Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the molecular mechanisms of osteosarcoma by the integrated analysis of mRNAs and miRNA microarrays

Osteosarcoma (OS) is the most frequently occurring primary bone malignancy with a rapid progression and poor survival. In the present study, in order to examine the molecular mechanisms of OS, we analyzed the microarray of GSE28425. GSE28425 was downloaded from Gene Expression Omnibus, which also included the miRNA expression profile, GSE28423, and the mRNA expression profile, GSE28424. Each of the expression profiles included 19 OS cell lines and 4 normal bones. The differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) were screened using the limma package in Bioconductor. The DEGs associated with tumors were screened and annotated. Subsequently, the potential functions of the DEGs were analyzed by Gene Ontology (GO) and pathway enrichment analyses. Furthermore, the protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software. Furthermore, modules of the PPI network were screened using the ClusterOne plugin in Cytoscape. Additionally, the transcription factor (TF)-DEG regulatory network, DE-miRNA-DEG regulatory network and miRNA-function collaborative network were separately constructed to obtain key DEGs and DE-miRNAs. In total, 1,609 DEGs and 149 DE-miRNAs were screened. Upregulated FOS-like antigen 1 (FOSL1) also had the function of an oncogene. MAD2 mitotic arrest deficient-like 1 (MAD2L1; degree, 65) and aurora kinase A (AURKA; degree, 64) had higher degrees in the PPI network of the DEGs. In the TF-DEG regulatory network, the TF, signal transducer and activator of transcription 3 (STAT3) targeted the most DEGs. Moreover, in the DE-miRNA-DEG regulatory network, downregulated miR-1 targeted many DEGs and estrogen receptor 1 (ESR1) was targeted by several highly expressed miRNAs. Moreover, in the miRNA-function collaborative networks of upregulated miRNAs, miR-128 targeted myeloid dendritic associated functions. On the whole, our data indicate that MAD2L1, AURKA, STAT3, ESR1, FOSL1, miR-1 and miR-128 may play a role in the development and/or progressio of OS.
Impact of Intermittent Preventive Treatment During Pregnancy on Plasmodium falciparum Drug Resistance–Mediating Polymorphisms in Uganda

Background In a recent trial of intermittent preventive treatment in pregnancy (IPTp) in Uganda, dihydroartemisinin-piperaquine (DP) was superior to sulfadoxine-pyrimethamine (SP) in preventing maternal and placental malaria. Methods We compared genotypes using sequencing, fluorescent microsphere, and quantitative polymerase chain reaction assays at loci associated with drug resistance in Plasmodium falciparum isolated from subjects receiving DP or SP. Results Considering aminoquinoline resistance, DP was associated with increased prevalences of mutations at pfmdr1 N86Y, pfmdr1 Y184F, and pfcrt K76T compared to SP (64.6% vs 27.4%, P < .001; 93.9% vs 59.2%, P < .001; and 87.7% vs 75.4%, P = .03, respectively). Increasing plasma piperaquine concentration at the time of parasitemia was associated with increasing pfmdr1 86Y prevalence; no infections with the N86 genotype occurred with piperaquine >2.75 ng/mL. pfkelch13 propeller domain polymorphisms previously associated with artemisinin resistance were not identified. Recently identified markers of piperaquine resistance were uncommon and not associated with DP. Considering antifolate resistance, SP was associated with increased prevalence of a 5-mutation haplotype (pfdhfr 51I, 59R, and 108N; pfdhps 437G and 581G) compared to DP (90.8% vs 60.0%, P = .001). Conclusions IPTp selected for genotypes associated with decreased sensitivity to treatment regimens, but genotypes associated with clinically relevant DP resistance in Asia have not emerged in Uganda.
Threats to bioethical principles in medical practice in Brazil: new medical ethics code period

We aimed to outline the profile of medical professionals in Brazil who have violated the deontological norms set forth in the ethics code of the profession, and whose cases were judged by the higher tribunal for medical ethics between 2010 and 2016. This survey was conducted using a database formed from professional ethics cases extracted from the plenary of the medical ethics tribunal of the Federal Council of Medicine. These were disciplinary ethics cases that were judged at appeal level between 2010 and 2016. Most of these professionals were male (88.5%) and their mean age was 59.9 years (SD=11.62) on the date of judgment of their appeals, ranging from 28 to 95 years. Most of them were based in the southeastern region of Brazil (50.89%). Articles 1 and 18 of the medical ethics code were the rules most frequently violated. The sentence given most often was the cancellation of their professional license (37.6%) and the acts most often sentenced involved malpractice, imprudence, and negligence (18.49%). It is acknowledged that concern for the principles of bioethics was present in the appeal decisions made by the plenary of the medical ethics tribunal of the Federal Council of Medicine.
Rituximab addition to chemotherapy in real world patients with chronic lymphocytic leukemia: effective in first line but indication of lack of efficacy in subsequent lines of therapy

