Miracle-dz/UniFAR-FTUs huggingface dataset:
Dung beetle movements at two spatial scales

To understand the dynamics of spatially structured populations, we need to know the level of movements at different spatial scales. This paper reports on Aphodius dung beetle movements at two scales: movements between dung pats within pastures, and movements between pastures. First, I test an assumption common to many recent models of spatially structured populations – that the probability of an individual moving between habitat patches decreases exponentially with distance. For dung beetles, I find sufficient evidence to reject this assumption. The distribution of dispersal distances was clearly leptokurtic, with more individuals moving short and long distances than expected on the basis of an exponential function. In contrast, the data were well described by a power function. I conclude that dung beetle movements include an element of non-randomness not captured by the simplistic exponential model. The power function offers a promising alternative, but the actual mechanisms behind the pattern need to be clarified. Second, I compare several species of Aphodius to each other. Although these species occur in the same network of habitat patches, their movement patterns are different enough to result in a mixture of different spatial population structures. Movements between pastures were more frequent the larger the species, the more specific its occurrence in relation to pat age, and the more specialized it is on cow dung and open pasture habitats. Within pastures, all species form “patchy” populations, with much movement among individual pats.
Unsupervised Does Not Mean Uninterpretable: The Case for Word Sense Induction and Disambiguation

The current trend in NLP is the use of highly opaque models, e.g. neural networks and word embeddings. While these models yield state-of-the-art results on a range of tasks, their drawback is poor interpretability. On the example of word sense induction and disambiguation (WSID), we show that it is possible to develop an interpretable model that matches the state-of-the-art models in accuracy. Namely, we present an unsupervised, knowledge-free WSID approach, which is interpretable at three levels: word sense inventory, sense feature representations, and disambiguation procedure. Experiments show that our model performs on par with state-of-the-art word sense embeddings and other unsupervised systems while offering the possibility to justify its decisions in human-readable form.
Phase-based frame interpolation for video

Standard approaches to computing interpolated (in-between) frames in a video sequence require accurate pixel correspondences between images e.g. using optical flow. We present an efficient alternative by leveraging recent developments in phase-based methods that represent motion in the phase shift of individual pixels. This concept allows in-between images to be generated by simple per-pixel phase modification, without the need for any form of explicit correspondence estimation. Up until now, such methods have been limited in the range of motion that can be interpolated, which fundamentally restricts their usefulness. In order to reduce these limitations, we introduce a novel, bounded phase shift correction method that combines phase information across the levels of a multi-scale pyramid. Additionally, we propose extensions for phase-based image synthesis that yield smoother transitions between the interpolated images. Our approach avoids expensive global optimization typical of optical flow methods, and is both simple to implement and easy to parallelize. This allows us to interpolate frames at a fraction of the computational cost of traditional optical flow-based solutions, while achieving similar quality and in some cases even superior results. Our method fails gracefully in difficult interpolation settings, e.g., significant appearance changes, where flow-based methods often introduce serious visual artifacts. Due to its efficiency, our method is especially well suited for frame interpolation and retiming of high resolution, high frame rate video.
iSyTE: integrated Systems Tool for Eye gene discovery.

PURPOSE To facilitate the identification of genes associated with cataract and other ocular defects, the authors developed and validated a computational tool termed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE uses a mouse embryonic lens gene expression data set as a bioinformatics filter to select candidate genes from human or mouse genomic regions implicated in disease and to prioritize them for further mutational and functional analyses. METHODS Microarray gene expression profiles were obtained for microdissected embryonic mouse lens at three key developmental time points in the transition from the embryonic day (E)10.5 stage of lens placode invagination to E12.5 lens primary fiber cell differentiation. Differentially regulated genes were identified by in silico comparison of lens gene expression profiles with those of whole embryo body (WB) lacking ocular tissue. RESULTS Gene set analysis demonstrated that this strategy effectively removes highly expressed but nonspecific housekeeping genes from lens tissue expression profiles, allowing identification of less highly expressed lens disease-associated genes. Among 24 previously mapped human genomic intervals containing genes associated with isolated congenital cataract, the mutant gene is ranked within the top two iSyTE-selected candidates in approximately 88% of cases. Finally, in situ hybridization confirmed lens expression of several novel iSyTE-identified genes. CONCLUSIONS iSyTE is a publicly available Web resource that can be used to prioritize candidate genes within mapped genomic intervals associated with congenital cataract for further investigation. Extension of this approach to other ocular tissue components will facilitate eye disease gene discovery.
Measurement of serum PODXL concentration for detection of pancreatic cancer

