Miracle-dz/UniFAR-FTUs huggingface dataset:
Towards a scalable, open-standards service for brokering cross-protocol data transfers across multiple sources and sinks

Data Transfer Service (DTS) is an open-source project that is developing a document-centric message model for describing a bulk data transfer activity, with an accompanying set of loosely coupled and platform-independent components for brokering the transfer of data between a wide range of (potentially incompatible) storage resources as scheduled, fault-tolerant batch jobs. The architecture scales from small embedded deployments on a single computer to large distributed deployments through an expandable ‘worker-node pool’ controlled through message-orientated middleware. Data access and transfer efficiency are maximized through the strategic placement of worker nodes at or between particular data sources/sinks. The design is inherently asynchronous, and, when third-party transfer is not available, it side-steps the bandwidth, concurrency and scalability limitations associated with buffering bytes directly through intermediary client applications. It aims to address geographical–topological deployment concerns by allowing service hosting to be either centralized (as part of a shared service) or confined to a single institution or domain. Established design patterns and open-source components are coupled with a proposal for a document-centric and open-standards-based messaging protocol. As part of the development of the message protocol, a bulk data copy activity document is proposed for the first time.
Nonparametric analysis of recurrent gap time data

Abstract Recurrent event data are frequently encountered in longitudinal studies. In many applications, the times between successive recurrent events (gap times) are often of interest and lead to problems that have received much attention recently. In this article, using the approach of inverse probability-of-censoring weights (IPCW), we propose nonparametric estimators for the estimation of the bivariate distribution and survival functions for gap times of recurrent event data. We also consider the estimation of Kendall’s tau for two gap times by expressing it as an integral functional of the bivariate survival function. The asymptotic properties of the proposed estimators are established. Simulation studies are conducted to investigate their finite sample performance.
Combined HER2 analysis of biopsies and surgical specimens to optimize detection of trastuzumab-eligible patients in eso-gastric adenocarcinoma: a GERCOR study.

BACKGROUND HER2 is overexpressed in 10 to 20% of gastro-esophageal adenocarcinoma (GE-ADK), and is a target for trastuzumab in metastatic patients. We conducted a study to compare HER2 expression between diagnostic biopsies (DBs) and surgical specimens (SSs) of GE-ADK, and to determine the influence of non-trastuzumab containing neoadjuvant chemotherapy (NAC) on this expression. PATIENTS AND METHODS Pathological specimens from biopsies of 228 patients operated on between 2004 and 2011 were collected. Two cohorts treated (n = 141) or not (n = 87) with a NAC were constituted. Two blind independent pathological HER2 analyses on DB and on SS were carried out using immunohistochemistry (IHC) and colorimetric in situ hybridization (CISH). HER-2 overexpression (HER2+) was defined by a score 3+ in IHC, or 2+ with a positive CISH test, according to the specific HER2 scoring guidelines for GE-ADK. RESULTS Paired HER2 status could be determined for 218 out of the 228 patients (95.6%). HER2+ rates were 13.3% on DB (29/218) and 14.7% on SS (32/218). HER2+ tumors were mainly cardial or esophageal adenocarcinomas, with a well-differentiated, intestinal histological type. HER2 status differed between DB and SS in 6% of cases. When DB analyses were added to SS analyses, the relative increase in HER2+ cases was 13.5% (17.1% for patients with NAC and 23.5% for patients with histological response to NAC, versus 7.1% for patients without NAC, P = 0.4, NS). Differences between DB and SS HER2 expression could be explained by intratumoral heterogeneity and by a HER2 expression decrease in SS after NAC in responding patients possibly due to a higher chemosensitivity of HER2-positive clones. CONCLUSION The determination of HER2 status on DB provides results that complete those obtained with SS. Combining the analysis of DB and of SS enables to optimize the selection of trastuzumab-eligible patients in case of metastatic relapse, and particularly in previously NAC-responding patients.
Sampling theorems for uniform and periodic nonuniform MIMO sampling of multiband signals

