accuracy to learning-based methods and for many videos is on par with average human accuracy.
Pigmented macrophages and related aggregates in the spleen of european sea bass dosed with heavy metals: Ultrastructure and explorative morphometric analysis

The ultrastructure and morphometrics of pigmented macrophages (PMs) were assessed in the spleen of European sea bass experimentally dosed with Cd and Hg. PMs occurred either as solitary cells or as variably structured aggregations, defined as macrophage aggregates (MAs). Light microscopy revealed a high degree of morphological heterogeneity amongst MAs of all experimental groups. At the ultrastructural level, MAs showed a heterogeneous pigment content that was not influenced by the treatment. Cytoplasm rarefaction/vacuolation and euchromatic nuclei, were observed in PMs of dosed fish. Undosed and Cd‐dosed samples differ significantly with regard to the following morphometric features: the Minor axis of the best fitting ellipse, Aspect Ratio, and Roundness. In Cd‐dosed fish, MAs showed reduced size and complexity. Lacunarity showed significant differences between undosed and both Cd and Hg‐dosed samples. These results suggest that heavy metals, and especially Cd, may influence the dynamics of PM aggregation/disaggregation. Variability in splenic MAs was observed both by light and electron microscopy. However, only the morphometric techniques adequately and objectively described the phenomenon, allowing a quantitative/statistical comparison of morphology among experimental groups. These morphometric analyses could be usefully applied in toxicological and ecotoxicological, as well as morpho‐functional studies.
Biallelic loss‐of‐function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome

Robinow syndrome (RS) is a well‐recognized Mendelian disorder known to demonstrate both autosomal dominant and autosomal recessive inheritance. Typical manifestations include short stature, characteristic facies, and skeletal anomalies. Recessive inheritance has been associated with mutations in ROR2 while dominant inheritance has been observed for mutations in WNT5A, DVL1, and DVL3. Through trio whole genome sequencing, we identified a homozygous frameshifting single nucleotide deletion in WNT5A in a previously reported, deceased infant with a unique constellation of features comprising a 46,XY disorder of sex development with multiple congenital malformations including congenital diaphragmatic hernia, ambiguous genitalia, dysmorphic facies, shortened long bones, adactyly, and ventricular septal defect. The parents, who are both heterozygous for the deletion, appear clinically unaffected. In conjunction with published observations of Wnt5a double knockout mice, we provide evidence for the possibility of autosomal recessive inheritance in association with WNT5A loss‐of‐function mutations in RS.
Impact of cocoa polyphenol extracts on the immune system and microbiota in two strains of young rats

A diet containing 10 % cocoa, a rich source of polyphenols and fibre, is able to modify intestinal immune status as well as microbiota composition. The present study was aimed at investigating whether cocoa flavonoid content is uniquely responsible for these modulatory effects of cocoa, and to establish whether these effects depend on the rat strain. To this end, 3-week-old Wistar and Brown Norway rats were fed, for 4 weeks, either a standard diet or the following three isoenergetic diets containing increasing proportions of cocoa flavonoids from different sources: one with 0·2 % polyphenols (from conventional defatted cocoa), and two others with 0·4 and 0·8 % polyphenols (from non-fermented cocoa, very rich in polyphenols). Serum Ig concentrations, faecal IgA levels, microbiota composition and IgA-coating bacterial proportion were evaluated at the beginning and at the end of the study. After the nutritional intervention, the composition of lymphocytes in Peyer's patches and mesenteric lymph nodes was evaluated. In some respects, the Wistar strain was more sensitive to the impact of the cocoa diets than the Brown Norway strain. After 4 weeks of dietary intervention, similar modulatory effects of the diets containing 0·2 and 0·8 % polyphenols on mucosal IgA levels and microbiota composition were found, although the 0·2 % diet, with a higher proportion of theobromine and fibre, had more impact, suggesting that polyphenols are not the only components involved in such effects.
EMT: Present and future in clinical oncology

