Miracle-dz/UniFAR-FTUs huggingface dataset:
Multivariate Computational Analysis of Gamma Delta T Cell Inhibitory Receptor Signatures Reveals the Divergence of Healthy and ART-Suppressed HIV+ Aging

Even with effective viral control, HIV-infected individuals are at a higher risk for morbidities associated with older age than the general population, and these serious non-AIDS events (SNAEs) track with plasma inflammatory and coagulation markers. The cell subsets driving inflammation in aviremic HIV infection are not yet elucidated. Also, whether ART-suppressed HIV infection causes premature induction of the inflammatory events found in uninfected elderly or if a novel inflammatory network ensues when HIV and older age co-exist is unclear. In this study we measured combinational expression of five inhibitory receptors (IRs) on seven immune cell subsets and 16 plasma markers from peripheral blood mononuclear cells (PBMC) and plasma samples, respectively, from a HIV and Aging cohort comprised of ART-suppressed HIV-infected and uninfected controls stratified by age (≤35 or ≥50 years old). For data analysis, multiple multivariate computational algorithms (cluster identification, characterization, and regression (CITRUS), partial least squares regression (PLSR), and partial least squares-discriminant analysis (PLS-DA)) were used to determine if immune parameter disparities can distinguish the subject groups and to investigate if there is a cross-impact of aviremic HIV and age on immune signatures. IR expression on gamma delta (γδ) T cells exclusively separated HIV+ subjects from controls in CITRUS analyses and secretion of inflammatory cytokines and cytotoxic mediators from γδ T cells tracked with TIGIT expression among HIV+ subjects. Also, plasma markers predicted the percentages of TIGIT+ γδ T cells in subjects with and without HIV in PSLR models, and a PLS-DA model of γδ T cell IR signatures and plasma markers significantly stratified all four of the subject groups (uninfected younger, uninfected older, HIV+ younger, and HIV+ older). These data implicate γδ T cells as an inflammatory driver in ART-suppressed HIV infection and provide evidence of distinct ‘inflamm-aging’ processes with and without ART-suppressed HIV infection.
Reduced mRNA and Protein Expression Levels of Tet Methylcytosine Dioxygenase 3 in Endothelial Progenitor Cells of Patients of Type 2 Diabetes With Peripheral Artery Disease

Endothelial progenitor cells (EPCs) with immunological properties repair microvasculature to prevent the complications in patients with diabetes. Epigenetic changes such as DNA methylation alter the functions of cells. Tet methylcytosine dioxygenases (TETs) are enzymes responsible for the demethylation of cytosine on genomic DNA in cells. We hypothesized that EPCs of diabetic patients with peripheral artery disease (D-PAD) might have altered expression levels of TETs. Subjects who were non-diabetic (ND, n = 22), with diabetes only (D, n = 29) and with D-PAD (n = 22) were recruited for the collection of EPCs, which were isolated and subjected to analysis. The mRNA and protein expression levels of TET1, TET2, and TET3 were determined using real-time PCR and immunoblot, respectively. The TET1 mRNA expression level in ND group was lower than that in the D and D-PAD groups. The TET3 mRNA level in the ND group was higher than that in the D group, which was higher than that in the D-PAD group. The TET1 protein level in the D-PAD group, but not the D group, was higher than that in the ND group. The TET2 protein level in the D-PAD group, but not the D group, was lower than that in the ND group. The TET3 protein level in the ND group was higher than that in the D group, which was higher than that in the D-PAD group, which is the lowest among the three groups. The changes of TETs protein levels were due to the alterations of their transcripts. These probably lead to epigenetic changes, which may be responsible for the reductions of EPCs numbers and functions in patients with the D-PAD. The expression pattern of TET3 mRNA and TET3 protein in EPCs may be a biomarker of angiopathy in diabetic patients.
Generating High Fidelity Images with Subscale Pixel Networks and Multidimensional Upscaling

