Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of a circulating CD45-, CD34dim cell population and validation of their endothelial phenotype

Summary Accurately detecting circulating endothelial cells (CECs) is important since their enumeration has been proposed as a biomarker to measure injury to the vascular endothelium. However, there is no single methodology for determining CECs in blood, making comparison across studies difficult. Many methods for detecting CECs rely on characteristic cell surface markers and cell viability indicators, but lack secondary validation. Here, a CEC population in healthy adult human subjects was identified by flow cytometry as CD45-, CD34dim that is comparable to a previously described CD45-, CD31bright population. In addition, nuclear staining with 7-aminoactinomycin D (7-AAD) was employed as a standard technique to exclude dead cells. Unexpectedly, the CD45-, CD34dim, 7-AAD- CECs lacked surface detectable CD146, a commonly used marker of CECs. Furthermore, light microscopy revealed this cell population to be composed primarily of large cells without a clearly defined nucleus. Nevertheless, immunostains still demonstrated the presence of the lectin Ulex europaeus and von Willebrand factor. Ultramicro analytical immunochemistry assays for the endothelial cell proteins CD31, CD34, CD62E, CD105, CD141, CD144 and vWF indicated these cells possess an endothelial phenotype. However, only a small amount of RNA, which was mostly degraded, could be isolated from these cells. Thus the majority of CECs in healthy individuals as defined by CD45-, CD34dim, and 7-AAD- have shed their CD146 surface marker and are senescent cells without an identifiable nucleus and lacking RNA of sufficient quantity and quality for transcriptomal analysis. This study highlights the importance of secondary validation of CEC identification.
Limited penetration of lopinavir into seminal plasma of HIV-1-infected men.

Joep M.A. Lange a,b,c and Jan M. Prins a , a Department of Internal Medicine, Division of Infectious Diseases, Tropical Medicine and AIDS, b International Antiviral Therapy Evaluation Center (IATEC), and c Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, the Netherlands; and Department of Clinical Pharmacy, University Medical Center, Nijmegen, the Netherlands.
Enforcing topological constraints in random field image segmentation

We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.
The Price of Political Uncertainty: Theory and Evidence from the Option Market

We empirically analyze the pricing of political uncertainty, guided by a theoretical model of government policy choice. To isolate political uncertainty, we exploit its variation around national elections and global summits. We find that political uncertainty is priced in the equity option market as predicted by theory. Options whose lives span political events tend to be more expensive. Such options provide valuable protection against the price, variance, and tail risks associated with political events. This protection is more valuable in a weaker economy and amid higher political uncertainty. The effects of political uncertainty spill over across countries.
Acute Effects of Different Stretching Techniques on Lower Limb Kinematics, Kinetics and Muscle Activities during Vertical Jump

The purpose of this study was to examine the acute effects of different stretching techniques on performance and lower limb kinematics, kinetics and muscle activities during vertical jump in female aerobics athletes. 10 female college aerobics athletes participated in this study. Three-dimensional kinematic and kinetic data, as well as electromyography of rectus femoris, biceps femoris and gastrocnemius medialis were collected using Vicon motion analysis system, Kistler force plate and Wireless surface electromyographic system respectively during the test. No significant differences in jump height had been determined among these 3 warm-up methods. Hip peak flexion and internal rotation angles decreased significantly after BSM and peak adduction angle decreased significantly after SSM and BSM during landing. Knee peak flexion and internal rotation angles increased significantly after SSM and BSM during take-off. Also, BSM showed significantly greater peak flexion compared with SSM. Ankle peak plantarflexion angle increased significantly after BSM. In addition, BSM showed significantly greater improvement in the variation range than SSM except for the ankle int-external rotation. Existence of no significant differences in the peak value of vertical ground reaction force during take-off and landing phase had been determined among these 3 warm-up methods, and muscle activities of rectus femoris, biceps femoris and gastrocnemius medialis were likewise not significantly different. The results of this study suggest that it would be suitable for female aerobics athletes to perform ballistic stretching in warm-up in order to improve flexibility without decreasing the following vertical jumping event and may also reduce the risk of ankle sprain injury.
Cytoskeleton reorganization of spreading cells on micro-patterned islands: a functional model

