Miracle-dz/UniFAR-FTUs huggingface dataset:
Motion-Based Object Segmentation Based on Dense RGB-D Scene Flow

Given two consecutive RGB-D images, we propose a model that estimates a dense three-dimensional (3D) motion field, also known as scene flow. We take advantage of the fact that in robot manipulation scenarios, scenes often consist of a set of rigidly moving objects. Our model jointly estimates the following: First, the segmentation of the scene into an unknown but finite number of objects, second, the motion trajectories of these objects, and finally, the object scene flow. We employ an hourglass, deep neural network architecture. In the encoding stage, the RGB and depth images undergo spatial compression and correlation. In the decoding stage, the model outputs three images containing a per-pixel estimate of the corresponding object center as well as object translation and rotation. This forms the basis for inferring the object segmentation and final object scene flow. To evaluate our model, we generated a new and challenging, large scale, synthetic dataset that is specifically targeted at robotic manipulation: It contains a large number of scenes with a very diverse set of simultaneously moving 3D objects and is recorded with a simulated, static RGB-D camera. In quantitative experiments, we show that we outperform state-of-the-art scene flow and motion-segmentation methods on this data set. In qualitative experiments, we show how our learned model transfers to challenging real-world scenes, visually generating better results than existing methods.
EMC10 governs male fertility via maintaining sperm ion balance

Infertility is a severe public health problem worldwide that prevails up to 15% in reproductive-age couples, and male infertility accounts for half of total infertility. Studies on genetically modified animal models have identified lots of genes involved in the pathogenesis of male infertility. The underlying causes, however, remain largely unclear. In this study, we provide evidence that EMC10, one subunit of endoplasmic reticulum (ER) membrane protein complex (EMC), is required for male fertility. EMC10 is significantly decreased in spermatozoa from patients with asthenozoospermia and positively associated with human sperm motility. Male mice lacking Emc10 gene are completely sterile. Emc10-null spermatozoa exhibit multiple defects including abnormal morphology, decreased motility, impaired capacitation, and impotency of acrosome reaction, thereby which are incapable of fertilizing intact or ZP-free oocytes. However, intracytoplasmic sperm injection could rescue this defect caused by EMC10 deletion. Mechanistically, EMC10 deficiency leads to inactivation of Na/K-ATPase, in turn giving rise to an increased level of intracellular Na+ in spermatozoa, which contributes to decreased sperm motility and abnormal morphology. Other mechanistic investigations demonstrate that the absence of EMC10 results in a reduction of HCO3- entry and subsequent decreases of both cAMP-dependent protein kinase A substrate phosphorylation and protein tyrosine phosphorylation. These data demonstrate that EMC10 is indispensable to male fertility via maintaining sperm ion balance of Na+ and HCO3-, and also suggest that EMC10 is a promising biomarker for male fertility and a potential pharmaceutical target to treat male infertility.
Effects of intraspecific phenotypic variation on species coexistence.

Intraspecific variation can promote or inhibit species coexistence, both by increasing species' competitive abilities, and by altering the relative strengths of intraspecific and interspecific competition. Effects of intraspecific variation on coexistence can occur via complementarity of different variants, and via a selection effect: initially-variable populations are more likely to contain highly competitive variants that might determine the ability of the population as a whole to both invade and resist invasion. We tested the effects of intraspecific variation and composition on coexistence by assaying the mutual invasibility of populations of two competing bean weevil species (Callosobruchus maculatus and C. chinensis) when each was initiated with one, three, or five genetically- and phenotypically-distinct lineages. Our results reveal that intraspecific variation is a double-edged sword for species coexistence. Increasing intraspecific variation increased species' abilities to invade, and to resist invasion, via selection effects and intraspecific niche complementarity among conspecific lineages, thereby creating the potential for exclusion among mismatched competitors. But intraspecific variation also increased the scope for resource partitioning, creating the potential for stable coexistence. Stable coexistence occurred only when intraspecific variation caused species to exhibit both relatively evenly-matched competitive abilities and sufficiently-strong resource partitioning. Our work explains the conflicting results of previous studies.
Sub-kilohertz excitation lasers for quantum information processing with Rydberg atoms