The unconditional generation of high fidelity images is a longstanding benchmark for testing the performance of image decoders. Autoregressive image models have been able to generate small images unconditionally, but the extension of these methods to large images where fidelity can be more readily assessed has remained an open problem. Among the major challenges are the capacity to encode the vast previous context and the sheer difficulty of learning a distribution that preserves both global semantic coherence and exactness of detail. To address the former challenge, we propose the Subscale Pixel Network (SPN), a conditional decoder architecture that generates an image as a sequence of sub-images of equal size. The SPN compactly captures image-wide spatial dependencies and requires a fraction of the memory and the computation required by other fully autoregressive models. To address the latter challenge, we propose to use Multidimensional Upscaling to grow an image in both size and depth via intermediate stages utilising distinct SPNs. We evaluate SPNs on the unconditional generation of CelebAHQ of size 256 and of ImageNet from size 32 to 256. We achieve state-of-the-art likelihood results in multiple settings, set up new benchmark results in previously unexplored settings and are able to generate very high fidelity large scale samples on the basis of both datasets.
Nanotechnology, an alternative with promising prospects and advantages for the treatment of cardiovascular diseases

Cardiovascular diseases (CVDs) are one of the most important causes of mortality and affecting the health status of patients. At the same time, CVDs cause a huge health and economic burden to the whole world. Although a variety of therapeutic drugs and measures have been produced to delay the progress of the disease and improve the quality of life of patients, most of the traditional therapeutic strategies can only cure the symptoms and cannot repair or regenerate the damaged ischemic myocardium. In addition, they may bring some unpleasant side effects. Therefore, it is vital to find and explore new technologies and drugs to solve the shortcomings of conventional treatments. Nanotechnology is a new way of using and manipulating the matter at the molecular scale, whose functional organization is measured in nanometers. Because nanoscale phenomena play an important role in cell signal transduction, enzyme action and cell cycle, nanotechnology is closely related to medical research. The application of nanotechnology in the field of medicine provides an alternative and novel direction for the treatment of CVDs, and shows excellent performance in the field of targeted drug therapy and the development of biomaterials. This review will briefly introduce the latest applications of nanotechnology in the diagnosis and treatment of common CVDs.
Identification of Integrin β1 as a Novel PAG1-Interacting Protein Involved in the Inherent Radioresistance of Human Laryngeal Carcinoma

Inherent radioresistance plays a crucial role in the failure of radiotherapy. Using the inherent radioresistant (Hep-2max) and radiosensitive (Hep-2min) cell lines established from the parental cell line Hep-2, we previously reported that phosphoprotein associated with glycosphingolipid-enriched microdomains 1(PAG1) overexpression in laryngeal carcinoma cells was correlated with inherent radioresistant phenotypes. However, the underlying mechanisms of this effect remain unknown. In the present study, we performed a proteomic screen to investigate the interactome of PAG1 in Hep-2max cells resulting in the identification of several interaction partners. Bioinformatic analysis and immunofluorescence experiments indicated the integrin β1 to be a crucial interaction partner of PAG1. PAG1 was also highly expressed in laryngeal carcinoma radioresistant tissues and showed co-localization with integrin β1. In addition, we demonstrated that integrin β1's binding to PAG1 could be interrupted by MβCD, an inhibitor of lipid rafts formation. Moreover, knockdown of integrin β1 by RNA interference sensitized radioresistant cells to irradiation. Importantly, we identified 2 potential interaction sites (Pro216-Arg232 and Asn356-Gly377) in the cytoplasmic domain of PAG1 using high throughput peptide arrays. Taken together, these results suggest that the binding of PAG1 to integrin β1 in lipid rafts is essential for inherent radioresistance of human laryngeal carcinoma.
Learning to Sample

: There is a growing number of tasks that work directly on point clouds. As the size of the point cloud grows, so do the computational demands of these tasks. A possible solution is to sample the point cloud first. Classic sampling approaches, such as farthest point sampling (FPS), do not consider the downstream task. A recent work showed that learning a task-specific sampling can improve results significantly. However, the proposed technique did not deal with the non-differentiability of the sampling operation and offered a workaround instead. We introduce a novel differentiable relaxation for point cloud sampling that approximates sampled points as a mixture of points in the primary input cloud. Our approximation scheme leads to consistently good results on classification and geometry reconstruction applications. We also show that the proposed sampling method can be used as a front to a point cloud registration network. This is a challenging task since sampling must be consistent across two different point clouds for a shared downstream task. In all cases, our approach outperforms existing non-learned and learned sampling alternatives.
ECC: Energy-Constrained Deep Neural Network Compression via a Bilinear Regression Model

