Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning

Sonic hedgehog (Shh) acts as a morphogen to mediate the specification of distinct cell identities in the ventral neural tube through a Gli-mediated (Gli1-3) transcriptional network. Identifying Gli targets in a systematic fashion is central to the understanding of the action of Shh. We examined this issue in differentiating neural progenitors in mouse. An epitope-tagged Gli-activator protein was used to directly isolate cis-regulatory sequences by chromatin immunoprecipitation (ChIP). ChIP products were then used to screen custom genomic tiling arrays of putative Hedgehog (Hh) targets predicted from transcriptional profiling studies, surveying 50-150 kb of non-transcribed sequence for each candidate. In addition to identifying expected Gli-target sites, the data predicted a number of unreported direct targets of Shh action. Transgenic analysis of binding regions in Nkx2.2, Nkx2.1 (Titf1) and Rab34 established these as direct Hh targets. These data also facilitated the generation of an algorithm that improved in silico predictions of Hh target genes. Together, these approaches provide significant new insights into both tissue-specific and general transcriptional targets in a crucial Shh-mediated patterning process.
RCDC: a relaxed consistency deterministic computer

Providing deterministic execution significantly simplifies the debugging, testing, replication, and deployment of multithreaded programs. Recent work has developed deterministic multiprocessor architectures as well as compiler and runtime systems that enforce determinism in current hardware. Such work has incidentally imposed strong memory-ordering properties. Historically, memory ordering has been relaxed in favor of higher performance in shared memory multiprocessors and, interestingly, determinism exacerbates the cost of strong memory ordering. Consequently, we argue that relaxed memory ordering is vital to achieving faster deterministic execution. This paper introduces RCDC, a deterministic multiprocessor architecture that takes advantage of relaxed memory orderings to provide high-performance deterministic execution with low hardware complexity. RCDC has two key innovations: a hybrid HW/SW approach to enforcing determinism; and a new deterministic execution strategy that leverages data-race-free-based memory models (e.g., the models for Java and C++) to improve performance and scalability without sacrificing determinism, even in the presence of races. In our hybrid HW/SW approach, the only hardware mechanisms required are software-controlled store buffering and support for precise instruction counting; we do not require speculation. A runtime system uses these mechanisms to enforce determinism for arbitrary programs. We evaluate RCDC using PARSEC benchmarks and show that relaxing memory ordering leads to performance and scalability close to nondeterministic execution without requiring any form of speculation. We also compare our new execution strategy to one based on TSO (total-store-ordering) and show that some applications benefit significantly from the extra relaxation. We also evaluate a software-only implementation of our new deterministic execution strategy.
Contract Monitoring Semantics as Patterns of Communication

We present a new approach to contract semantics which expresses myriad monitoring strategies using a small core of foundational communication primitives. This approach allows multiple existing contract monitoring approaches, ranging from Findler and Felleisen’s original model of higher-order contracts to semi-eager, parallel, or asynchronous monitors, to be expressed in a single language built on well-understood constructs. We prove that this approach accurately simulates the original semantics of higher-order contracts. A straightforward implementation in Racket demonstrates the practicality of our approach which can not only enrich existing Racket monitoring strategies, but also support a new style of monitoring in which collections of contracts collaborate to establish a global invariant.
A survey of transport protocols for wireless sensor networks

In this article we present a survey of transport protocols for wireless sensor networks (WSNs). We first highlight several unique aspects of WSNs, and describe the basic design criteria and challenges of transport protocols, including energy-efficiency, quality of service, reliability, and congestion control. We then provide a summary and comparison of existing transport protocols for WSNs. Finally, we discuss several open research problems.
The Validity of Conscientiousness Is Overestimated in the Prediction of Job Performance

Introduction Sensitivity analyses refer to investigations of the degree to which the results of a meta-analysis remain stable when conditions of the data or the analysis change. To the extent that results remain stable, one can refer to them as robust. Sensitivity analyses are rarely conducted in the organizational science literature. Despite conscientiousness being a valued predictor in employment selection, sensitivity analyses have not been conducted with respect to meta-analytic estimates of the correlation (i.e., validity) between conscientiousness and job performance. Methods To address this deficiency, we reanalyzed the largest collection of conscientiousness validity data in the personnel selection literature and conducted a variety of sensitivity analyses. Results Publication bias analyses demonstrated that the validity of conscientiousness is moderately overestimated (by around 30%; a correlation difference of about .06). The misestimation of the validity appears to be due primarily to suppression of small effects sizes in the journal literature. These inflated validity estimates result in an overestimate of the dollar utility of personnel selection by millions of dollars and should be of considerable concern for organizations. Conclusion The fields of management and applied psychology seldom conduct sensitivity analyses. Through the use of sensitivity analyses, this paper documents that the existing literature overestimates the validity of conscientiousness in the prediction of job performance. Our data show that effect sizes from journal articles are largely responsible for this overestimation.
Trajectory Tracking Controller Design for Percutaneous Interventional Procedures

