Miracle-dz/UniFAR-FTUs huggingface dataset:
Hidden in Plain Sight: The Ecology and Physiology of Organismal Transparency

Despite the prevalence and importance of transparency in organisms, particularly pelagic species, it is a poorly understood characteristic. This article reviews the current state of knowledge on the distribution, ecology, and physical basis of biological transparency. Particular attention is paid to the distribution of transparent species relative to their optical environment, the relationship between transparency and visual predation, the physics of transparency, and what is known about the anatomical and ultrastructural modifications required to achieve this condition. Transparency is shown to be primarily a pelagic trait, uncommon in other aquatic habitats and extremely rare on land. Experimental and theoretical studies in terrestrial, freshwater, and marine ecosystems have shown that transparency is a successful form of camouflage, and that several visual adaptations seem to counter it. The physical basis of transparency is still poorly understood, but anatomical observations and mathematical models show that there are various routes to transparency. Future avenues for research include examination of the ultrastructure and optical properties of transparent tissue, exploring the link between transparent species and special visual modifications in the species they interact with, and analysis of the evolution of transparency using comparative methods.
The Spatial and Temporal Origin of Chandelier Cells in Mouse Neocortex

Building Cross Connectivity Chandelier cells innervate the initial segment of axons from pyramidal neurons and are thus placed to regulate pyramidal cell circuits in the brain. Chandelier cells of mice are marked by expression of the NKX2.1 transcription factor. Taniguchi et al. (p. 70, published online 22 November) followed the development of these neurons and found that chandelier cells originate from the ventral germinal zone. The nascent cells migrate and integrate with cortical neurons following specific developmental pathways. Chandelier interneurons migrate along well-defined paths as they mingle with pyramidal neurons to build circuits. Diverse γ-aminobutyric acid–releasing interneurons regulate the functional organization of cortical circuits and derive from multiple embryonic sources. It remains unclear to what extent embryonic origin influences interneuron specification and cortical integration because of difficulties in tracking defined cell types. Here, we followed the developmental trajectory of chandelier cells (ChCs), the most distinct interneurons that innervate the axon initial segment of pyramidal neurons and control action potential initiation. ChCs mainly derive from the ventral germinal zone of the lateral ventricle during late gestation and require the homeodomain protein Nkx2.1 for their specification. They migrate with stereotyped routes and schedule and achieve specific laminar distribution in the cortex. The developmental specification of this bona fide interneuron type likely contributes to the assembly of a cortical circuit motif.
PERBANDINGAN DECISION TREE, MAXIMUM ENTROPY, DAN ASSOCIATION RULES PADA RESOLUSI KOREFERENSI UNTUK BAHASA INDONESIA

Metode Decision Tree, Maximum Entropy, dan Association Rules pernah diaplikasikan untuk melakukan penelitian resolusi koreferensi untuk Bahasa Inggris. Sedangkan penelitian resolusi koreferensi untuk Bahasa Indonesia baru dilakukan dengan menggunakan Association Rules. Penelitian ini dilakukan untuk membandingkan ketiga metode untuk melakukan resolusi koreferensi. Pengujian dilakukan terhadap 500 dokumen yang diambil dari sumber koran online. Kata Kunci: resolusi koreferensi, Decision Tree, Maximum Entropy, Association Rules
Optimal task rate selection in fixed priority systems

The design phase of any real-time system requires balancing the limited computational resources against the functional requirements and the performance of the application. The optimal design solution can be obtained by solving an optimization problem where the system performance is maximized within the schedulability constraints. In this paper, we provide a procedure that finds the task activation rates maximizing a performance function within the deadline constraints in systems scheduled by fixed priorities. First, we describe the exact feasibility region in the domain of task frequencies. Then, we introduce a procedure that starts by finding an initial solution, and incrementally improves it by using an original branch and bound search, until the global optimum is reached. Experiments show that our algorithm finds the optimal task periods for practical problems with a remarkable speedup, if compared with existing techniques. When the size of the problem makes the global search intractable, the experiments show that the algorithm can still find a high quality solution in the very early steps
Flexure of Lithosphere Beneath Apennine and Carpathian Foredeep Basins: Evidence for an Insufficient Topographic Load