Many DNN-enabled vision applications constantly operate under severe energy constraints such as unmanned aerial vehicles, Augmented Reality headsets, and smartphones. Designing DNNs that can meet a stringent energy budget is becoming increasingly important. This paper proposes ECC, a framework that compresses DNNs to meet a given energy constraint while minimizing accuracy loss. The key idea of ECC is to model the DNN energy consumption via a novel bilinear regression function. The energy estimate model allows us to formulate DNN compression as a constrained optimization that minimizes the DNN loss function over the energy constraint. The optimization problem, however, has nontrivial constraints. Therefore, existing deep learning solvers do not apply directly. We propose an optimization algorithm that combines the essence of the Alternating Direction Method of Multipliers (ADMM) framework with gradient-based learning algorithms. The algorithm decomposes the original constrained optimization into several subproblems that are solved iteratively and efficiently. ECC is also portable across different hardware platforms without requiring hardware knowledge. Experiments show that ECC achieves higher accuracy under the same or lower energy budget compared to state-of-the-art resource-constrained DNN compression techniques.
Composition and Comparison of the Ocular Surface Microbiome in Infants and Older Children

Purpose Unlike other microbiomes of the body, the composition of the ocular surface microbiome (OSM) in children has yet to be thoroughly explored. Our goal was to evaluate the OSM in young infants and compare its composition to older children using both culture dependent and independent methodologies to assess for differences with age. Methods Prospective, observational, cross-sectional study of children <18 years of age at a university-based institution. The mucosal surfaces of both eyes, nose and throat were swabbed with a forensic-quality swab. Half of the swab was plated for culture and the other half underwent 16S sequencing. Culture results and microbiome diversity were analyzed. Results Fifty patients (mean age 37 months, range 1–168 months) were enrolled. Forty-seven eyes of 30 patients had positive cultures; four eyes grew >1 species. Culture positive patients were older (43 vs. 29 months, P = 0.19). Additionally, older children had greater diversity than children under 6 months of age by 16S sequencing (P = 0.05). Staphylococcus species were predominant by culture (35/52 isolates) and by 16S sequencing. The OSM was fairly similar to the nose microbiome, whereas the throat microbiome differed significantly and had a higher abundance of Streptococcaceae (P = 0.001). Conclusions The OSM is predominantly composed of Staphylococcus species in children, as demonstrated by both culture dependent and culture independent methods. Older children were more likely to have growth on culture and have more a complex bacterial milieu with 16S sequencing. Translational Relevance 16S sequencing provides more robust information regarding the composition of the microbiomes than culture dependent methods.
Henoch-schonlein Purpura Nephritis with Renal Interstitial Lesions

Abstract Objective To investigate the clinical pathology and prognosis & outcome of Henoch-Schonlein purpura nephritis (HSPN) with renal interstitial lesions. Methods All 148 patients were analyzed for clinical, renal pathological, and prognostic features. Patients with no, mild, and moderate- severe renal tubulo-interstitial lesions were included in group A, B and C, respectively. Results The estimated glomerular filtration rate (eGFR) of group B was significantly lower than that of group A. The levels of serum creatinine and blood urea nitrogen in group C were significantly higher than those in groups A and B. Clinical type II was correlated with pathological types II and IIIa; pathological type IV and IIIb were correlated with clinical type VI and IV. There were significant differences in the level of red blood cells in urinary sediment, levels of urine occult blood and in the prognosis among the 3 groups. Conclusion Clinically, Type II is the most common cause; pathologically, Type IIIa is more common. The severity of renal tubulo-interstitial lesions is positively correlated with a decline in renal function and GFR. There is a correlation between the severity of renal tubulo-interstitial lesions and the severity of hematuria. Most patients with HSPN have a good prognosis.
Playing Text-Adventure Games with Graph-Based Deep Reinforcement Learning