Epithelial/mesenchymal transition (EMT) has emerged as a key regulator of metastasis by facilitating tumor cell invasion and dissemination to distant organs. Recent evidences support that the reverse mesenchymal/epithelial transition (MET) is required for metastatic outgrowth; moreover, the existence of hybrid epithelial/mesenchymal (E/M) phenotypes is increasingly being reported in different tumor contexts. The accumulated data strongly support that plasticity between epithelial and mesenchymal states underlies the dissemination and metastatic potential of carcinoma cells. However, the translation into the clinics of EMT and epithelial plasticity processes presents enormous challenges and still remains a controversial issue. In this review, we will evaluate current evidences for translational applicability of EMT and depict an overview of the most recent EMT in vivo models, EMT marker analyses in human samples as well as potential EMT therapeutic approaches and ongoing clinical trials. We foresee that standardized analyses of EMT markers in solid and liquid tumor biopsies in addition to innovative tools targeting the E/M states will become promising strategies for future translation to the clinical setting.
Accumulation of 2,4‐dinitroanisole in the earthworm Eisenia fetida from chemically spiked and aged natural soils

An initiative within the US military is targeting the replacement of traditional munitions constituents with insensitive munitions to reduce the risk of accidental detonation. The bioavailability and bioaccumulative potential of the insensitive munitions compound 2,4‐dinitroanisole (DNAN) to Eisenia fetida was assessed in soils with different geochemical characteristics. Prior to exposure, soils were chemically spiked with DNAN and aged for 1 wk or 29 wk. Transformation products 2‐ and 4‐amino‐nitroanisole (2A‐4NAN and 4A‐2NAN) occurred in aged soils and their porewater but never at concentrations higher than the residual DNAN. The sum of DNAN, 2A‐4NAN, and 4A‐2NAN (sumDNAN) in soil decreased with aging, likely by irreversible binding. Both clay and organic matter contents of the soil appeared to affect the bioavailability of DNAN. The sumDNAN body residues of earthworms approached apparent steady state after 1 d and remained relatively constant through to day 7. Higher concentrations of 2A‐4NAN and 4A‐2NAN measured in worm tissues relative to those in soil suggest reductive transformation of DNAN in the tissues. Mean bioaccumulation factors (ratio of tissue to soil concentrations) varied from 1.2 to 4.3, whereas mean bioconcentration factors (ratio of tissue to porewater concentrations) ranged from 1.4 to 3.2. Porewater seems to play a significant role in the accumulation of DNAN in earthworms, consistent with equilibrium partitioning theory. The concentration of DNAN in soil porewater could serve as an indicator of bioavailability as well as a predictor of the concentration of that compound in earthworms. Environ Toxicol Chem 2016;35:1835–1842. Publlished 2015 SETAC. This article is a US Government work, and as such, is in the public domain in the United States of America.
The Effect of Particles on the Phase Separation of Waxy Corn Starch plus Galactomannan gums

This thesis was initiated with the aim of studying the effect of small particles on phase separation of polysaccharide mixtures with the expectation of stabilising the mixture for a longer period of time, completely inhibiting phase separation, or changing the phase-separated microstructure. The phase separation of a model system consisting 2 wt. % waxy corn starch + 0.25 wt. % guar gum or 0.3 wt. % locust bean gum was studied at 25 °C at pH 7. Phase separated networks occurred within 30 minutes after preparation where the upper phase was enriched with galactomannan gum whereas the lower phase contained starch. Macroscopic phase separation of mixed polysaccharides was studied at vary concentrations, i.e., 0.5 – 4 wt. % and 0.05 – 0.6 wt. % galactomannan gums. The phase diagram illustrating the binodal lines almost coincided with the axes representing the polysaccharide concentrations. Microscopic results showed that the morphology of both mixtures exhibited thermodynamic incompatibility via spinodal decomposition structure. The model systems were also studied in the presence of different kinds of particles. There are three main types of particles that were selected in this thesis; silica nanoparticles (at different hydrophobicities), oil-in-water stable microdroplets and whey protein microgel particles with an initial particle size of 20 nm, 280 nm and 149 nm, respectively. The key parameters investigated were particle concentration, size and effect of pH. This particle-stablised model W/W emulsion was shown to induce long-term stability. With silica particles, the results showed that the rate of phase separation was inversely proportional to particle concentration. The observation also showed that the phase separation of polysaccharide mixtures was significantly slowed down in the presence of 0.5 wt. % of the 80-SiOH and 65-SiOH particles and fully inhibited at 1 wt. % particle concentration. The microdroplets appeared to slow down the rate of phase separation but within one month of storage all mixtures showed the sign of phase separation. The phase separation of a model system, starch + locust bean gum, was significantly inhibited in the presence of 1 vol.% whey protein microgel particles at pH 4, whilst the microgel particles were not as effective in starch + guar gum systems.
Circulating biomarkers in schizophrenia : a proteomics perspective REVIEW