The Pliocene foredeep basin external to the Apennine thrust belt and the late Miocene foredeep basin external to the outer East Carpathians are considered typical molassic foredeeps that formed contemporaneously with thrusting in the adjacent mountain belts. A simple mechanical model in which the response of the lithosphere to loading was approximately by a semi-infinite (broken) elastic plate overlying a weak fluid was used to analyze the deflection of the foreland lithosphere beneath the Apennine and outer East Carpathian foredeep basins along three transects perpendicular to the thrust belts. Comparison between the calculated and observed depth to basement suggests that the emplacement of thrust sheets onto the foreland lithosphere during mountain building failed to pr duce a sufficient load to create the observed foredeep basins and observed topography regardless of the position of the slab end or the flexural rigidity assumed for the foreland lithosphere. We infer that an additional subsurface load must be present and that its magnitude must be roughly equal to the load created by that part of the thrust belt that is above sea level. For the two Apennine transects, an acceptable fit to the shape and size of the observed foredeep basin was generated by assuming effective elastic plate thicknesses of 8 and 15 km (4.9 and 9.3 mi) and applied vertical forces of 2 × 1015 dynes/cm and 1.3 × 1015 dynes/cm at the slab end. For the Carpathian transect, an effective plate thickness of 30 km (18.6 mi) and an applied force of 1.5 #215; 1015 dynes/cm generated an acceptable fit. This study suggests a method whereby an estimate of the depth to autochthonous basement rocks beneath overthrust belts can be made in some areas where this information is not available from seismic or drilling data. Such an approach may enable exploration geologists to determine if crystalline rocks encountered in drilling overthrust terranes are a part of the autochthonous basement, or if they are part of an overthrust sheet. In the latter situation, oil-bearing sequences of sedimentary rocks might lie below crystalline rocks contained in the allochthonous sheet.
Timing-driven routing for symmetrical-array-based FPGAs

In this paper, we present a timing-driven global router for symmetrical-array-based FPGAs. The routing resources in the symmetrical-array-based FPGAs consist of segments of various lengths. Researchers have shown that the number of segments, instead of wirelength, used by a net is the most critical factor in controlling routing delay in an FPGA. Thus, traditional measure of routing delay based on the geometric distance of a signal is not accurate. To consider wirelength and delay simultaneously, we study a model of timing-driven routing trees, arising from the special properties of FPGA routing architectures. We explore the complexity of the routing-tree problem and present efficient and effective approximation algorithms for the problem. Based on the solutions to the routing-tree problem, we present a global-routing algorithm which is able to utilize various routing segments with global consideration to meet the timing constraints. Experimental results on benchmark circuits show that our approach is promising.
Influence of the Fibroblastic Reticular Network on Cell-Cell Interactions in Lymphoid Organs

Secondary lymphoid organs (SLO), such as lymph nodes and the spleen, display a complex micro-architecture. In the T cell zone the micro-architecture is provided by a network of fibroblastic reticular cells (FRC) and their filaments. The FRC network is thought to enhance the interaction between immune cells and their cognate antigen. However, the effect of the FRC network on cell interaction cannot be quantified to date because of limitations in immunological methodology. We use computational models to study the influence of different densities of FRC networks on the probability that two cells meet. We developed a 3D cellular automaton model to simulate cell movements and interactions along the FRC network inside lymphatic tissue. We show that the FRC network density has only a small effect on the probability of a cell to come into contact with a static or motile target. However, damage caused by a disruption of the FRC network is greatest at FRC densities corresponding to densities observed in the spleen of naïve mice. Our analysis suggests that the FRC network as a guiding structure for moving T cells has only a minor effect on the probability to find a corresponding dendritic cell. We propose alternative hypotheses by which the FRC network might influence the functionality of immune responses in a more significant way.
On the upscaling of mass transfer rate expressions for interpretation of source zone partitioning tracer tests

