Miracle-dz/UniFAR-FTUs huggingface dataset:
Object-Based Image Classification of Summer Crops with Machine Learning Methods

The strategic management of agricultural lands involves crop field monitoring each year. Crop discrimination via remote sensing is a complex task, especially if different crops have a similar spectral response and cropping pattern. In such cases, crop identification could be improved by combining object-based image analysis and advanced machine learning methods. In this investigation, we evaluated the C4.5 decision tree, logistic regression (LR), support vector machine (SVM) and multilayer perceptron (MLP) neural network methods, both as single classifiers and combined in a hierarchical classification, for the mapping of nine major summer crops (both woody and herbaceous) from ASTER satellite images captured in two different dates. Each method was built with different combinations of spectral and textural features obtained after the segmentation of the remote images in an object-based framework. As single classifiers, MLP and SVM obtained maximum overall accuracy of 88%, slightly higher than LR (86%) and notably higher than C4.5 (79%). The SVM+SVM classifier (best method) improved these results to 89%. In most cases, the hierarchical classifiers considerably increased the accuracy of the most poorly classified class (minimum sensitivity). The SVM+SVM method offered a significant improvement in classification accuracy for all of the studied crops compared to the conventional decision tree classifier, ranging between 4% for safflower and 29% for corn, which suggests the application of object-based image analysis and advanced machine learning methods in complex crop classification tasks.
Specific Rescue of Cystic Fibrosis Transmembrane Conductance Regulator Processing Mutants Using Pharmacological Chaperones

Most mutants of the cystic fibrosis transmembrane conductance regulator (CFTR) that cause severe symptoms of cystic fibrosis do not reach the cell surface because they are defective in folding. Many CFTR folding mutants, however, including the ΔF508 mutant found in more than 90% of cystic fibrosis patients, are potentially functional at the cell surface if they can be induced to fold correctly. In a previous study (Mol Pharm 2:407–413, 2005), we reported that a quinazoline derivative (CFcor-325) could rescue CFTR processing mutants. The corrector was not specific however, as it could also rescue a processing mutant of CFTR's sister protein, the multidrug resistance P-glycoprotein. The goal of this study was to test whether it was possible to specifically rescue CFTR processing mutants using a pharmacological chaperone. In this article, we report that two compounds, 4-methyl-2-(5-phenyl-1H-pyrazol-3-yl)-phenol (CFpot-532) and 2-phenylamino-4-(4-ethylene-phenyl)-thiazole (corr-2b) could rescue CFTR processing mutants such as ΔF508 CFTR but not a P-glycoprotein processing mutant. The compound CFpot-532 also acts as a potentiator of ΔF508 CFTR channel activity. Therefore, the results suggest that the mechanism whereby CFpot-532 and corr-2b promote folding of CFTR processing mutants is through direct interaction with the CFTR mutant proteins. The compound CFpot-532 could be a particularly useful lead compound for treatment of cystic fibrosis because it is both a CFTR channel potentiator as well as a specific pharmacological chaperone.
Morphology-Density Relation for Simulated Clusters of Galaxies in Cold Dark Matter-dominated Universes

We present a model to investigate the formation and evolution of cluster galaxies using cosmological high-resolution N-body simulations. The N-body simulations are used to construct merging history trees of dark halos. Gas cooling, star formation, supernova feedback, and mergers of galaxies within dark halos are included by using simple prescriptions taken from semianalytic models of galaxy formation. In this paper, we examine the merger-driven bulge formation model and represent the morphology-density relation of cluster galaxies at z = 0. We find that this morphological evolution model can explain the distribution of elliptical galaxies in the clusters well and cannot reproduce the distribution of S0 galaxies. This result suggests that the elliptical galaxies are mainly formed by the major mergers, while, in the S0 formation, processes other than major mergers play an important role.
Extensive Reorganization of Primary Afferent Projections into the Gustatory Brainstem Induced by Feeding a Sodium-Restricted Diet during Development: Less Is More