Background The aim of this study was to investigate the use of podocalyxin (PODXL) and secretoglobin family 1D, member 2 (SCGB1D2) expressions in whole blood as diagnostic biomarkers to distinguish between patients with pancreatic cancer and control participants, in comparison with serum cancer antigen 19-9 (CA19-9), which is the current clinical standard. Patients and methods Flow cytometric analysis was performed to determine the expressions of PODXL and SCGB1D2 on the surface of cultured pancreatic cancer cells. Immunoblotting was performed to determine whether PODXL and SCGB1D2 were detectable in the media of cultured pancreatic cancer cells. A discovery-stage clinical study was performed in a cohort of 23 patients with pancreatic cancer and 51 control individuals without pancreatic disease who had been treated in the Department of Gastroenterology and Hepatology at Kochi Medical School Hospital from April 2014 to January 2016. Serum PODXL and SCGB1D2 levels were measured by enzyme-linked immunosorbent assay (ELISA). Results PODXL and SCGB1D2 accumulated in the protrusions of cultured pancreatic cancer cells, and they were detectable both on the cell surface and in the cultured media from these cells. The discovery-stage clinical study showed that the area under the receiver-operating characteristic curve (AUC) was 0.96 (95% confidence interval [CI] 0.91–1.000) for PODXL, 0.80 (95% CI 0.67–0.94) for SCGB1D2, and 0.78 (95% CI 0.66–0.90) for CA19-9. The AUC for PODXL was thus significantly higher than that for CA19-9 (P = 0.006). The combination of SCGB1D2 with CA19-9 did not significantly increase the AUC (0.83; 95% CI 0.70–0.96) compared with the AUC for either SCGB1D2 or CA19-9 alone (P = 0.563). Conclusion PODXL may be a novel, non-invasive diagnostic biomarker for the detection of pancreatic cancer.
Determination of Reddening and Extinction Due to Dust in APM Galaxy Clusters

Existing observations are consistent with rich clusters of galaxies having no dust on scales of approximately megaparsecs or greater, while galaxy groups most probably do have dust distributed over scales of roughly megaparsecs or less. Dust in groups accounts for the observed redshift asymmetries of their galaxy distributions, and about E(B-V) ∼ 0.1–0.2 mag of reddening. Motivated by these results, we develop a new technique for determining the degree of reddening and extinction due to widely distributed dust in nearby moderately rich and poor galaxy clusters. The method compares the color-magnitude plane distributions of galaxies from cluster and control regions on the sky, where control regions are assumed to be unaffected by dust. The method is statistical in nature; it can distinguish between uniformly, nonuniformly, and clumpily distributed dust, and can determine the amount of reddening and obscuration without a priori assuming an AR/E(BJ-R) ratio. We apply the method to nearby, z ≤ 0.08, medium-rich and poor APM galaxy clusters. We detect no dust in these on 1.3 Mpc scales (we assume h = 0.75), and derive 99% confidence upper limits on extinction of AR = 0.025 mag and reddening of E(BJ-R) = 0.025 mag [which corresponds to E(B-V) ≈ 0.02 mag]. We test the method using clusters whose galaxies have been artificially reddened and obscured by various amounts, and conclude that it robustly recovers the input values for reddening, its distribution, and the ratio of total to selective extinction. The method can be applied to any set of galaxy clusters or groups constructed out of homogeneous and uniform two-color galaxy catalogs.
Endoprosthetic Replacement for Giant Cell Tumour of the Proximal Femur