We examine a multiple-input multiple-output (MIMO) sampling scheme for a linear time-invariant continuous-time MIMO channel. The input signals are modeled as multiband signals with different spectral supports, and the channel outputs are sampled on either uniform or periodic nonuniform sampling sets, with possibly different but commensurate intervals on the different outputs. This scheme encompasses Papoulis' generalized sampling and several nonuniform sampling schemes as special cases. We derive necessary and sufficient conditions on the channel and the sampling rate that allow stable perfect reconstruction of the inputs or, equivalently, perfect inversion of the channel. From an implementation viewpoint, we note that it is desirable that the reconstruction filters have continuous frequency responses. We derive necessary and sufficient conditions that guarantee this continuity property. The frequency responses of the reconstruction filters are specified as solutions to a system of linear equations. Finally, we demonstrate that perfect reconstruction may be possible, even when the channel outputs are sampled at an average rate that does not allow the reconstruction of any output from its samples alone. In certain instances, this average rate can achieve the recently presented fundamental bounds on MIMO sampling density.
Two Arabidopsis circadian oscillators can be distinguished by differential temperature sensitivity

Circadian rhythms are widespread in nature and reflect the activity of an endogenous biological clock. In metazoans, the circadian system includes a central circadian clock in the brain as well as distinct clocks in peripheral tissues such as the retina or liver. Similarly, plants have distinct clocks in different cell layers and tissues. Here, we show that two different circadian clocks, distinguishable by their sensitivity to environmental temperature signals, regulate the transcription of genes that are expressed in the Arabidopsis thaliana cotyledon. One oscillator, which regulates CAB2 expression, responds preferentially to light–dark versus temperature cycles and fails to respond to the temperature step associated with release from stratification. The second oscillator, which regulates CAT3 expression, responds preferentially to temperature versus light–dark cycles and entrains to the release from stratification. Finally, the phase response curves of these two oscillators to cold pulses are distinct. The phase response curve of the oscillator component TOC1 to cold pulses is similar to that of CAB2, indicating that CAB2 is regulated by a TOC1-containing clock. The existence of two clocks, distinguishable on the basis of their sensitivity to temperature, provides an additional means by which plants may integrate both photoperiodic and temperature signals to respond to the changing seasons.
Topology Maintenance in Asynchronous Sensor Networks

In most sensor networks the nodes are static. Nevertheless, the node connectivity is subject to changes because of disruptions in wireless connectivity, transmission power changes, or loss of synchronization between neighboring nodes. Hence, even after a sensor is aware of its immediate neighbors, it must continuously maintain its view, a process we call topology maintenance. This work is the first to distinguish between neighbor discovery during sensor network initialization and topology maintenance. Whereas many works focus on the former task, we focus on the latter. We view topology maintenance as a joint task of all the connected sensors. Each sensor employs a simple protocol in a coordinate effort to reduce power consumption without increasing the time required to detect hidden sensors.
Flexible Hardware Acceleration for Instruction-Grain Lifeguards

Instruction-grain lifeguards monitor executing programs at the granularity of individual instructions to quickly detect bugs and security attacks, but their fine-grain nature incurs high monitoring overheads. This article identifies three common sources of these overheads and proposes three techniques that together constitute a general-purpose hardware acceleration framework for lifeguards.
Myofibroblasts. II. Intestinal subepithelial myofibroblasts.