Neural development is especially vulnerable to environmental influences during periods of neurogenesis and rapid maturation. In fact, short periods of environmental manipulations confined to embryonic development lead to significant changes in morphology and function. A guiding principal emerging from studies of sensory systems is that experimentally induced effects are most dramatic in higher neural levels (e.g., cortex) and primarily involve postnatal synaptic refinements. In contrast to other sensory systems, the gustatory system is particularly susceptible to the effects of deprivation much earlier and with profound changes evident in the brainstem. Here we show that feeding pregnant rats a custom diet featuring a low-sodium content for 9 d before the tongue appears in the fetus produces extensive restructuring of the gustatory brainstem. Rats born to mothers fed the custom diet from embryonic day 3 (E3) to E12 have terminal field volumes of the greater superficial petrosal, chorda tympani, and glossopharyngeal nerves at adulthood that are expanded as much as 10 times beyond that found in rats fed a standard rat chow. The widespread alterations are not attributable to increased numbers of nerve cells, increased target size, or obvious changes in peripheral taste function. Moreover, we show that the limited period of feeding the custom diet has much larger effects than if rats were fed the diet to postweaning ages. Our results suggest that early periods of altered experience, especially during nucleus of the solitary tract neurogenesis, leads to a restructuring of the gustatory brainstem, which in turn may impact the control of sensory and homeostatic processes.
Improving effective bandwidth through compiler enhancement of global cache reuse

Reusing data in cache is critical to achieving high performance on modern machines because it reduces the impact of the latency and bandwidth limitations of direct memory access. To date, most studies of software memory hierarchy management have focused on the latency problem. However today's machines are increasingly limited by insufficient memory bandwidth-on these machines, latency-oriented techniques are inadequate because they do not seek to minimize the total memory traffic over the whole program. This paper explores the potential for addressing bandwidth limitations by increasing global cache reuse-that is, reusing data across whole program and over the entire data collection. To this end, the paper explores a two-step global strategy. The first step fuses computations on the same data to enable the caching of repeated accesses. The second step groups data used by the same computation to bring about contiguous access to memory. While the first step reduces the frequency of memory accesses, the second step improves their efficiency. The paper demonstrates the effectiveness of this strategy and shows how to automate it in a production compiler.
Morphological segmentation and partial volume analysis for volumetry of solid pulmonary lesions in thoracic CT scans

Volumetric growth assessment of pulmonary lesions is crucial to both lung cancer screening and oncological therapy monitoring. While several methods for small pulmonary nodules have previously been presented, the segmentation of larger tumors that appear frequently in oncological patients and are more likely to be complexly interconnected with lung morphology has not yet received much attention. We present a fast, automated segmentation method that is based on morphological processing and is suitable for both small and large lesions. In addition, the proposed approach addresses clinical challenges to volume assessment such as variations in imaging protocol or inspiration state by introducing a method of segmentation-based partial volume analysis (SPVA) that follows on the segmentation procedure. Accuracy and reproducibility studies were performed to evaluate the new algorithms. In vivo interobserver and interscan studies on low-dose data from eight clinical metastasis patients revealed that clinically significant volume change can be detected reliably and with negligible computation time by the presented methods. In addition, phantom studies were conducted. Based on the segmentation performed with the proposed method, the performance of the SPVA volumetry method was compared with the conventional technique on a phantom that was scanned with different dosages and reconstructed with varying parameters. Both systematic and absolute errors were shown to be reduced substantially by the SPVA method. The method was especially successful in accounting for slice thickness and reconstruction kernel variations, where the median error was more than halved in comparison to the conventional approach.
Morphological Study of Isolated Ovarian Preantral Follicles Using Fibrin Gel Plus Platelet Lysate after Subcutaneous Transplantation