Quantum information processing using atomic qubits requires narrow linewidth lasers with long-term stability for high-fidelity coherent manipulation of Rydberg states. In this paper, we report on the construction and characterization of three continuous-wave narrow linewidth lasers stabilized simultaneously to an ultra-high finesse Fabry–Perot cavity made of ultra-low expansion glass, with a tunable offset-lock frequency. One laser operates at 852 nm, while the two locked lasers at 1018 nm are frequency doubled to 509 nm for excitation of Cs133 atoms to Rydberg states. The optical beat note at 509 nm is measured to be 260(5) Hz. We present measurements of the offset between the atomic and cavity resonant frequencies using electromagnetically induced transparency for high-resolution spectroscopy on a cold atom cloud. The long-term stability is determined from repeated spectra over a period of 20 days, yielding a linear frequency drift of ∼1 Hz/s.
An Efficient HOG-Centroid Descriptor for Human Gait Recognition

Automatic recognition of human gait have gained much attention nowadays. Histogram of Oriented Gradient (HOG) is a widely adopted descriptor for object’s shape analysis. In this paper, combination of HOG descriptor with silhouette centroid for human gait recognition is proposed. The resultant descriptor, namely HOG-Centroid, achieves better recognition performance on comparison with HOG descriptor individually as well as other existing gait recognition methods. Experiments are carried out with CASIA gait dataset B and cumulative matching scores of 95.3%, 98.1% and 99.2% are obtained for rank 1, rank 5 and rank 10 respectively.
Osteoporosis Therapy With Denosumab in Organ Transplant Recipients

Objective Osteoporosis and fragility fractures represent serious complications for the solid organ transplant population. The recommended osteoporosis therapy for organ recipients involves supplementation with calcium and vitamin D and bisphosphonate administration. However, these options can prove limited for patients with impaired renal function. An alternative therapy option is offered by denosumab, a monoclonal antibody that targets receptor activator of nuclear factor kappa-B ligand. Patients and methods We evaluated 63 patients with osteoporosis (23 males and 40 females, age 56.4 ± 13.1 years) following solid organ transplantation (15 diabetic patients after simultaneous transplantation of the kidney and pancreas, 34 patients after kidney transplantation, and 14 patients with liver grafts). Osteoporosis was diagnosed according to standard DEXA examination using the Lunar Prodigy apparatus. Transplanted patients with impaired renal function were treated for osteoporosis of the lumbar spine (L-spine) and/or proximal femur with calcium and vitamin D supplementation and 60 mg of denosumab every 6 months between the years 2012 and 2017. The mean duration of the therapy was 1.65 ± 0.7 years. Results After denosumab therapy, L-spine T-scores improved across the whole group, ranging from −2.7 ± 0.09 to −1.8 ± 1.0 (p < 0.001). T-score values for the proximal femur increased from −2.5 ± 0.8 to −2.0 ± 0.7 after the therapy (p < 0.01). We observed only a mild, statistically insignificant improvement in distal forearm T-scores. The mean increase in L-spine bone mineral density (BMD) was 11.5 ± 6.2% in subjects with osteoporosis at this site and 10.4 ± 6.1% in the case of all patients. BMD of the proximal femur increased by 10.4 ± 8.3% in patients with osteoporosis and by 7.5 ± 7.3% in all patients. Denosumab therapy decreased the prevalence of osteoporosis in the L-spine from 75 to 27% (p < 0.001) and proximal femur osteoporosis from 54 to 36% (p < 0.05). Denosumab therapy reduced elevated levels of osteocalcin and beta-crosslaps (βCTX) in comparison with baseline levels (p < 0.001) across the whole group of graft recipients. Conclusion Denosumab therapy was well-tolerated and improved bone density in our group of solid organ transplant recipients. The indications are that denosumab could be a viable therapeutic option for transplanted patients with osteoporosis, especially in those with renal function impairment or bisphosphonate intolerance.
Development of an in vitro method for modeling drug release and subsequent tissue drug uptake and deposition in a pulsatile flow network