Predictive numerical models of cellular response to biophysical cues have emerged as a useful quantitative tool for cell biology research. Cellular experiments in silico can augment in vitro and in vivo investigations by filling gaps in what is possible to achieve through ‘wet work’. Biophysics-based numerical models can be used to verify the plausibility of mechanisms regulating tissue homeostasis derived from experiments. They can also be used to explore potential targets for therapeutic intervention. In this perspective article we introduce a single cell model developed towards the design of novel biomaterials to elicit a regenerative cellular response for the repair of diseased tissues. The model is governed by basic mechanisms of cell spreading (lamellipodial and filopodial extension, formation of cell–matrix adhesions, actin reinforcement) and is developed in the context of cellular interaction with functionalized substrates that present defined points of potential adhesion. To provide adequate context, we first review the biophysical underpinnings of the model as well as reviewing existing cell spreading models. We then present preliminary benchmarking of the model against published experiments of cell spreading on micro-patterned substrates. Initial results indicate that our mechanistic model may represent a potentially useful approach in a better understanding of cell interactions with the extracellular matrix.
Three-dimensional analyses of ultrasonic scaler oscillations.

BACKGROUND It is stated that the oscillation patterns of dental ultrasonic scalers are dependent upon whether the instrument is of a magnetostrictive or piezoelectric design. These patterns are then linked to differences in root surface debridement in vitro. MATERIAL AND METHODS Piezoelectric (A, P) and magnetostrictive (Slimline, TFI-3) ultrasonic scalers (three of each) were evaluated, loaded (100 g/200 g) and unloaded with a 3D laser vibrometer. Loads were applied to the probe tips via teeth mounted in a load-measuring device. RESULTS Elliptical motion was demonstrated for all probes under loaded and unloaded conditions. Loading flattened the elliptical motion along the length of the probe. Unloaded, Slimline tip 1 was significantly different to tips 2 and 3 (p<0.0001). There were no differences between the A-tips (p>0.207). All TFI-3 tips were different to each other (p<0.0001). P-tips 1 and 2 were different to each other (p=0.046). Loaded, Slimline tips were different to each other (p<0.001). There were no differences between the P probes (p>0.867). Generator power increased all Slimline and P tip vibrations (p<0.0001). CONCLUSIONS Probe oscillation patterns are independent of ultrasound production mechanism and are dependent upon probe shape and generator power. Loaded probes oscillated with an elliptical pattern.
Molecular detection of Peronospora variabilis in quinoa seed and phylogeny of the quinoa downy mildew pathogen in South America and the United States.

Quinoa (Chenopodium quinoa) is an important export of the Andean region, and its key disease is quinoa downy mildew, caused by Peronospora variabilis. P. variabilis oospores can be seedborne and rapid methods to detect seedborne P. variabilis have not been developed. In this research, a polymerase chain reaction (PCR)-based detection method was developed to detect seedborne P. variabilis and a sequencing-based method was used to validate the PCR-based method. P. variabilis was detected in 31 of 33 quinoa seed lots using the PCR-based method and in 32 of 33 quinoa seed lots using the sequencing-based method. Thirty-one of the quinoa seed lots tested in this study were sold for human consumption, with seed originating from six different countries. Internal transcribed spacer (ITS) and cytochrome c oxidase subunit 2 (COX2) phylogenies were examined to determine whether geographical differences occurred in P. variabilis populations originating from Ecuador, Bolivia, and the United States. No geographical differences were observed in the ITS-derived phylogeny but the COX2 phylogeny indicated that geographical differences existed between U.S. and South American samples. Both ITS and COX2 phylogenies supported the existence of a Peronospora sp. , distinct from P. variabilis, that causes systemic-like downy mildew symptoms on quinoa in Ecuador. The results of these studies allow for a better understanding of P. variabilis populations in South America and identified a new causal agent for quinoa downy mildew. The PCR-based seed detection method allows for the development of P. variabilis-free quinoa seed, which may prove important for management of quinoa downy mildew.
Influence of soil properties on the abundance of plant species in ferruginous rocky soils vegetation, southeastern Brazil