Objective Ovarian and follicle transplantation may preserve fertility in young cancer survivors. In this study, we have transplanted preantral follicles using fibrin gel as a carrier and fibrin gel supplemented with platelet lysate (PL) as a rich source of angiogenic and growth factors. The purpose of this study was to evaluate the role of fibrin gel and PL in follicle transplantation. Materials and Methods In this experimental study, ovaries were taken from 14-day- old Naval Medical Research Institute (NMRI) mice. Preantral follicles were dissected from the ovaries and encapsulated into fibrin gel supplemented with 5, 10, 15 or 20% PL, then transplanted back into the same donor mice. Fibrin gels supplemented with PL that contained preantral follicles were placed in a subcutaneous pocket in the back of the neck of the recipient, donor mouse (the same mouse that follicles were collected). After 14 days the grafts were processed and embedded in paraffin blocks, then serially sectioned for histological evaluation. We counted the follicles and classified them according to stage (preantral or antral). Data were presented as mean ± standard error of mean (SEM) and analysed by analysis of variance (ANOVA) and the Kruskal-Wallistest. Results The mean percentage of recovered follicles encapsulated and transplanted in each group were 33.30 ± 2.47 (fibrin gel), 31.96 ± 1.90 (fibrin gel+5% PL), 34.02 ± 2.44 (fibrin gel+10% PL), 48.31 ± 2.06 (fibrin gel+15% PL) and 17.60 ± 2.79 (fibrin gel+20% PL). There was a significant increase in the recovery rate of grafted follicles with fibrin gel+15% PL (48.31%; p<0.001). The percentage of preantral follicles showed no significant difference in all groups (p<0.05). The percentage of antral follicles showed a significant decrease in follicles grafted with fibrin gel+20% PL when compared to the other groups (11.77%; p<0.005) but no significant difference was observed in the other groups. Conclusion The use of PL in follicle transplantation can improve ovarian follicular survival rate.
Replicated Server Placement with QoS Constraints

The network planning problem of placing replicated servers with QoS constraints is considered. Each server site may consist of multiple server types with varying capacities and each site can be placed in any location among those belonging to a given set. Each client can be served by more than one location as long as the round-trip delay of data requests satisfies predetermined upper bounds. Our main focus is to minimize the cost of using the servers and utilizing the link bandwidth, while serving requests according to their delay constraint. This is an NP-hard problem. A pseudopolynomial and a polynomial algorithm that provide guaranteed approximation factors with respect to the optimal for the problem at hand are presented
Tyrosyltubulin ligase and colchicine binding activity in synchronized Chinese hamster cells

Tyrosyltubulin ligase (TTL) was found to be present in CHO and V79 Chinese hamster cells grown in tissue culture. The enzyme is soluble and requires potassium, magnesium, and ATP for maximum activity and requires tubulin as a substrate. TTL was analyzed through the cell cycle of V79 and CHO Chinese hamster cells. The enzyme showed two peaks of activity in V79 cells at 4 h and 7 h after mitotic selection, corresponding to the early S and mid to late S phases of the cell cycle. In CHO cells the enzyme displayed a major peak of activity at mid S and a minor peak or plateau during early S. Tubulin, as measured by (3H)colchicine binding, was shown to increase through S phase and reach a maximum late in the cycle during G2 approx. 3 h after maximum TTL activity.
Subsequence kernel-based Chinese recommender system

With the rapid growth of Chinese websites in several years, how to get the useful information for users on Chinese websites has become a critic issue. This paper proposes the subsequence kernel-based Chinese recommender system, and subsequence kernel provides a flexible method to make the Chinese recognition easier, which overcomes the weakness of efficiency degrading for large scale users. Subsequence based on Kernel Matrix Factorization (KMF) is used to indicate that a phrase/word occurs contiguously within another phrase, and subsequence to allow the possibility that gaps separate the different characters resulting in a noncontiguous occurrence within the phrase. Experiments show that this method outperforms the others.
Coordinated Beamforming with Limited BS Cooperation for Multicell Multiuser MIMO Broadcast Channel

The capacity of downlink multi-input multi-output (MIMO) systems is significantly limited by inter-cell co-channel interference (CCI). Improving the performance of cell edge users who suffers strong inter-cell CCI is still a crucial issue. In this paper, coordinated beamforming (CBF) algorithm for multicell multiuser MIMO system is proposed to cope with the presence of intel-cell CCI. In multicell environment with MIMO channel, limited base station (BS) cooperation is considered to design optimal transmit and receive beamformers which make interference-free at the receiver. Simulation results show that the proposed algorithms can improve the capacity of cell edge user effectively as well as the overall system capacity for multiuser multicell MIMO system.
P2x Receptors in Peripheral Neurons