The aim of this research work is to implement a trajectory tracking controller for a flexible needle within a tissue region, using a neural network-based approach. Initially, a kinematic model for steerable needle inside the tissue domain is considered based on a unicycle model while considering nonholonomic constraints. Subsequently, a neural network (NN) architecture based closed loop control strategy is implemented to track a desired trajectory on a specified plane. The efficacy of the developed controller is confirmed through simulation studies. Furthermore, a comparative study is conducted, involving a standard Proportional-Integral-Derivative (PID) controller, to demonstrate the efficacy of the proposed controller. The simulation outcomes demonstrate that the proposed control scheme outperforms the conventional PID approach.
Pore structure and fractal characteristics of a tight gas sandstone: A case study of Sulige area in the Ordos Basin, China

To understand the pore structure and fractal characteristics of tight gas reservoirs, thin sections, nuclear magnetic resonance, rate-controlled mercury injection, microcomputed tomography scanning, and field emission scanning electron microscopy investigations under laboratory conditions were conducted on a suite of core samples from the Middle Permian Shihezi Formation of Sulige area in the Ordos Basin, China. The investigated tight gas sandstones comprise three types of pores, i.e. residual intergranular pore, secondary dissolution pore, and micropore. The pore–throat size distribution is extremely wide and multiscale (10 nm–400 μm) co-existing in tight gas reservoirs. The submicron- and micron-scale pore–throats with radius above 0.05 μm, which are characterized by combining rate-controlled mercury injection with nuclear magnetic resonance, are considered to be the effective pores and throats that dominated the reservoirs flow capacity. Tight gas sandstones have stage fractal characteristics, and the intrusion pressure of approximately 1 MPa is regarded as an inflection point. Fractal dimension is negatively correlated with permeability, average throat radius and mainstream throat radius, positively correlated with heterogeneous coefficient, while there are no obvious relationships with porosity and average pore radius. Additionally, the percolation characteristics of tight gas reservoirs can be characterized by fractal structure. When the pore structure does not follow the fractal structure (i.e. intrusion pressure is lower than 1 MPa), the mercury intrusion saturation is dominated by pores; in contrast, the mercury intrusion saturation is almost solely dominated by throats. This research sheds light on the pore–throat size distribution of tight gas reservoirs by identifying the role of multiple techniques and the relationships between the pore structure parameters and percolation characteristics of tight gas reservoirs and fractal dimension.
Immunopathogenesis and immunotherapy in rheumatoid arthritis: an area in transition

Abstract. In years to come, new therapeutic modalities for the treatment of chronic arthritis will be launched for general clinical use. These therapies, until today only used in clinical studies, are based on knowledge obtained from animal models of chronic arthritis. This knowledge not only ushers therapeutic use in humans: in many settings, the animal studies have proven to be irreplacable tools to get insights into the pathogenesis of chronic arthritis. Rheumatoid arthritis (RA) shows a strong linkage of susceptibility to a certain epitope common to some HLA‐DRβ chains; this immunogenetic linkage is the strongest evidence for specific, T‐cell dependent immunity in the pathogenesis of the disease. Despite intense efforts, no unequivocal proofs of T‐cell specificity or oligoclonality have been found in RA. Therapeutic efforts directed against T‐cells or T‐cell functions have also at the best showed partial effects. As compared to the local production of T‐cell cytokines in the joint, monokine production is abundant. Therapies aimed at neutralizing the effects of the cartilage‐devastating monokine TNF‐a have showed remarkable results in small clinical trials. The possibility of increasing the presence of the regulatory cytokines IL‐4, IL‐10 and TGF‐β has also been explored, but only in animal studies. Immunology has also shed light on the mode of action of the commonly used ‘disease modifying’ drugs, and combinations of such drugs have shown increased potentials in recent clinical studies. The possibility of combining traditional anti‐arthritic drugs with recent immunological tools seem promising for the future. This review discusses recent advances in the understanding of pathogenesis and delineate new therapeutic approaches for chronic arthritis from the point of view of the immunologically oriented clinician.
Value of fluorine-18-fluorodeoxyglucose and thallium-201 in the detection of pancreatic cancer.