Purpose. To evaluate the functional and oncological outcomes of 12 patients with giant cell tumour (GCT) of the proximal femur treated with customised endoprosthesis. Methods. Nine men and 3 women aged 26 to 52 (mean, 36) years with Campanacci stage-III GCTs of the proximal femur were included. All underwent a wide excision of the tumour with clear margins and replacement using a customised, bipolar, cemented proximal femoral megaprosthesis. Functional outcomes were evaluated using the Musculoskeletal Tumor Society functional scores. Results. The mean follow-up period was 4.8 (range, 4–6) years. There were no instances of recurrence, dislocation, aseptic loosening, deep infection, or death. At the end of 4 years, 8 patients were walking unassisted, 2 used a cane to support during outdoor activities, one used a walking frame at home and outdoors, and one was lost to follow-up. The mean pain relief score was 5.0, the mean functional score was 4.3, the mean emotional acceptance of the procedure and its outcome was 4.7, the mean lower extremity score for support use was 4.7, for walking ability was 4.5, and for gait was 4.3, and the mean total score was 28.3 (out of the maximum of 30). Conclusion. Endoprosthetic replacement for Campanacci stage-III GCT of the proximal femur achieves good to excellent functional and oncological outcomes.
Laryngeal Aerodynamics in Children with Hearing Impairment versus Age and Height Matched Normal Hearing Peers

Lack of proper auditory feedback in hearing-impaired subjects results in functional voice disorder. It is directly related to discoordination of intrinsic and extrinsic laryngeal muscles and disturbed contraction and relaxation of antagonistic muscles. A total of twenty children in the age range of 5–10 years were considered for the study. They were divided into two groups: normal hearing children and hearing aid user children. Results showed a significant difference in the vital capacity, maximum sustained phonation, and fast adduction abduction rate having equal variance for normal and hearing aid user children, respectively, but no significant difference was found in the peak flow value with being statistically significant. A reduced vital capacity in hearing aid user children suggests a limited use of the lung volume for speech production. It may be inferred from the study that the hearing aid user children have poor vocal proficiency which is reflected in their voice. The use of voicing component in hearing impaired subjects is seen due to improper auditory feedback. It was found that there was a significant difference in the vital capacity, maximum sustained phonation (MSP), and fast adduction abduction rate and no significant difference in the peak flow.
Can more than one incremental cycling test be performed within one day?

Abstract Changes in performance parameters over four consecutive maximal incremental cycling tests were investigated to determine how many tests can be performed within one single day without negatively affecting performance. Sixteen male and female subjects (eight trained (T): 25 ± 3 yr, BMI 22.6 ± 2.5 kg·m−2, maximal power output (Pmax) 4.6 ± 0.5 W·kg−1; eight untrained (UT): 27 ± 3 yr, BMI 22.3 ± 1.2 kg·m−2, Pmax 2.9 ± 0.3 W·kg−1) performed four successive maximal incremental cycling tests separated by 1.5 h of passive rest. Individual energy requirements were covered by standardised meals between trials. Maximal oxygen uptake (O2max) remained unchanged over the four tests in both groups (P = 0.20 and P = 0.33, respectively). Pmax did not change in the T group (P = 0.32), but decreased from the third test in the UT group (P < 0.01). Heart rate responses to submaximal exercise were elevated from the third test in the T group and from the second test in the UT group (P < 0.05). The increase in blood lactate shifted rightward over the four tests in both groups (P < 0.001 and P < 0.01, respectively). Exercise-induced net increases in epinephrine and norepinephrine were not different between the tests in either group (P ≥ 0.15). If O2max is the main parameter of interest, trained and untrained individuals can perform at least four maximal incremental cycling tests per day. However, because other parameters changed after the first and second test, respectively, no more than one test per day should be performed if parameters other than O2max are the prime focus.
Granulomatous Inflammation in Pineal Germinoma: A Cause of Diagnostic Failure at Stereotaxic Brain Biopsy