Text-based adventure games provide a platform on which to explore reinforcement learning in the context of a combinatorial action space, such as natural language. We present a deep reinforcement learning architecture that represents the game state as a knowledge graph which is learned during exploration. This graph is used to prune the action space, enabling more efficient exploration. The question of which action to take can be reduced to a question-answering task, a form of transfer learning that pre-trains certain parts of our architecture. In experiments using the TextWorld framework, we show that our proposed technique can learn a control policy faster than baseline alternatives. We have also open-sourced our code at https://github.com/rajammanabrolu/KG-DQN.
Effects of waste stream combinations from brewing industry on performance of Black Soldier Fly, Hermetia illucens (Diptera: Stratiomyidae)

Background In recent years, there has been a rapidly growing demand for readily accessible substrates for mass production of Black Soldier Fly, Hermetia illucens Linnaeus. Beer production results in various by-products that typically end up in uncontrolled dumpsites constituting pollution problems, which merits urgent attention. The present study investigated whether the 12 formulated diets composed of brewers’ spent grains (BSGs), brewers’ yeast and cane molasses can serve as substrate for H. illucens production. Methods Four different BSGs were selected and formulated into 12 diets, aiming at varying protein and net energy levels. The diets were offered to newly hatched (∼1 h old) H. illucens larvae and the influence on developmental duration, survival, wet weight, pre-oviposition time, fecundity, and longevity were compared. Results Developmental duration of the larvae (16–21 days) and pre-pupae (8–11 days) differed significantly across the different diets. The developmental duration of the pupae (8.7–9.1 days) was not affected by diet. The larval (86–99.2%), pre-pupal (71–95%), and pupal (65–91%) survival rates varied significantly between flies reared on the different diets. The pre-oviposition time was similar for flies provided with water (7–11 days) and 10% sugar solution (8–14 days) or across the different diets. The mean fecundity per female ranged from 324–787 eggs and did not differ between females provided with water or sugar solution. However, the number of eggs laid per female varied significantly across the different diets when provided with water. The longevity of starved H. illucens adults was significantly lower (5 days) compared to those provided with water (11–14 days) or sugar solution (14–15 days). Discussion The implications of these findings as part of a quality control procedure for commercial production of high-quality H. illucens larvae as an alternative protein ingredient in livestock and aquaculture feed are discussed.
Tenascin-C Modulates Cell Cycle Progression to Enhance Tumour Cell Proliferation through AKT/FOXO1 Signalling in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is a disease with an extremely poor prognosis that is characterized by a rich extracellular matrix (ECM). Tenascin-C (TNC) is a component of the ECM and plays a role in tumour progression. In this study, we reported that TNC is overexpressed in PDAC tissues and is correlated with tumour stage and cyclin D1 expression. Cyclin D1 is key regulator of the cell cycle G1/S transition. Further experiments revealed that TNC promotes G1/S transition through AKT signalling. TNC/AKT increases the expression of cyclin D1 by enhancing the transcriptional activity of β-catenin, whereas the translocation of FOXO1 from the nucleus results in the downregulation of p27Kip1. Cyclin D1 and p27Kip1 regulate the activity of cyclin D1-CDK4 complexes and retinoblastoma (Rb), and then they stimulate the progression of G1/S transition and tumour cell proliferation. In conclusion, TNC exerts its activating effect on the proliferation of pancreatic cancer cells in vitro and in vivo through its functional target AKT/FOXO1/β-catenin. The molecular mechanisms that drive PDAC progression will be useful for the development of molecular markers and the evaluation of patient prognosis.
Benchmarking Keyword Spotting Efficiency on Neuromorphic Hardware

Using Intel's Loihi neuromorphic research chip and ABR's Nengo Deep Learning toolkit, we analyze the inference speed, dynamic power consumption, and energy cost per inference of a two-layer neural network keyword spotter trained to recognize a single phrase. We perform comparative analyses of this keyword spotter running on more conventional hardware devices including a CPU, a GPU, Nvidia's Jetson TX1, and the Movidius Neural Compute Stick. Our results indicate that for this real-time inference application, Loihi outperforms all of these alternatives on an energy cost per inference basis while maintaining equivalent inference accuracy. Furthermore, an analysis of tradeoffs between network size, inference speed, and energy cost indicates that Loihi's comparative advantage over other low-power computing devices improves for larger networks.
Endothelial-specific FoxO1 depletion prevents obesity-related disorders by increasing vascular metabolism and growth