Schizophrenia (SCZ) is one of the most severe and devastating major mental disorders, with an onset typically in late adolescence or early adulthood affecting about 0.5–1.2% of the population worldwide. It is one of the most debilitating medical conditions, with striking socio-economic burden to society due to lost employment and social support that largely surpass direct costs of treatment. SCZ is listed by the World Health Organization (WHO) among the top 20 leading causes of disability worldwide. Its diagnosis is syndromic, based in clinical interviewing and anamnesis, as there is to date no biochemical test to aid in this diagnosis. On the other hand, SCZ treatment is mostly based in antipsychotic drugs which are in several aspects somehow ineffective, and some of these medications have low tolerability with severe side effects. For all these reasons, the current search for new panels of biomarkers is of the utmost importance to aid in the correct diagnosis and stratification of the patients, prognosis, and prediction of treatment effectiveness.
Long-Term Dexamethasone Exposure Down-Regulates Hepatic TFR1 and Reduces Liver Iron Concentration in Rats

Exposure to stress is known to cause hepatic iron dysregulation, but the relationship between prolonged stress and liver iron metabolism is not yet fully understood. Thirty 13-week-old female Sprague–Dawley rats were randomly divided into two groups, as follows: the control group (saline-injection) and the dexamethasone group (Dexamethasone (Dex)-injection 0.1 mg/kg/day). After the 21-day stress trial, the results showed that chronic Dex administration not only impaired serum corticosterone (p = 0.00) and interleukin-6 (IL-6) (p = 0.01) levels, but also decreased white blood cell counts (p = 0.00), and reduced blood lymphocyte counts (p = 0.00). The daily Dex-injection also significantly reduced body weight (p < 0.01) by inhibiting food intake. Consecutive Dex administration resulted in decreased iron intake (p = 0.00), enhanced serum iron levels (p = 0.01), and increased the serum souble transferrin receptor (sTfR) content (p = 0.00) in rats. Meanwhile, long-term Dex exposure down-regulated duodenal cytochrome b (DCYTB) (p = 0.00) and the divalent metal transporter 1 (DMT1) (p = 0.04) protein expression, but up-regulated ferroportin (FPN) protein expression (p = 0.04). Chronic Dex administration reduced liver iron concentration (p = 0.02) in rats. Hepatic transferrin receptor 1 (TFR1) expression was lowered at the protein level (p = 0.03), yet with uncoupled mRNA abundance in Dex-treated rats. Enhanced iron-regulatory protein (IRP)/iron-responsive element (IRE) binding activity was observed, but did not line up with lowered hepatic TFR1 protein expression. This study indicates that long-term Dex exposure reduces liver iron content, which is closely associated with down-regulated hepatic TFR1 protein expression.
Targeting hepatocarcinogenesis model in C56BL6 mice with pan-aurora kinase inhibitor Danusertib

Background: To elucidate the expression of Aurora kinases (AURK) and the anticancer effects of pan-aurora kinase inhibitor Danusertib in hepatocarcinogenesis model in C56Bl6 mice. Methods: Thirty mice C56Bl6 were randomly divided into Group A or control, Group B animals who underwent experimental hepatocarcinogenesis with diethylnitrosamine (DEN), and Group C animals with DEN-induced hepatocarcinogenenesis that treated with pan-aurora kinase inhibitor Danusertib. Primary antibodies for immunochistochemistry (IHC) included rabbit antibodies against Ki-67, DKK1, INCENP, cleaved caspase-3, NF-κB p65, c-Jun, β-catenin. Hepatocyte growth factor receptor (C-MET/HGFR) and Bcl-2 antagonist of cell death (BAD) serum levels were determined using a quantitative sandwich enzyme immunoassay technique. Results: Inhibition of AURK reduced the number of DEN-induced liver tumours. Apoptosis and proliferation was very low in both DEN-induced and anti- AURK groups respectively. The hepatocellular adenoma cells of DEN-treated mice uniformly had ample nuclear INCENP whereas in anti- AURK markedly decreased. Expression of β-catenin, NF-kB and c-Jun did not differ in liver tumors of both AURK -depleted and non-depleted mice. Conclusions: Depletion of AURK reduced the number of DEN-induced hepatic tumours. However, their size did not differ significantly between the groups.