Lina van der Straten , Avinash G. Dinmohamed , Peter E. Westerweel, Anton W. Langerak, Jurgen Riedl, Jeanette K. Doorduijn, Arnon P. Kater and Mark-David Levin Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands; Department of Research, Netherlands Comprehensive Cancer Organisation (IKNL), Utrecht, The Netherlands; Department of Public Health, Erasmus University Medical Centre, Rotterdam, The Netherlands; Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands; Department of Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands; Department of Clinical Chemistry, Result laboratories, Albert Schweitzer Hospital, Dordrecht, The Netherland; Department of Hematology, Academic Medical Centre, Amsterdam, the Netherlands
Turbo Trellis-Coded Hierarchical-Modulation Assisted Decode-and-Forward Cooperation

Hierarchical modulation (HM), which is also known as layered modulation, has been widely adopted across the telecommunication industry. Its strict backward compatibility with single-layer modems and its low complexity facilitate the seamless upgrading of wireless communication services. The potential employment of HM in cooperative communications has the promise of increasing the achievable throughput at low power consumption. In this paper, we propose a single-relay-aided hierarchical-modulation-based cooperative communication system. The source employs a pair of turbo trellis-coded modulation (TTCM) schemes relying on specially designed HM, whereas the relay invokes the decode-and-forward (DAF) protocol. We have analyzed the system's achievable rate, as well as its bit error ratio (BER), using Monte Carlo simulations. The results demonstrate that the power consumption of the entire system is reduced to 3.62 dB per time slot (TS) by our scheme.
Ultrastructural localisation of protein interactions using conditionally stable nanobodies

We describe the development and application of a suite of modular tools for high-resolution detection of proteins and intracellular protein complexes by electron microscopy (EM). Conditionally stable GFP- and mCherry-binding nanobodies (termed csGBP and csChBP, respectively) are characterized using a cell-free expression and analysis system and subsequently fused to an ascorbate peroxidase (APEX) enzyme. Expression of these cassettes alongside fluorescently labelled proteins results in recruitment and stabilisation of APEX, whereas unbound APEX nanobodies are efficiently degraded by the proteasome. This greatly simplifies correlative analyses, enables detection of less-abundant proteins, and eliminates the need to balance expression levels between fluorescently labelled and APEX nanobody proteins. Furthermore, we demonstrate the application of this system to bimolecular complementation (‘EM split-fluorescent protein’), for localisation of protein–protein interactions at the ultrastructural level.
Feature saliency based SLAM of mobile robot

We propose a stable CV-SLAM (Ceiling Vision based Simultaneous Localization and Mapping) technique, which uses both circle and corner features as landmarks in the scene and improves the process stability using saliency measurement. It provides a method which utilizes different feature detection algorithms to detect various key points. And then we measure saliency strength of every points to pick out more stable feature points and generate a hybrid map based on Delaunay triangles among these points. Moreover, we complete SLAM using an extended Kalman filter(EKF), which is fundament for robotic SLAM. Simulation results show the effects of proposed methods.
Verifying the CPA Networking Stack using SPIN/Promela

This paper presents a verification of the CPA Networking Stack, using the SPIN Model Checker. Our work shows that the system developed for general networking within CPA applications works under the conditions defined for it. The model itself focuses on ensuring deadlock freedom, and work still needs to be undertaken to verify expected behaviour of the architecture.
Activation of voltage‐gated sodium current and inhibition of erg‐mediated potassium current caused by telmisartan, an antagonist of angiotensin II type‐1 receptor, in HL‐1 atrial cardiomyocytes

Telmisartan (TEL) is a non‐peptide blocker of angiotensin II type‐1 (AT1) receptor. However, the mechanisms through which this drug interacts directly with ion currents in hearts remain largely unclear. Herein, we aim to investigate the effects of TEL the on ionic currents and membrane potential of murine HL‐1 cardiomyocytes. In whole‐cell recordings, addition of TEL stimulated the peak and late components of voltage‐gated Na+ currents (INa) with different potencies. The EC50 values required to achieve the stimulatory effect of this drug on peak and late INa were 0.2 and 1.2 μmol/L, respectively, and the current‐voltage relationship of peak INa shifted toward less‐depolarized potentials during exposure to TEL. Telmisartan not only increased peak INa but also prolonged the inactivation time course of late INa. Amiodarone (Amio) or ranolazine (Ran), but not angiotensin II, could reverse TEL‐mediated effects. The drug enhanced the recovery rate of INa inactivation and exerted an inhibitory effect on erg‐mediated K+ and L‐type Ca2+ currents. In whole‐cell current‐clamp recordings, addition of the drug resulted in prolongation of the duration of action potentials (APs) in a dose‐dependent manner in HL‐1 cells; Amio or Ran could reverse this increase in AP durations. Telmisartan‐mediated prolongation of AP was attenuated in KCNH2 siRNA‐transfected HL‐1 cells. In cultured smooth muscle cells of the human coronary artery, TEL enhanced INa amplitudes and slowed current inactivation. Stimulation by TEL of INa in HL‐1 cells did not simply increase current magnitude but altered current kinetics, thereby suggesting state‐dependent activation. Telmisartan may have greater affinity to the open/inactivated state than to the resting state residing in NaV channels. Collectively, TEL‐mediated stimulation of INa and inhibition of IK(erg) could be an important ionic mechanism underlying the increased cell excitability of HL‐1 cells; these actions, however, cannot be entirely explained by its blockade of AT1 receptor.
Boosting Handwriting Text Recognition in Small Databases with Transfer Learning