We report four patients with pineal germinoma in whom the initial procedure for obtaining a tissue diagnosis was a stereotaxic biopsy. In all four cases, the biopsy showed granulomatous inflammation with epithelioid cells and lymphocytes. In one case, the granulomatous inflammation was accompanied by classical germinoma. Another case exhibited malignant cells considered nondiagnostic for a specific neoplasm. Two cases had no evidence of a malignant tumor; they were composed entirely of granulomatous inflammation. In two of the three cases where the diagnosis was not established by the first biopsy, a second stereotaxic biopsy showed pineal germinoma. Tissue obtained at resection in the third patient revealed large areas of granulomatous inflammation accompanying the germinoma. Immunoperoxidase stains for ferritin and placental alkaline phosphatase did not increase diagnostic yield. We conclude that a finding of granulomatous inflammation in a stereotaxic biopsy specimen of a pineal mass should suggest a diagnosis of germinoma, followed by sampling from several different target points within the lesion.
Intrapericardial bevacizumab safely and effectively treats malignant pericardial effusion in advanced cancer patients

We evaluated the safety and efficacy of intrapericardial bevacizumab (BEV) for treating symptomatic malignant pericardiac effusion (MPCE) in seven advanced cancer patients. All patients had previously undergone multiple lines of systemic therapy. Each patient received paracentesis and intrapericardial infusions of 100 or 200 mg of BEV every two weeks. Systemic treatments for primary tumors continued for all patients during BEV treatment. Of the seven patients, three achieved a complete response, two achieved a partial response, and two showed no response with regard to MPCE after BEV infusion. The median overall survival time was 168 days (range, 22-224 days). In six of the seven patients, effusion did not recur before death. Toxicity associated with BEV treatment was mild and manageable in all patients. This study provides preliminary evidence that intrapericardial BEV may be an effective and safe treatment for MPCE in patients with advanced cancers.
LAP-like process as an immune mechanism downstream of IFN-γ in control of the human malaria Plasmodium vivax liver stage

Significance IFN-γ plays an important role in the elimination of liver-stage Plasmodium parasites, but the mechanism involved in this process is unclear. In this study, we demonstrate that IFN-γ treatment induces a noncanonical autophagy pathway in human hepatocytes dubbed an LC3-associated phagocytosis (LAP)-like process, in which the parasitophorous vacuole membrane of the parasites is decorated with LC3, resulting in the colocalization of parasite compartments with lysosomes. Downstream autophagy-related proteins are involved in this pathway, whereas the upstream autophagy-initiating protein is not. Our work shows that a LAP-like process serves as a previously unidentified downstream effector of IFN-γ in elimination of the liver-stage human malarial parasite Plasmodium vivax. IFN-γ is a major regulator of immune functions and has been shown to induce liver-stage Plasmodium elimination both in vitro and in vivo. The molecular mechanism responsible for the restriction of liver-stage Plasmodium downstream of IFN-γ remains uncertain, however. Autophagy, a newly described immune defense mechanism, was recently identified as a downstream pathway activated in response to IFN-γ in the control of intracellular infections. We thus hypothesized that the killing of liver-stage malarial parasites by IFN-γ involves autophagy induction. Our results show that whereas IFN-γ treatment of human hepatocytes activates autophagy, the IFN-γ–mediated restriction of liver-stage Plasmodium vivax depends only on the downstream autophagy-related proteins Beclin 1, PI3K, and ATG5, but not on the upstream autophagy-initiating protein ULK1. In addition, IFN-γ enhanced the recruitment of LC3 onto the parasitophorous vacuole membrane (PVM) and increased the colocalization of lysosomal vesicles with P. vivax compartments. Taken together, these data indicate that IFN-γ mediates the control of liver-stage P. vivax by inducing a noncanonical autophagy pathway resembling that of LC3-associated phagocytosis, in which direct decoration of the PVM with LC3 promotes the fusion of P. vivax compartments with lysosomes and subsequent killing of the pathogen. Understanding the hepatocyte response to IFN-γ during Plasmodium infection and the roles of autophagy-related proteins may provide an urgently needed alternative strategy for the elimination of this human malaria.
B-Type Natriuretic Peptide Predicts Sudden Death in Patients With Chronic Heart Failure