A novel benchtop model of drug elution and arterial drug deposition following stent implantation has been developed. The model contains a single drug loaded strut and a compartment simulating the vessel wall, housed in a flow chamber under a pulsatile flow regime. Each component has programmable transport properties that can be implemented into a computational model of drug elution. An initial experiment determining the effects of luminal flow on drug deposition patterns was performed. The results show that spatial distribution of drug correlates with areas of low and recirculating flow surrounding the strut. This spatial distribution of drug was shown to be dependent on both transient release behavior and the local flow field surrounding the strut. Furthermore, these results showed that the novel method could be used to study the effects of luminal flow in the presence of single or multiple struts. The method could also be used to explore more complex drug release strategies.
Empirical evaluation of data normalization methods for molecular classification

Background Data artifacts due to variations in experimental handling are ubiquitous in microarray studies, and they can lead to biased and irreproducible findings. A popular approach to correct for such artifacts is through post hoc data adjustment such as data normalization. Statistical methods for data normalization have been developed and evaluated primarily for the discovery of individual molecular biomarkers. Their performance has rarely been studied for the development of multi-marker molecular classifiers—an increasingly important application of microarrays in the era of personalized medicine. Methods In this study, we set out to evaluate the performance of three commonly used methods for data normalization in the context of molecular classification, using extensive simulations based on re-sampling from a unique pair of microRNA microarray datasets for the same set of samples. The data and code for our simulations are freely available as R packages at GitHub. Results In the presence of confounding handling effects, all three normalization methods tended to improve the accuracy of the classifier when evaluated in an independent test data. The level of improvement and the relative performance among the normalization methods depended on the relative level of molecular signal, the distributional pattern of handling effects (e.g., location shift vs scale change), and the statistical method used for building the classifier. In addition, cross-validation was associated with biased estimation of classification accuracy in the over-optimistic direction for all three normalization methods. Conclusion Normalization may improve the accuracy of molecular classification for data with confounding handling effects; however, it cannot circumvent the over-optimistic findings associated with cross-validation for assessing classification accuracy.
Targeting the Leukemia Antigen PR1 with Immunotherapy for the Treatment of Multiple Myeloma

Purpose: PR1 is a human leukocyte antigen (HLA)-A2 nonameric peptide derived from neutrophil elastase (NE) and proteinase 3 (P3). We have previously shown that PR1 is cross-presented by solid tumors, leukemia, and antigen-presenting cells, including B cells. We have also shown that cross-presentation of PR1 by solid tumors renders them susceptible to killing by PR1-targeting immunotherapies. As multiple myeloma is derived from B cells, we investigated whether multiple myeloma is also capable of PR1 cross-presentation and subsequently capable of being targeted by using PR1 immunotherapies. Experimental Design: We tested whether multiple myeloma is capable of cross-presenting PR1 and subsequently becomes susceptible to PR1-targeting immunotherapies, using multiple myeloma cell lines, a xenograft mouse model, and primary multiple myeloma patient samples. Results: Here we show that multiple myeloma cells lack endogenous NE and P3, are able to take up exogenous NE and P3, and cross-present PR1 on HLA-A2. Cross-presentation by multiple myeloma utilizes the conventional antigen processing machinery, including the proteasome and Golgi, and is not affected by immunomodulating drugs (IMiD). Following PR1 cross-presentation, we are able to target multiple myeloma with PR1-CTL and anti-PR1/HLA-A2 antibody both in vitro and in vivo. Conclusions: Collectively, our data demonstrate that PR1 is a novel tumor-associated antigen target in multiple myeloma and that multiple myeloma is susceptible to immunotherapies that target cross-presented antigens. Clin Cancer Res; 24(14); 3386–96. ©2018 AACR.
Coordinated regulation of the dorsal‐ventral and anterior‐posterior patterning of Xenopus embryos by the BTB/POZ zinc finger protein Zbtb14