P2X receptors are a family of ligand-gated ion channels, activated by extracellular ATP. The seven subunits cloned (P2X 1–7) can assemble to form homomeric and heteromeric receptors. Peripheral neurons of neural crest origin (e.g. those in dorsal root, trigeminal, sympathetic and enteric ganglia) and placodal origin (e.g. those in nodose and petrosal ganglia) express mRNAs for multiple P2X subunits. In this review, we summarize the molecular biological, electrophysiological and immunohistochemical evidence for P2X receptor subunits in sensory, sympathetic, parasympathetic, pelvic and myenteric neurons and adrenomedullary chromaffin cells. We consider the pharmacological properties of these native P2X receptors and their physiological roles. The responses of peripheral neurons to ATP show considerable heterogeneity between cells in the same ganglia, between ganglia and between species. Nevertheless, these responses can all be accounted for by the presence of P2X 2 and P2X 3 subunits, giving rise to varying proportions of homomeric and heteromeric receptors. While dorsal root ganglion neurons express predominantly P2X 3 and rat sympathetic neurons express mainly P2X 2 receptors, nodose and guinea-pig sympathetic neurons express mixed populations of P2X 2 and heteromeric P2X 2/3 receptors. P2X receptors are important for synaptic transmission in enteric ganglia, although their roles in sympathetic and parasympathetic ganglia are less clear. Their presence on sensory neurons is essential for some processes including detection of filling of the urinary bladder. The regulation of P2X receptor expression in development and in pathological conditions, along with the interactions between purinergic and other signalling systems, may reveal further physiological roles for P2X receptors in autonomic and sensory ganglia.
User willingness to accept friend requests on SNS: A facebook experiment

Based on a dual approach, which incorporated both a literature survey as well as a direct experiment without the preamble to support any hypothesis, the objectives of the research was to determine the likeliness of a SNS users from two different parts of South Africa to accept a friend request from a totally unknown and fictitious user. The results seem to point to a general willingness to accept a friend requests from a total stranger.
Machine learning‐based classification of diffuse large B‐cell lymphoma patients by eight gene expression profiles

Gene expression profiling (GEP) had divided the diffuse large B‐cell lymphoma (DLBCL) into molecular subgroups: germinal center B‐cell like (GCB), activated B‐cell like (ABC), and unclassified (UC) subtype. However, this classification with prognostic significance was not applied into clinical practice since there were more than 1000 genes to detect and interpreting was difficult. To classify cancer samples validly, eight significant genes (MYBL1, LMO2, BCL6, MME, IRF4, NFKBIZ, PDE4B, and SLA) were selected in 414 patients treated with CHOP/R‐CHOP chemotherapy from Gene Expression Omnibus (GEO) data sets. Cutoffs for each gene were obtained using receiver–operating characteristic curves (ROC) new model based on the support vector machine (SVM) estimated the probability of membership into one of two subgroups: GCB and Non‐GCB (ABC and UC). Furtherly, multivariate analysis validated the model in another two cohorts including 855 cases in all. As a result, patients in the training and validated cohorts were stratified into two subgroups with 94.0%, 91.0%, and 94.4% concordance with GEP, respectively. Patients with Non‐GCB subtype had significantly poorer outcomes than that with GCB subtype, which agreed with the prognostic power of GEP classification. Moreover, the similar prognosis received in the low (0–2) and high (3–5) IPI scores group demonstrated that the new model was independent of IPI as well as GEP method. In conclusion, our new model could stratify DLBCL patients with CHOP/R‐CHOP regimen matching GEP subtypes effectively.
A high-resolution TDC implemented in a 90nm process FPGA