Background—Given the high incidence of sudden death in patients with chronic heart failure (CHF) and the efficacy of implantable cardioverter-defibrillators, an appropriate tool for the prediction of sudden death is desirable. B-type natriuretic peptide (BNP) has prognostic significance in CHF, and the stimuli for its production cause electrophysiological abnormalities. This study tests BNP levels as a predictor of sudden death. Methods and Results—BNP levels, in addition to other neurohormonal, clinical, and hemodynamic variables, were obtained from 452 patients with a left ventricular ejection fraction (LVEF) ≤35%. For prediction of sudden death, only survivors without heart transplantation (HTx) or a mechanical assist device and patients who died suddenly were analyzed. Up to 3 years, 293 patients survived without HTx or a mechanical assist device, 89 patients died, and 65 patients underwent HTx. Mode of death was sudden in 44 patients (49%), whereas 31 patients (35%) had pump failure and 14 patients (16%) died from other causes. Univariate risk factors of sudden death were log BNP (P =0.0006), log N-terminal atrial natriuretic peptide (P =0.003), LVEF (P =0.005), log N-terminal BNP (P =0.006), systolic blood pressure (P =0.01), big endothelin (P =0.03), and NYHA class (P =0.04). In the multivariate model, log BNP level was the only independent predictor of sudden death (P =0.0006). Using a cutoff point of log BNP <2.11 (130 pg/mL), Kaplan-Meier sudden death–free survival rates were significantly higher in patients below (99%) compared with patients above (81%) this cutoff point (P =0.0001). Conclusion—BNP levels are a strong, independent predictor of sudden death in patients with CHF.
Effect of Cd-Enriched Sewage Sludge on Plant Growth, Nutrients and Heavy Metals Concentrations in the Soil–Plant System

Abstract Greenhouse pot experiment was conducted to evaluate the changes in soil fertility and nutrient and heavy metal uptake by radish grown in calcareous soil amended with sewage sludge (SS). SS was applied at zero (control), 20, 40 and 80 ton ha-1. Additional treatments were also included (160 ton Cd-enriched SS ha-1; and 80 kg diammonium phosphate ha-1 . Three radish seedlings per pot were planted in a seven-liter pots and were grown for 12 weeks. Radish tuber weight increased with increasing SS rates where the response followed a quadratic relationship and where the rate of 40 ton ha-1 was enough to reach the highest fresh weight. However, doubling the rate of the Cd-enriched SS resulted in a drastic decrease in tuber fresh weight. Addition of 20 ton SS ha-1 was as effective as the addition of the recommended DAP fertilizer. Shoot and tuber Cd concentrations increased with both rates of Cd-enriched SS. However, only the highest rate of original SS slightly increased Cd concentration. Soil pH decreased similarly by all rates and soil salinity increased with increasing SS rates. Soil organic mater, available P and micronutrients and DTPA-Extractable Pb increased by all SS rates. However, Cd sharply increased with application of Cd-enriched SS. Plant Cd concentration was significantly related to the DTPA-extractable soil Cd. It was concluded that SS can be applied to improve plant growth and soil fertility, however, high rates and SS rich in Cd should be avoided.
Melatonin reduces induction of Bax, caspase and cell death in methamphetamine-treated human neuroblastoma SH-SY5Y cultured cells

Abstract: Several studies demonstrated that methamphetamine (MA)‐treated human neuroblastoma cells exhibit increased oxidative stress, which regulates intracellular signaling cascades leading to cell death. Melatonin has a potential as a direct free radical scavenger and protects against cell death caused by MA. The objective of this study was to investigate the neuroprotective properties of melatonin on MA‐induced induction of death signaling cascade and neuronal cell degeneration in human neuroblastoma SH‐SY5Y cultured cells. The results of the present study demonstrate that MA significantly reduced cell viability in SH‐SY5Y cultured cells. Desipramine, a monoamine uptake blocker, and melatonin reversed the toxic effect of MA in reducing cell viability. Induction of Bax, Bcl‐2 and cleaved caspase‐3 protein levels were observed in SH‐SY5Y cultured cells treated with MA, whereas the induction of Bax and cleaved caspase‐3 was diminished by melatonin. Visualization of the induction of Bax using immunofluorescence but a reduction in mitochondrial sites using red‐fluorescent mitochondria‐staining dye was more obviously apparent in MA‐treated cells than in untreated control cells and, again, this effect was abolished by melatonin. These findings demonstrate important roles of Bax and caspase in death signaling cascade, and the protective effects of melatonin in MA‐treated SH‐SY5Y cells.