UNLABELLED This study compares the diagnostic value of 18F-FDG PET imaging and 201TI-SPECT imaging in patients with pancreatic cancer. METHODS Twenty-five patients with histologically-proven pancreatic cancer were studied. Following PET transmission scanning, 3 mCi of 201TI were administered after patients had fasted overnight. Thallium-201-SPECT images were obtained 15 min later. Immediately after 201TI-SPECT imaging, 4 mCi of FDG were administered and PET images were obtained 60 min later. The PET and SPECT images were compared qualitatively and quantitatively. For quantitative analysis, 10 x 10 mm2 regions of interest (ROIs) were selected in areas of the tumor showing the highest tracer accumulation and in the normal pancreas. The tumor to nontumor activity ratio (T/N ratio) was calculated. RESULTS Although both techniques delineated focal lesions with an increase in tracer accumulation in 16 patients, PET identified eight additional patients in whom 201TI-SPECT images did not visualize any lesion. Thus, FDG-PET provided significantly higher sensitivity (96%) than 201TI-SPECT (64%). Among the patients showing increased tracer accumulation, the T/N ratio was significantly higher with FDG-PET (3.24 +/- 1.27) than with 201TI-SPECT (1.77 +/- 0.37) (p < 0.0001). CONCLUSION We conclude that FDG-PET has a larger clinical value for noninvasive detection of pancreatic cancer than 201TI-SPECT. If a PET camera is available, FDG-PET is considered to be the method of choice for the evaluation of patients with suspected pancreatic cancer.
Induction of Pro- and Anti-Inflammatory Cytokines by Borrelia burgdorferi Lipoproteins in Monocytes Is Mediated by CD14

ABSTRACT We previously showed that heat-killed Borrelia burgdorferi spirochetes and lipidated outer surface protein A (L-OspA) stimulated the in vitro production of interleukin-10 (IL-10) in peripheral blood mononuclear cells (PBMC) from uninfected humans and rhesus monkeys (G. Giambartolomei et al., Infect. Immun. 66:2691–2697, 1998). Here we demonstrate that uninfected human peripheral blood monocytes, but not B or T cells, are the cells that transcribe the IL-10 cytokine gene in response to heat-killed B. burgdorferi. B. burgdorferi similarly induced an upregulation of the IL-1β and IL-6 cytokine genes in monocytes and the production of IL-10 and IL-6 in culture supernatants of the human monocytic cell line THP-1. Purified L-OspA (but not unlipidated OspA [U-OspA] or U-OspC) also stimulated the production of both cytokines in THP-1 cells in a dose-dependent fashion, suggesting that acylation of the OspA protein molecule is required for the production of both anti- and pro-inflammatory cytokines in naive monocytes. A lipohexapeptide that contained the tripalmitoyl-modified cysteine motif (Pam3Cys-Hex) of B. burgdorferi lipoproteins but with an arbitrary peptide sequence had the same effect. Monoclonal antibodies (MAbs) MY4 and 60bca, both of which bind to CD14 and are known to block lipopolysaccharide (LPS)-mediated cytokine production, were able to block L-OspA-mediated IL-10 and IL-6 cytokine production. In contrast, MAb 26ic, which also binds to CD14 but does not block LPS function, failed to inhibit L-OspA-mediated cytokine production. These data suggest that activation of monocytes and production of both anti- and pro-inflammatory cytokines induced by lipoproteins proceeds via the CD14 receptor. LPS binding protein was not required for OspA-induced cytokine production. Our results demonstrate that pro- and anti-inflammatory cytokines induced by B. burgdorferilipoproteins in PBMC are produced by monocytes and that lipoprotein and LPS signaling pathways share at least the initial signaling event that involves the CD14 receptor.
An Integrated Target Recognition Method Based on Improved Faster-RCNN for Apple Detection, Counting, Localization, and Quality Estimation

Aiming at the problems of the dense target distribution, poor positioning ability to pick robots, and inaccurate ripeness judgment in the picking orchard scene, this paper proposes an apple image recognition model with a high recognition rate, high speed, and high accuracy, which can effectively analyze the data of quantity, location, ripeness and quality estimation in the apple image. Firstly, the Faster R-CNN network is improved by introducing Efficient Channel Attention (ECA) and multi-scale fusion feature pyramid (FPN) for fruit detection and recognition localization. Then the distance transform-based watershed algorithm is used for image segmentation to fit the apple edge image while combining with the fitted circle determination algorithm to establish a mathematical model for apple volume estimation to calculate the quantity as well as the quality of apples. Finally, the apples are classified into four categories according to their ripeness, and the improved Faster R-CNN network is used to improve the ripeness detection effect, and the results show that the average fruit recognition accuracy of the improved method proposed in this paper is 95.42%, which significantly improves the accuracy of fruit detection.
SL-Defender: Decentralized Defense for Adversarial Robustness in Federated Learning