During early vertebrate embryogenesis, bone morphogenetic proteins (BMPs) belonging to the transforming growth factor‐β (TGF‐β) family of growth factors play a central role in dorsal–ventral (DV) patterning of embryos, while other growth factors such as Wnt and fibroblast growth factor (FGF) family members regulate formation of the anterior–posterior (AP) axis. Although the establishment of body plan is thought to require coordinated formation of the DV and AP axes, the mechanistic details underlying this coordination are not well understood. Here, we show that a Xenopus homologue of zbtb14 plays an essential role in the regulation of both DV and AP patterning during early Xenopus development. We show that overexpression of Zbtb14 promotes neural induction and inhibits epidermal differentiation, thereby regulating DV patterning. In addition, Zbtb14 promotes the formation of posterior neural tissue and suppresses anterior neural development. Consistent with this, knock‐down experiments show that Zbtb14 is required for neural development, especially for the formation of posterior neural tissues. Mechanistically, Zbtb14 reduces the levels of phosphorylated Smad1/5/8 to suppress BMP signaling and induces an accumulation of β‐Catenin to promote Wnt signaling. Collectively, these results suggest that Zbtb14 plays a crucial role in the formation of DV and AP axes by regulating both the BMP and Wnt signaling pathways during early Xenopus embryogenesis.
Oleic acid promotes prostate cancer malignant phenotype via the G protein‐coupled receptor FFA1/GPR40

Prostate cancer (PCa) is the most commonly diagnosed malignancy in men and the second leading cause of cancer‐related death in industrialized countries. Epidemiologic evidence suggests that obesity promotes aggressive PCa. Recently, a family of Free Fatty Acid (FFA) receptors (FFARs) has been identified and reported to affect several crucial biological functions of tumor cells such as proliferation, invasiveness, and apoptosis. Here we report that oleic acid (OA), one of the most prevalent FFA in human plasma, increases proliferation of highly malignant PC3 and DU‐145 PCa cells. Furthermore, docetaxel cytotoxic action, the first‐line chemotherapeutic agent for the treatment of androgen‐independent PCa, was significantly reduced in the presence of OA, when measured by the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide assay, suggesting that this FFA plays also a role in chemoresistance. OA induced intracellular calcium increase, in part due to the store operated calcium entry (SOCE), measured by a calcium imaging technique. Moreover, PI3K/Akt signaling pathway was enhanced, as revealed by increased Akt phosphorylation levels. Intriguingly, attenuating the expression of FFA1/GPR40, a receptor for long chain FFA including OA, prevented the OA‐induced effects. Of relevance, we found that FFA1/GPR40 is significantly overexpressed in tissue specimens of PCa, compared to benign prostatic hyperplasia tissues, at both mRNA and protein expression level, analyzed by Real Time RT‐PCR and immunofluorescence experiments, respectively. Our data suggest that OA promotes an aggressive phenotype in PCa cells via FFA1/GPR40, calcium and PI3K/Akt signaling. Thus, FFA1/GPR40, might represent a potential useful prognostic biomarker and therapeutic target for the treatment of advanced PCa.
miR-132 couples the circadian clock to daily rhythms of neuronal plasticity and cognition

The microRNA miR-132 serves as a key regulator of a wide range of plasticity-associated processes in the central nervous system. Interestingly, miR-132 expression has also been shown to be under the control of the circadian timing system. This finding, coupled with work showing that miR-132 is expressed in the hippocampus, where it influences neuronal morphology and memory, led us to test the idea that daily rhythms in miR-132 within the forebrain modulate cognition as a function of circadian time. Here, we show that hippocampal miR-132 expression is gated by the time-of-day, with peak levels occurring during the circadian night. Further, in miR-132 knockout mice and in transgenic mice, where miR-132 is constitutively expressed under the control of the tetracycline regulator system, we found that time-of-day dependent memory recall (as assessed via novel object location and contextual fear conditioning paradigms) was suppressed. Given that miRNAs exert their functional effects via the suppression of target gene expression, we examined the effects that transgenic miR-132 manipulations have on MeCP2 and Sirt1—two miR-132 targets that are associated with neuronal plasticity and cognition. In mice where miR-132 was either knocked out, or transgenically expressed, rhythmic expression of MeCP2 and Sirt1 was suppressed. Taken together, these results raise the prospect that miR-132 serves as a key route through which the circadian timing system imparts a daily rhythm on cognitive capacity.
VPRS-Based Regional Decision Fusion of CNN and MRF Classifications for Very Fine Resolution Remotely Sensed Images