Intestinal subepithelial myofibroblasts (ISEMF) and the interstitial cells of Cajal are the two types of myofibroblasts identified in the intestine. Intestinal myofibroblasts are activated and proliferate in response to various growth factors, particularly the platelet-derived growth factor (PDGF) family, which includes PDGF-BB and stem cell factor (SCF), through expression of PDGF receptors and the SCF receptor c-kit. ISEMF have been shown to play important roles in the organogenesis of the intestine, and growth factors and cytokines secreted by these cells promote epithelial restitution and proliferation, i.e., wound repair. Their role in the fibrosis of Crohn's disease and collagenous colitis is being investigated. Through cyclooxygenase (COX)-1 and COX-2 activation, ISEMF augment intestinal ion secretion in response to certain secretagogues. By forming a subepithelial barrier to Na(+) diffusion, they create a hypertonic compartment that may account for the ability of the gut to transport fluid against an adverse osmotic gradient. Through the paracrine secretion of prostaglandins and growth factors (e.g., transforming growth factor-beta), ISEMF may play a role in colonic tumorigenesis and metastasis. COX-2 in polyp ISEMF may be a target for nonsteroidal anti-inflammatory drugs (NSAIDs), which would account for the regression of the neoplasms in familial adenomatous polyposis and the preventive effect of NSAIDs in the development of sporadic colon neoplasms. More investigation is needed to clarify the functions of these pleiotropic cells.
Accuracy of Mass Spectrometry with the Ease of Immunoassay ? LC-MS / MS Workflow improvements for Primary Aldosteronism Screening

Primary aldosteronism (PA) is the most common form of secondary hypertension and is responsible for 10% of hypertension in allcomers [1]. The two most common forms of PA are idiopathic adrenal hyperplasia (IAH) and unilateral aldosterone producing adenoma (APA). IAH is amenable to treatment with aldosterone antagonists (spironolactone, eplelrenone) and unilateral adrenalectomy for APA often leads to complete cure of PA. In addition to the all of the expected sequelae of hypertension (increased risk of: atherosclerosis, stroke, chronic renal impairment, coronary heart disease), patients with PA have risk of cardiac [2] and renal disease [3] that is out of proportion to their hypertension, indicating the specific pathogenetic role that aldosterone plays in PA. For this reason, identification and treatment of PA is important from the standpoint of public health.
MHD Slip Flow of Casson Fluid along a Nonlinear Permeable Stretching Cylinder Saturated in a Porous Medium with Chemical Reaction, Viscous Dissipation, and Heat Generation/Absorption

The aim of the present analysis is to provide local similarity solutions of Casson fluid over a non-isothermal cylinder subject to suction/blowing. The cylinder is placed inside a porous medium and stretched in a nonlinear way. Further, the impact of chemical reaction, viscous dissipation, and heat generation/absorption on flow fields is also investigated. Similarity transformations are employed to convert the nonlinear governing equations to nonlinear ordinary differential equations, and then solved via the Keller box method. Findings demonstrate that the magnitude of the friction factor and mass transfer rate are suppressed with increment in Casson parameter, whereas heat transfer rate is found to be intensified. Increase in the curvature parameter enhanced the flow field distributions. The magnitude of wall shear stress is noticed to be higher with an increase in porosity and suction/blowing parameters.
Intestinal Retransplant in a Patient after Fungal Sepsis: Considerations and Issues

An adolescent female received an isolated intestinal transplant. She developed severe exfoliative rejection and required complete enterectomy. The patient developed a septic hip and lung lesions with biopsy-proven Aspergillus nidulans and was treated with caspofungin, ambiosome, and voriconizole. After completing a year of treatment and extensive physical therapy, the patient requested retransplant. The case was presented to the ethics committee, which determined that the patient demonstrated understanding of the risks and benefits. Infectious disease consultants presented data showing high risk for fungal recurrence. Quality of life as observed by our transplant team seemed good and the patient had no other indications. Retransplant is associated with higher risk than first transplants. Does the team have the right to deny retransplant if the competent patient requests transplant despite high risk? Guidelines for this indication are complex and evolving.
Gait recognition using occluded data