Ferruginous "campos rupestres" are a particular type of vegetation growing on iron-rich primary soils. We investigated the influence of soil properties on plant species abundance at two sites of ferruginous "campos rupestres" and one site of quartzitic "campo rupestre", all of them in "Quadrilatero Ferrifero", in Minas Gerais State, southeastern Brazil. In each site, 30 quadrats were sampled to assess plant species composition and abundance, and soil samples were taken to perform chemical and physical analyses. The analyzed soils are strongly acidic and presented low fertility and high levels of metallic cations; a principal component analysis of soil data showed a clear segregation among sites due mainly to fertility and heavy metals content, especially Cu, Zn, and Pb. The canonical correspondence analysis indicated a strong correlation between plant species abundance and soil properties, also segregating the sites.
Residual Tumor Cells That Drive Disease Relapse after Chemotherapy Do Not Have Enhanced Tumor Initiating Capacity

Although chemotherapy is used to treat most advanced solid tumors, recurrent disease is still the major cause of cancer-related mortality. Cancer stem cells (CSCs) have been the focus of intense research in recent years because they provide a possible explanation for disease relapse. However, the precise role of CSCs in recurrent disease remains poorly understood and surprisingly little attention has been focused on studying the cells responsible for re-initiating tumor growth within the original host after chemotherapy treatment. We utilized both xenograft and genetically engineered mouse models of non-small cell lung cancer (NSCLC) to characterize the residual tumor cells that survive chemotherapy treatment and go on to cause tumor regrowth, which we refer to as tumor re-initiating cells (TRICs). We set out to determine whether TRICs display characteristics of CSCs, and whether assays used to define CSCs also provide an accurate readout of a cell’s ability to cause tumor recurrence. We did not find consistent enrichment of CSC marker positive cells or enhanced tumor initiating potential in TRICs. However, TRICs from all models do appear to be in EMT, a state that has been linked to chemoresistance in numerous types of cancer. Thus, the standard CSC assays may not accurately reflect a cell’s ability to drive disease recurrence.
Control of Non-Equilibrium Dynamics in Communication Networks

We propose a novel, dynamical systems-based approach for analysis and control of the complex dynamic behavior arising in communication networks. Specifically, we consider the active queue management (AQM) problem and study the non-equilibrium behavior observed as a result of the interaction between deterministic queueing and nonlinear flow-control dynamics using a stochastic characterization. The asymptotic dynamics are interpreted using invariant measures of certain stochastic operators. For computational tractability, we use set-oriented numerical methods to construct finite-dimensional Markov models including control Markov chains and hidden Markov models. Based on the stochastic model constructed, we pose and solve the AQM control problem using Markov decision processes (MDPs). The framework developed is demonstrated through a numerical study of an example AQM scheme, which shows persistent non-equilibrium queue behavior under the optimal control strategy
Report of the 19th follow‐up survey of primary liver cancer in Japan