In this paper we deal with the offline handwriting text recognition (HTR) problem with reduced training data sets. Recent HTR solutions based on artificial neural networks exhibit remarkable solutions in referenced databases. These deep learning neural networks are composed of both convolutional (CNN) and long short-term memory recurrent units (LSTM). In addition, connectionist temporal classification (CTC) is the key to avoid segmentation at character level, greatly facilitating the labeling task. One of the main drawbacks of the CNN-LSTM-CTC (CRNN) solutions is that they need a considerable part of the text to be transcribed for every type of calligraphy, typically in the order of a few thousands of lines. Furthermore, in some scenarios the text to transcribe is not that long, e.g. in the Washington database. The CRNN typically overfits for this reduced number of training samples. Our proposal is based on the transfer learning (TL) from the parameters learned with a bigger database. We first investigate, for a reduced and fixed number of training samples, 350 lines, how the learning from a large database, the IAM, can be transferred to the learning of the CRNN of a reduced database, Washington. We focus on which layers of the network could not be re-trained. We conclude that the best solution is to re-train the whole CRNN parameters initialized to the values obtained after the training of the CRNN from the larger database. We also investigate results when the training size is further reduced. For the sake of comparison, we study the character error rate (CER) with no dictionary or any language modeling technique. The differences in the CER are more remarkable when training with just 350 lines, a CER of 3.3% is achieved with TL while we have a CER of 18.2% when training from scratch. As a byproduct, the learning times are quite reduced. Similar good results are obtained from the Parzival database when trained with this reduced number of lines and this new approach.
Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat

To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598–50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.
Economic burden of comorbid chronic kidney disease and diabetes

Abstract Objective: To estimate real-world healthcare utilization and expenditures across the spectrum of chronic kidney disease (CKD), as determined by estimated glomerular filtration rate (eGFR) categories in patients with diabetes. Methods: This study employed a retrospective cohort study design using the Truven Healthcare and Claims Dataset from 2009–2012. Index date was defined as the first eGFR value during a continuous enrollment period of 24 months. Cohorts of patients were stratified by Kidney Disease: Improving Global Outcomes CKD stage based on eGFR (stages 1: ≥90 mL/min/1.73 m2; 2: 60–89; 3A: 45–59; 3B: 30–44; 4: 15–29; 5: <15). Healthcare expenditures (total patient and payer paid claims) and utilization (number of claims or visits) were estimated 12-months post-index date using generalized linear modeling and negative binomial modeling, respectively, after adjusting for baseline characteristics. Results: Of 130,098 patients with an index eGFR value and 24-months continuous enrolment, 64,521 (49.59%) were in stage 1 CKD, 47,816 (36.75%) were in stage 2, 13,377 (10.28%) were in stage 3A, 3,217 (2.47%) were in stage 3B, 898 (0.69%) were in stage 4, and 269 (0.21%) were in stage 5. Patients in stages 3A, 3B, and 4 CKD had 1.32 (95% CI = 1.22–1.43), 1.59 (95% CI = 1.41–1.80), and 2.65 (95% CI = 2.23–3.14) times higher rates of diabetes-associated inpatient visits, respectively, compared with stage 1 CKD patients. Patients in stages 3A, 3B, and 4 CKD had increased incremental total annual healthcare expenditures of $1,732 (95% CI = $1,109–$2,356), $2,632 (95% CI = $1,647–$3,619), and $6,949 (95% CI = $5,466–$8,432), respectively, compared with stage 1 CKD patients. Limitations: The claims data were generated for billing and reimbursement, not for research purposes. Conclusions: These real-world data suggest an incremental and significant increase in economic burden in diabetes as kidney function declines, starting with moderate (stage 3A) CKD.
Fundus Autofluorescence Lifetime Patterns in Retinitis Pigmentosa.