Gait is an attractive biometrics for use in monitoring and surveillance applications. In such settings, occlusion is common and may affect recognition. This paper investigates the performance of gait using occluded data. To reconstruct the data, interpolation is applied to the occluded data using the Support Vector Machines for Regression (SVR) framework. Then the Principal Component Analysis (PCA) and Canonical Analysis (CA) are applied to reduce the dimensionality of the reconstructed data and classification. Comparison is made between the recognition accuracy rates obtained using the occluded and visible data of the same subject.
A Nonlinear Method for Improving the Active Control Efficiency of Smart Structures Subjected to Rigid Body Motions

Smart components are commonly used for their compactness and ability to control the vibrations in an embedded flexible structure. Their relative actuation capabilities can limit the active control efficiency. This paper introduces a nonlinear method to improve their action using independent controllers for flexible modes and for rigid body modes. The nonlinear control of each flexible mode uses fuzzy logic controllers designed to improve the mechanical work of smart actuators by taking into account their actuation capabilities. The control law parameters are iteratively adjusted by taking into account the estimated disturbance levels until obtaining the desired compromise between efficiency and spillover. In addition, an independent fuzzy control for rigid body motions is then developed and adjusted in order to reduce the vibrations of the structure without decreasing the tracking efficiency. These two independent nonlinear strategies are described, implemented, and experimentally tested to control an articulated smart structure.
Pilot study of reduced‐intensity conditioning followed by allogeneic stem cell transplantation from related and unrelated donors in patients with myelofibrosis

A prospective pilot study was performed to evaluate the effect of reduced‐intensity conditioning with busulphan (10 mg/kg), fludarabine (180 mg/qm) and anti‐thymocyte globulin followed by allogeneic stem cell transplantation from related (n = 8) and unrelated donors (n = 13) in 21 patients with myelofibrosis. The median age of the patients was 53 years (range, 32–63). No primary graft failure occurred. The median time until leucocyte (>1·0 × 109/l) and platelet (>20 × 109/l) engraftment was 16 (range, 11–26) and 23 d (range, 9–139) respectively. Complete donor chimaerism on day 100 was seen in 20 patients (95%). Acute graft‐versus‐host disease (GvHD) grades II–IV and III/IV occurred in 48% and 19% of cases and 55% of the patients had chronic GvHD. Treatment‐related mortality was 0% at day 100 and 16% [95% confidence interval (CI): 0–32%] at 1 year. Haematological response was seen in 100% and complete histopathological remission was observed in 75% of the patients and 25% of the patients showed partial histopathological remission with a continuing decline in the grade of fibrosis. After a median follow‐up of 22 months (range, 4–59), the 3‐year estimated overall and disease‐free survival was 84% (95% CI: 67–100%).
EEG in the ICU : What Should One Treat , What Not ?

Les tracés paroxysmaux et périodiques se rencontrent souvent lors de l’enregistrement en continu de l’EEG aux soins neuro-intensifs. L’identification précise et la gestion adéquate de ces tracés posent souvent un défi. Le présent article offre une vue d’ensemble des tracés EEG les plus courants. Malheureusement, il manque des directives basées sur l’évidence concernant leur maniement : le texte présente des suggestions pratiques.
Cold-induced angiogenesis in seasonally acclimatized rainbow trout (Oncorhynchus mykiss)

Seasonal acclimatization of rainbow trout induced an inverse relationship between environmental temperature and the capillary:fibre ratio of slow locomotory muscle, which increased from 1.73±0.09 in the summer (18 °C) to 2.50±0.15 in the winter (4 °C). However, the rate of capillary growth (angiogenesis) was exceeded by that of fibre growth at low temperatures such that the extensive fibre hypertrophy found at 4 °C led to a decrease in capillary density, NA(c,f), to 57 % of that found at 11 °C and 85 % of that at 18 °C. Cold-induced angiogenesis resulted in an expanded capillary bed of similar topology to the existing network, with capillary orientation deviating from that of muscle fibres by only 4­7 %. Capillary length density was maximal at 11 °C, JV(c,f)=2421±239 mm-2, which as previously described corresponds to the point when muscle blood flow is highest and the scope for aerobic swimming is greatest, reflecting an integrated response to optimize aerobic performance at intermediate temperatures. In contrast, ventricular NA(c,f) parallels heart rate and hence was highest at 18 °C, while there was no seasonal variation in myocyte diameter. Although a systemic response to seasonal adjustments in humoral factors may occur, the data reported here suggest that angiogenesis is probably stimulated by different mechanical factors in these two muscles.
Evaluative Cognition