The 19th Nationwide Follow‐up Survey of Primary Liver Cancer in Japan comprised 20 850 primary liver cancer patients newly registered at 482 medical institutions over a period of 2 years (from 1 January 2006 to 31 December 2007). Of these, 94.7% had hepatocellular carcinoma (HCC) and 4.4% had intrahepatic cholangiocarcinoma (ICC). In addition, follow‐up data were obtained regarding 34 752 patients who were registered in the previous survey. Epidemiological and clinicopathological factors, diagnosis, and treatment were examined in newly registered patients. Compared with the 18th follow‐up survey, the present follow‐up survey suggested an increase in the number of elderly and female patients, a reduction in the number of hepatitis B surface antigen‐ and anti‐hepatitis C virus antibody‐positive patients, and a reduction in tumor size at the time of clinical diagnosis. In terms of local ablation therapy, the number of patients receiving radiofrequency ablation therapy increased. The cumulative survival rates for newly registered patients between 1996 and 2007 were calculated for each histological type (HCC, ICC, and combined HCC and ICC) and stratified according to background factors and treatments. The cumulative survival rates of newly registered patients between 1978 and 2007 were calculated after dividing individuals into groups according to registration date (1978–1987, 1988–1997, and 1998–2007). The data obtained from this follow‐up survey will contribute to the medical management of primary liver cancer and facilitate future research.
Outcomes of Open Versus Laparoscopic Procedure for Synchronous Radical Resection of Liver Metastatic Colorectal Cancer: A Comparative Study

Background: The laparoscopic resection of colorectal cancer (CRC) along with synchronous liver metastases has been attempted and reported in multiple single series. In this study, we aimed to examine the feasibility, procedural safety, and oncological integrity of 1-stage totally laparoscopic procedure for the radical resection of liver metastatic CRC in a head-to-head comparison with the 1-stage open procedure simultaneously. Methods: The patients who underwent selective 1-stage concomitant resection of CRC and synchronous liver metastases between January 2004 and December 2008 (laparoscopy group, n=13) were retrospectively enrolled in the study. Patients receiving open 1-stage resection (laparotomy group) were retrospectively included at the ratio of 1:1 (n=13 out of 71), matching the laparoscopy group in sex, age, body mass index, site and stage of primary tumor, location and size of liver metastases, and adjuvant therapies. Results: All the thirteen 1-stage laparoscopic procedures were successfully completed, without conversion to open procedure or additional incision. The operative duration of laparoscopic procedure was shorter than that of open procedure (313±44 vs. 350±46 min, P<0.05). The volume of blood loss was comparable between the 2 groups (259±111 vs. 273±95 mL, P>0.05). Patients undergoing laparoscopic procedure resumed off-bed activities, bowel movement, and oral intake earlier than those undergoing open procedure, and also had a shorter hospitalization stay (8.5±1.9 vs. 11.2±1.8 d, P<0.05). Only 1 clinically significant adverse event occurred in a patient who developed bile leak after the laparoscopic resection. The 1-, 3-, and 5-year survival rates were comparable between the 2 groups (P>0.05). Conclusions: One-stage synchronous laparoscopic resection of liver metastatic CRC is a feasible, effective, and safe modality in specifically indicated patients, both accelerating postoperative recovery and shortening hospitalization time.
Bacterial meningitis: diagnosis by latex agglutination test and clinical features.

To know the usefulness of Latex Agglutination Test (LAT) for the diagnosis of bacterial meningitis (BM), it was performed in all the 114 consecutive samples of CSF with polymorphs from 114 prospectively recruited children aged 2 months to 11 years. Definite diagnosis of BM based on culture and/or LAT was evident in 55. Among the 46 LAT positive, culture was positive in 3 only. Major organisms identified by LAT were H. influenzae B (HiB) in 28 and S. pneumoniae (SP) in 15. Ninety per cent of HiB and 67% of SP bacterial meningitis were under one year of age. Fever > 7 days prior to admission was not uncommon (38%) and 26% had received prior antibiotics. Meningeal signs were present in 64%. CSF cells were < 500/mm3 in 24% and sugar was > 50% of blood level in 23%. There was no significant difference in the immediate outcome between HiB and SP meningitis. The case fatality was 22% and was significantly high in cases who had altered level of consciousness on admission (p = 0.02). It is concluded that LAT is very useful for rapid diagnosis of BM.
Big-data streaming applications scheduling with online learning and concept drift detection