Purpose We investigated whether fundus autofluorescence (FAF) lifetimes in patients with retinitis pigmentosa display a disease-specific lifetime pattern. Methods Fundus autofluorescence lifetime imaging ophthalmoscopy (FLIO) was performed in two spectral channels (498-560 and 560-720 nm) after excitation with a 473 nm pulsed laser in patients with retinitis pigmentosa and compared to healthy controls of a similar age range. Corresponding FAF intensity and spectral domain optical coherence tomography (OCT) data, as well as best corrected visual acuity (BCVA) were acquired and compared to fluorescence lifetime data. Results We investigated 43 eyes from 43 patients with retinitis pigmentosa (mean age 45 ± 15 years) and compared them to eyes of 13 age-matched healthy participants. Mean FAF lifetimes were prolonged in areas of photoreceptor atrophy with preserved retinal pigment epithelium (RPE) (P = 0.0036) and even longer in areas with total atrophy of photoreceptors and RPE (P = 0.0002). The prevalence of perifoveal ring structures characterized by prolonged fluorescence lifetimes in FLIO was higher (63% vs. 49%) and the rings were wider compared to the hyperautofluorescent rings in qualitative fundus autofluorescence intensity images. In the central fovea with intact retinal layer structure identified by OCT, fluorescence lifetimes were slightly prolonged compared to those of age-matched healthy controls (short spectral channel [SSC], P = 0.0044; long spectral channel [LSC], P = 0.0128). Short lifetimes within the macular center were negatively correlated with BCVA (R2 = 0.33, P < 0.0001) as well as the greatest diameter of the ellipsoid band in OCT. Conclusions FLIO in retinitis pigmentosa reveals characteristic patterns that allow identification of areas of photoreceptor atrophy, RPE atrophy, and remaining photoreceptor segments in areas of RPE atrophy. Fluorescence lifetimes can be used to identify ellipsoid zone loss that correlates with functional parameters.
Advances in the Preclinical Study of Some Flavonoids as Potential Antidepressant Agents

Flavonoids are phenolic compounds found commonly in plants that protect them against the negative effects of environmental insults. These secondary metabolites have been widely studied in preclinical research because of their biological effects, particularly as antioxidant agents. Diverse flavonoids have been studied to explore their potential therapeutic effects in the treatment of disorders of the central nervous system, including anxiety and depression. The present review discusses advances in the study of some flavonoids as potential antidepressant agents. We describe their behavioral, physiological, and neurochemical effects and the apparent mechanism of action of their preclinical antidepressant-like effects. Natural flavonoids produce antidepressant-like effects in validated behavioral models of depression. The mechanism of action of these effects includes the activation of serotonergic, dopaminergic, noradrenergic, and γ-aminobutyric acid-ergic neurotransmitter systems and an increase in the production of neural factors, including brain-derived neurotrophic factor and nerve growth factor. Additionally, alterations in the function of tropomyosin receptor kinase B and activity of the enzyme monoamine oxidase A have been reported. In conclusion, preclinical research supports the potential antidepressant effects of some natural flavonoids, which opens new possibilities of evaluating these substances to develop complementary therapeutic alternatives that could ameliorate symptoms of depressive disorders in humans.
Decision Tree-Based Contextual Location Prediction from Mobile Device Logs

Contextual location prediction is an important topic in the field of personalized location recommendation in LBS (location-based services). With the advancement of mobile positioning techniques and various sensors embedded in smartphones, it is convenient to obtain massive human mobile trajectories and to derive a large amount of valuable information from geospatial big data. Extracting and recognizing personally interesting places and predicting next semantic location become a research hot spot in LBS. In this paper, we proposed an approach to predict next personally semantic place with historical visiting patterns derived from mobile device logs. To address the problems of location imprecision and lack of semantic information, a modified trip-identify method is employed to extract key visit points from GPS trajectories to a more accurate extent while semantic information are added through stay point detection and semantic places recognition. At last, a decision tree model is adopted to explore the spatial, temporal, and sequential features in contextual location prediction. To validate the effectiveness of our approach, experiments were conducted based on a trajectory collection in Guangzhou downtown area. The results verified the feasibility of our approach on contextual location prediction from continuous mobile devices logs.
Practically Classifying Unmanned Aerial Vehicles Sound Using Convolutional Neural Networks

In this work, we analyze the effectiveness of a simple neural network for the task of determining, by sound, if small unmanned vehicles are carrying potentially harmful payloads The goal of this work is to contribute to a real-time UAV detection system that requires a means of assessing threat level of incoming vehicles whose positions are determined by other sensors. Further, we operated under a minimal cost constraints to enable eventual adoption at scale by law enforcement agencies. Our system classifies payload carrying vs. non-payload carrying DJI Phantom II UAVs by presenting sound spectrum data to a simple Convolutional Neural Networks (CNN). These networks, along with a simple voting system, provided a 99.92% recognition rate for this problem without a need to violate our minimal cost constraint.