Impaired angiogenesis is a hallmark of metabolically dysfunctional adipose tissue in obesity. However, the underlying mechanisms restricting angiogenesis within this context remain ill-defined. Here, we demonstrate that induced endothelial-specific depletion of the transcription factor Forkhead Box O1 (FoxO1) in male mice led to increased vascular density in adipose tissue. Upon high-fat diet feeding, endothelial cell FoxO1-deficient mice exhibited even greater vascular remodeling in the visceral adipose depot, which was paralleled with a healthier adipose tissue expansion, higher glucose tolerance and lower fasting glycemia concomitant with enhanced lactate levels. Mechanistically, FoxO1 depletion increased endothelial proliferative and glycolytic capacities by upregulating the expression of glycolytic markers, which may account for the improvements at the tissue level ultimately impacting whole-body glucose metabolism. Altogether, these findings reveal the pivotal role of FoxO1 in controlling endothelial metabolic and angiogenic adaptations in response to high-fat diet and a contribution of the endothelium to whole-body energy homeostasis.
Bacterial profile, antibiotic resistance pattern and associated factors among cancer patients at University of Gondar Hospital, Northwest Ethiopia

Introduction Cancer is alarmingly increased in developing countries like Ethiopia, where multidrug resistant bacterial infection is rampant. The aim of this study was to determine the bacterial profile, antimicrobial resistance pattern, and associated factors among cancer patients attending University of Gondar Hospital. Methods A consecutive 216 cancer patients were recruited from February to April, 2017. Socio-demographic and clinical data were collected using a structured questionnaire. Culture and antibiotic resistance were done following standard microbiological procedures. Result The overall prevalence of bacterial infection was 19.4%. The predominant bacterial isolates were Staphylococcus aureus (28.6%), followed by coagulase negative staphylococci (26.2%) and Escherichia coli (21.4%). Multidrug resistance was detected in 46.5% bacterial isolates. Methicillin resistance was detected in 25% of S. aureus and in 45.5% of coagulase negative staphylococci. Fluoroquinolone resistance was detected in 33.3% of E. coli isolates. Cancer patients with solid tumor, started cancer therapy, and being symptomatic had higher odds of culture positivity. Conclusion The overall burden of bacterial infection among cancer patients is considerably high. The findings of this study inform baseline information for policymakers and call for additional studies with large isolates in different cancer treatment centers in the region and in the country to better understand the bacterial isolate and resistance pattern.
Extensively drug-resistant Acinetobacter baumannii and Proteeae association in a Romanian intensive care unit: risk factors for acquisition

Purpose The purpose of this study was to identify risk factors for extensively drug-resistant (XDR) Acinetobacter baumannii (AB) and XDR Proteeae association in the largest intensive care unit (ICU) in Western Romania. Materials and methods This retrospective case-controlled study was conducted between January 2016 and December 2016 in the ICU of the “Pius Brînzeu” County Emergency Clinical Hospital of Timi oara. Data were collected, in strict confidentiality, from the electronic database of the Microbiology Laboratory and the hospital’s electronic medical records. Risk factors were ș investigated by logistic regression. Independent variables with P≤0.05 and OR >1 (95% CI >1) in the univariate analysis were entered into multivariate sequenced analysis. Findings The incidence density of coinfection with XDR AB and XDR Proteeae was 5.31 cases per 1,000 patient-days. Independent risk factors for the association of XDR AB and XDR Proteeae were represented by the presence of tracheostomy and naso-/orogastric nutrition ≥ 8 days. In addition, pressure ulcers were independent predictive factors for infections with all three infection types. Previous antibiotic therapy was an independent risk factor for the acquisition of XDR-AB strains, alone or in association, while the prolonged hospitalization in the ICU, blood transfusion, and hemodialysis appear as independent risk factors for single infections. Conclusion This association of XDR AB and XDR Proteeae may well not be limited to our hospital or our geographical area.