Several techniques have been proposed to adapt Big-Data streaming applications to resource constraints. These techniques are mostly implemented at the application layer and make simplistic assumptions about the system resources and they are often agnostic to the system capabilities. Moreover, they often assume that the data streams characteristics and their processing needs are stationary, which is not true in practice. In fact, data streams are highly dynamic and may also experience concept drift, thereby requiring continuous online adaptation of the throughput and quality to each processing task. Hence, existing solutions for Big-Data streaming applications are often too conservative or too aggressive. To address these limitations, we propose an online energy-efficient scheduler which maximizes the QoS (i.e., throughput and output quality) of Big-Data streaming applications under energy and resources constraints. Our scheduler uses online adaptive reinforcement learning techniques and requires no offline information. Moreover, our scheduler is able to detect concept drifts and to smoothly adapt the scheduling strategy. Our experiments realized on a chain of tasks modeling real-life streaming application demonstrate that our scheduler is able to learn the scheduling policy and to adapt it such that it maximizes the targeted QoS given energy constraint as the Big-Data characteristics are dynamically changing.
A Simple Competitive Account of Some Response Properties of Visual Neurons in Area MSTd

A simple and biologically plausible model is proposed to simulate the optic flow computation taking place in the dorsal part of medial superior temporal (MSTd) area of the visual cortex in the primates' brain. The model is a neural network composed of competitive learning layers. The input layer of the network simulates the neurons in the middle temporal (MT) area that selectively respond to the visual stimuli of the input motion patterns with different local velocities. The output layer of the network simulates the MSTd neurons that selectively respond to different types of optic flow motion patterns including planar, circular, radial, and spiral motions. Simulation results obtained from this model show that the behaviors of the output nodes of the network resemble very closely the known responsive properties of the MSTd neurons found neurophysiologically, such as the existence of three types of MSTd neurons that respond, respectively, to one, two, or three types of the input motion patterns with different position dependences, and the continuum of response selectivity formed by the three types of neurons.
Non-Linear Genetic Representations

The limitations of linear chromosomes and conventional recombination operators are reviewed. It is argued that there are at least three classes of problems for which such representations and operators are likely to be ineffective. Methods for constructing operators which manipulate more complex structures with evolutionary search methods are presented, and it is argued that whenever possible, genetic operators and analogues of schemata should be defined directly in space of phenotypes, rather than in the genotype (representation) space. This paper considers the implications of earlier theoretical work on evolutionary search concerning the relationship between genetic representation, idealised genetic operators and performance correlations between solutions in the search space. The central thesis of the paper is that for many problems conventional linear chromosomes and recombination operators are inadequate for effective genetic search, and that for general problems non-linear representations are required. Section 2 considers representation issues in the abstract, focusing initially on the genotype-phenotype mapping, intrinsic parallelism and the ability of schemata to capture important regularities in performance characteristics in the search space, before discussing the various ways in which different workers have tried to respond to perceived limitations. Section 3 discusses various generalisations of the standard analysis of genetic algorithms, which are then used to explore three specific limitations of linear chromosomes with conventional operators. Briefly, these limitations arise when schemata are unable to describe important subsets of the search space (section 4), when key characteristics of solutions cannot by independently assigned (section 5), and when constraints are involved (section 6). The paper closes with a summary.
Stability of cell‐free DNA from maternal plasma isolated following a single centrifugation step

Cell‐free fetal DNA can be used for prenatal testing with no procedure‐related risk to the fetus. However, yield of fetal DNA is low compared with maternal cell‐free DNA fragments, resulting in technical challenges for some downstream applications. To maximize the fetal fraction, careful blood processing procedures are essential. We demonstrate that fetal fraction can be preserved using a single centrifugation step followed by postage of plasma to the laboratory for further processing.