Recent advances in computer vision and pattern recognition have demonstrated the superiority of deep neural networks using spatial feature representation, such as convolutional neural networks (CNNs), for image classification. However, any classifier, regardless of its model structure (deep or shallow), involves prediction uncertainty when classifying spatially and spectrally complicated very fine spatial resolution (VFSR) imagery. We propose here to characterize the uncertainty distribution of CNN classification and integrate it into a regional decision fusion to increase classification accuracy. Specifically, a variable precision rough set (VPRS) model is proposed to quantify the uncertainty within CNN classifications of VFSR imagery and partition this uncertainty into positive regions (correct classifications) and nonpositive regions (uncertain or incorrect classifications). Those “more correct” areas were trusted by the CNN, whereas the uncertain areas were rectified by a multilayer perceptron (MLP)-based Markov random field (MLP-MRF) classifier to provide crisp and accurate boundary delineation. The proposed MRF-CNN fusion decision strategy exploited the complementary characteristics of the two classifiers based on VPRS uncertainty description and classification integration. The effectiveness of the MRF-CNN method was tested in both urban and rural areas of southern England as well as semantic labeling data sets. The MRF-CNN consistently outperformed the benchmark MLP, support vector machine, MLP-MRF, CNN, and the baseline methods. This paper provides a regional decision fusion framework within which to gain the advantages of model-based CNN, while overcoming the problem of losing effective resolution and uncertain prediction at object boundaries, which is especially pertinent for complex VFSR image classification.
A novel histochemistry assay to assess and quantify focal cytochrome c oxidase deficiency

Defects in the respiratory chain, interfering with energy production in the cell, are major underlying causes of mitochondrial diseases. In spite of this, the surprising variety of clinical symptoms, disparity between ages of onset, as well as the involvement of mitochondrial impairment in ageing and age‐related diseases continue to challenge our understanding of the pathogenic processes. This complexity can be in part attributed to the unique metabolic needs of organs or of various cell types. In this view, it remains essential to investigate mitochondrial dysfunction at the cellular level. For this purpose, we developed a novel enzyme histochemical method that enables precise quantification in fresh‐frozen tissues using competing redox reactions which ultimately lead to the reduction of tetrazolium salts and formazan deposition in cytochrome c oxidase‐deficient mitochondria. We demonstrate that the loss of oxidative activity is detected at very low levels – this achievement is unequalled by previous techniques and opens up new opportunities for the study of early disease processes or comparative investigations. Moreover, human biopsy samples of mitochondrial disease patients of diverse genotypic origins were used and the successful detection of COX‐deficient cells suggests a broad application for this new method. Lastly, the assay can be adapted to a wide range of tissues in the mouse and extends to other animal models, which we show here with the fruit fly, Drosophila melanogaster. Overall, the new assay provides the means to quantify and map, on a cell‐by‐cell basis, the full extent of COX deficiency in tissues, thereby expending new possibilities for future investigation. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Validation of respiratory signal derived from suprasternal notch acceleration for sleep apnea detection

This study evaluates the respiration signal derived from an accelerometer mounted on the suprasternal notch in three body positions and three respiration types simulating normal sleep conditions. The Acceleration Derived Respiratory signal (ADR) is compared with single strain gauge belt and a standard spirometry signal taken as reference. The results demonstrate the potential of ADR as a simple, low cost and unintrusive method of screening breath disorders such as obstructive sleep apnea/hypopnea.