Adversarial poisoning attacks are growing threats to federated deep learning systems, as models can be poisoned from any of the compromised participants. Existing solutions attempt to detect and defend these attacks by assuming that there is an honest central parameter aggregator on which the detection and defense techniques can be applied. This assumption can give rise to a single point of failure (SPOF) and an easy target for attackers to compromise the whole federated learning system. They also lack a robust mechanism to isolate the malicious node so as to protect the rest of the federated system. We propose SL-Defender, a novel solution that overcomes these limitations by using a decentralized method to detect and defend against attacks based on Swarm Learning. Our solution uses the selected layers from each of the federated learning participants and projects their parameters into a lower dimensional subspace and performs clustering analysis in this subspace. The proposed methodology adds the ability to act on identified malicious participants and contain their impact on the federated learning process or remove them if needed. The proposed SL-Defender thus eliminates the need for honest central aggregator and distributes computation to peers and dynamically monitors them and defends them from the federating poisoned parameters without interrupting the learning process. With the support of experimental results on MNIST Dataset, we prove that SL-Defender will offer a unique position to improve the reliability and trustworthiness of Swarm Learning and Federated Machine learning in general.
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism

Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a “tipping point” mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
Identifying coseismic subsidence in tidal‐wetland stratigraphic sequences at the Cascadia subduction zone of western North America

Tidal-wetland stratigraphy reveals that great plate boundary earthquakes have caused hundreds of kilometers of coast to subside at the Cascadia subduction zone. However, determining earthquake recurrence intervals and mapping the coastal extent of past great earthquake ruptures in this region are complicated by the effects of many sedimentologic, hydrographic, and oceanographic processes that occur on the coasts of tectonically passive as well as active continental margins. Tidal-wetland stratigraphy at many Cascadia estuaries differs little from that at similar sites on passive-margin coasts where stratigraphic sequences form through nonseismic processes unrelated to coseismic land level changes. Methods developed through study of similar stratigraphic sequences in Europe provide a framework for investigating the Cascadia estuarine record. Five kinds of criteria must be evaluated when inferring regional coastal subsidence due to great plate boundary earthquakes: the suddenness and amount of submergence, the lateral extent of submerged tidal-wetland soils, the coincidence of submergence with tsunami deposits, and the degree of synchroneity of submergence events at widely spaced sites. Evaluation of such criteria at the Cascadia subduction zone indicates regional coastal subsidence during at least two great earthquakes. Evidence for a coseismic origin remains equivocal, however, for the many peat-mud contacts in Cascadia stratigraphic sequences that lack (1) contrasts in lithology or fossils indicative of more than half a meter of submergence, (2) well-studied tsunami deposits, or (3) precise ages needed for regional correlation. Paleoecologic studies of fossil assemblages are particularly important in estimating the size of sudden sea level changes recorded by abrupt peat-mud contacts and in helping to distinguish erosional and gradually formed contacts from coseismic contacts. Reconstruction of a history of great earthquakes for the Cascadia subduction zone will require rigorous application of the above criteria and many detailed investigations.
Structural and Magnetic Response in Bimetallic Core/Shell Magnetic Nanoparticles

Bimagnetic monodisperse CoFe2O4/Fe3O4 core/shell nanoparticles have been prepared by solution evaporation route. To demonstrate preferential coating of iron oxide onto the surface of ferrite nanoparticles X-ray diffraction (XRD), High resolution transmission electron microscope (HR-TEM) and Raman spectroscopy have been performed. XRD analysis using Rietveld refinement technique confirms single phase nanoparticles with average seed size of about 18 nm and thickness of shell is 3 nm, which corroborates with transmission electron microscopy (TEM) analysis. Low temperature magnetic hysteresis loops showed interesting behavior. We have observed large coercivity 15.8 kOe at T = 5 K, whereas maximum saturation magnetization (125 emu/g) is attained at T = 100 K for CoFe2O4/Fe3O4 core/shell nanoparticles. Saturation magnetization decreases due to structural distortions at the surface of shell below 100 K. Zero field cooled (ZFC) and Field cooled (FC) plots show that synthesized nanoparticles are ferromagnetic till room temperature and it has been noticed that core/shell sample possess high blocking temperature than Cobalt Ferrite. Results indicate that presence of iron oxide shell significantly increases magnetic parameters as compared to the simple cobalt ferrite.