This paper represents a Time-to-digital Converter (TDC) architecture based in a FPGA. The proposed architecture relies on a single tapped-delay line to implement time-to-digital conversion, taking advantage of the fast dedicated carry chains available within FPGAs. The results of post-route simulation indicate that this architecture offered a time resolution of 34ps with a 12 ps precision. In a Virtex-4 FPGA that is fabricated in the 90nm process this structure achieved a resolution of 48ps and a precision of 35ps.Commonly, to design a TDC on a FPGA requires iterative manual adjustment in the placement and route of the circuit; however, in the architecture presented in this paper, we controls the performance of pivotal parts of the circuit with user constraints instead of manual adjustment, which makes this TDC architecture access to portability.
Development of robust speech recognition middleware on microprocessor

We have developed speech recognition middleware on a RISC microprocessor which has robust processing functions against environmental noise and speaker differences. The speech recognition middleware enables developers and users to use a speech recognition process for many possible speech applications, such as car navigation systems and handheld PCs. We report implementation issues of speech recognition process in middleware of microprocessors and propose robust noise handling functions using ANC (adaptive noise cancellation) and noise adaptive models. We also propose a new speaker adaptation algorithm in which the relationships among HMMs (hidden Markov models) transfer vectors are provided as a set of pre-trained interpolation coefficients. Experimental evaluations on 1000-word vocabulary speech recognition showed promising results for both robust processing functions of the proposed noise handling methods and the proposed speaker adaptation method.
Are endothelial progenitor cells a prognostic factor in patients with heart failure?

For the last two decades, endothelial progenitor cells (EPCs) have been proposed as a novel prognostic marker and potential therapeutic target in patients with cardiovascular diseases. EPCs are involved in the process of adult vasculogenesis and repair of dysfunctional endothelium. Endothelial dysfunction has been documented in the peripheral and coronary arteries of chronic heart failure (HF) patients, and has proved to be an independent predictor of morbidity and mortality in HF patients. This has led researchers to analyze the association of EPCs and disease severity in HF patients. In this paper, we review studies analyzing the prognostic role of EPCs in patients with HF. Through a systematic search, we identified 14 relevant studies. Only one study analyzed mortality as an outcome; the others evaluated the association between EPC levels and patients’ characteristics. Overall, results were inconsistent and suggested that levels of EPCs may vary according to factors such as disease severity, underlying cause of cardiomyopathy and medical therapy.
Proprioceptive Rehabilitation of Upper Limb Dysfunction in Movement Disorders: A Clinical Perspective

Movement disorders (MDs) are frequently associated with sensory abnormalities. In particular, proprioceptive deficits have been largely documented in both hypokinetic (Parkinson’s disease) and hyperkinetic conditions (dystonia), suggesting a possible role in their pathophysiology. Proprioceptive feedback is a fundamental component of sensorimotor integration allowing effective planning and execution of voluntary movements. Rehabilitation has become an essential element in the management of patients with MDs, and there is a strong rationale to include proprioceptive training in rehabilitation protocols focused on mobility problems of the upper limbs. Proprioceptive training is aimed at improving the integration of proprioceptive signals using “task-intrinsic” or “augmented feedback. ” This perspective article reviews the available evidence on the effects of proprioceptive stimulation in improving upper limb mobility in patients with MDs and highlights the emerging innovative approaches targeted to maximizing the benefits of exercise by means of enhanced proprioception.
Application of Molecular Dynamics Simulation to Small Systems

The study of chemical behavior includes answering questions as ’which isomer is the most stable? ’, ’which relative orientation is the most favorable for such-and-such interaction? ’, ’which conformer is the global minimum? ’, ’what are the lowest energy configurations and their relative energies? ’. The answer to these questions–and many others–depends on the ability to find and study a variety of configurations of the system of interest. Recently, (Atilgan, 2007) briefly reviewed the use of molecular dynamics simulation for conformational search in the process of drug design, concluding that its use could reduce the errors in estimating binding affinities and finding more viable conformations. In addition, (Corbeil, 2009) considered the need to include ring flexibility in the conformational searches used in flexible docking. Most of the flexible docking algorithms skip searching for conformations in rings, even though a protein may stabilize a conformation other than the most stable one.