Cognitive agents form beliefs representing the world, evaluate the world as represented, form plans for making the world more to their liking, and perform actions executing the plans. Then the cycle repeats. This is the doxastic-conative loop, diagrammed in figure one. Both human beings and the autonomous rational agents envisaged in AI are cognitive agents in this sense. The cognition of a cognitive agent can be subdivided into two parts. Epistemic cognition is that kind of cognition responsible for producing and maintaining beliefs. Practical cognition evaluates the world, adopts plans, and initiates action. There is a massive literature both in philosophy and artificial intelligence concerning various aspects of epistemic cognition, and large parts of it are well understood. Practical cognition is less well understood. We can usefully divide practical cognition into five parts: (1) the evaluation of the world as represented by the agent’s beliefs, (2) the adoption of goals for changing it, (3) the construction of plans for achieving goals, (4) the adoption of plans, and (5) the execution of plans. There is a substantial literature in AI concerning the construction and execution of plans, and I will say nothing further about those topics here. This paper will focus on the evaluative aspects of practical cognition. Evaluation plays an essential role in both goal selection and plan adoption. My concern here is the investigation of evaluation as a cognitive enterprise performed by cognitive agents. I am interested both in how it is performed in human beings and how it might be performed in artificial rational agents.
Redox-sensitive materials for drug delivery: targeting the correct intracellular environment, tuning release rates, and appropriate predictive systems.

SIGNIFICANCE The development of responsive drug delivery systems (DDS) holds great promise as a tool for improving the pharmacokinetic properties of drug compounds. Redox-sensitive systems are particularly attractive given the rich variety of redox gradients present in vivo. These gradients, where the circulation is generally considered oxidizing and the cellular environment is substantially more reducing, provide attractive options for targeted, specific cargo delivery. RECENT ADVANCES Experimental evidence suggests that a "one size fits all" redox gradient does not exist. Rather, there are subtle differences in redox potential within a cell, while the chemical nature of reducing agents in these microenvironments varies. Recent works have demonstrated an ability to modulate the degradation rate of redox-susceptible groups and, hence, provide new tools to engineer precision-targeted DDS. CRITICAL ISSUES Modern synthetic and macromolecular chemistry provides access to a wide range of redox-susceptible architectures. However, in order to utilize these in real applications, the actual chemical nature of the redox-susceptible group, the sub-cellular location being targeted, and the redox microenvironment being encountered should be considered in detail. This is critical to avoid the over-simplification possible when using non-biological reducing agents, which may provide inaccurate kinetic information, and to ensure these materials can be advanced beyond simple "on/off" systems. Furthermore, a strong case can be made for the use of biorelevant reducing agents such as glutathione when demonstrating a materials redox response. FUTURE DIRECTIONS A further understanding of the complexities of the extra- and intracellular microenvironments would greatly assist with the design and application of DDS.
Evolutionary Optimization of Echo State Networks: Multiple Motor Pattern Learning

Echo State Networks are a special class of recurrent neural networks, that are well suited for attractor based learning of motor patterns. Using structural multiobjective optimization, the tradeoff between network size and accuracy can be identified. This allows to choose a feasible model capacity for a follow-up full weight optimization. Both optimization steps can be combined into a nested, hierarchical optimization procedure. It is shown to produce small and efficient networks, that are capable of storing multiple motor patterns in a single net. Especially the smaller networks can interpolate between learned patterns using bifurcation inputs.