Analysis of partitioning tracer tests conducted in dense nonaqueous phase liquid (DNAPL) source zones relies on conceptual models that describe mass exchange between the DNAPL and aqueous phases. Such analysis, however, is complicated by the complex distribution of entrapped DNAPL mass and formation heterogeneity. Due to parameter uncertainty in heterogeneous regions and the desire to reduce model complexity, the effect of mass transfer limitations is often neglected, and an equilibrium‐based model is typically used to interpret test results. This work explores the consequences of that simplifying assumption on test data interpretation and develops an alternative upscaled modeling approach to quantify effective mass transfer rates. To this end, a series of partitioning tracer tests is numerically simulated in heterogeneous two‐dimensional PCE‐DNAPL source zones, representative of a range of hydraulic conductivity and DNAPL mass distribution characteristics. The effective mass transfer coefficient corresponding to each test is determined by fitting an upscaled model to the simulated data, and regression analysis is performed to explore the correlation between various source zone metrics and the effective mass transfer coefficient. Results suggest that vertical DNAPL spreading, Reynolds number, pool fraction, and the effective organic phase saturation are the most significant parameters controlling tracer partitioning rates. Finally, a correlation for prediction of the effective (upscaled) mass transfer coefficient is proposed and verified using existing experimental data. The developed upscaled model incorporates the influence of physical heterogeneity on the rate of tracer partitioning and, thus, can be used for the estimation of source zone mass distribution characteristics from tracer test results.
In-Situ Evaluation of Strength and Dilatancy of Sands Based on CPT Results

ABSTRACT In-situ tests have been increasingly used to estimate the shear strength of soils. In this paper, we propose methods to evaluate in-situ strength and dilatancy of sandy soils based on cone penetration test (CPT) results. It takes into account the silt content, relative density and stress state of the sand. A series of laboratory test results from fundamental property tests and triaxial tests are analyzed to develop methods for in-situ evaluation of strength and dilatancy for sands. Based on test results, modified and simplified dilatancy equations, in terms of the cone penetration resistance qc and intrinsic soil variables, are proposed. Results from proposed and original dilatancy indexes show close agreements for various soil conditions. Values of intrinsic variables for the proposed dilatancy relationships were proposed as a function of silt content. Based on TX test results, a direct CPT-based correlation, applicable to both clean and silty sands, is proposed as well. In order to verify the proposed methods, calibration chamber CPT results obtained in this study and collected from the literature are adopted. It is observed that the results from the proposed methods show good agreement with the measured results.
Characterization of SodC, a Periplasmic Superoxide Dismutase from Burkholderia cenocepacia

ABSTRACT Burkholderia cenocepacia is a gram-negative, non-spore-forming bacillus and a member of the Burkholderia cepacia complex. B. cenocepacia can survive intracellularly in phagocytic cells and can produce at least one superoxide dismutase (SOD). The inability of O2− to cross the cytoplasmic membrane, coupled with the periplasmic location of Cu,ZnSODs, suggests that periplasmic SODs protect bacteria from superoxide that has an exogenous origin (for example, when cells are faced with reactive oxygen intermediates generated by host cells in response to infection). In this study, we identified the sodC gene encoding a Cu,ZnSOD in B. cenocepacia and demonstrated that a sodC null mutant was not sensitive to a H2O2, 3-morpholinosydnonimine, or paraquat challenge but was killed by exogenous superoxide generated by the xanthine/xanthine oxidase method. The sodC mutant also exhibited a growth defect in liquid medium compared to the parental strain, which could be complemented in trans. The mutant was killed more rapidly than the parental strain was killed in murine macrophage-like cell line RAW 264.7, but killing was eliminated when macrophages were treated with an NADPH oxidase inhibitor. We also confirmed that SodC is periplasmic and identified the metal cofactor. B. cenocepacia SodC was resistant to inhibition by H2O2 and was unusually resistant to KCN for a Cu,ZnSOD. Together, these observations establish that B. cenocepacia produces a periplasmic Cu,ZnSOD that protects this bacterium from exogenously generated O2− and contributes to intracellular survival of this bacterium in macrophages.
Experimental Mycobacterium tuberculosis Infection of Cynomolgus Macaques Closely Resembles the Various Manifestations of Human M. tuberculosis Infection

ABSTRACT Nonhuman primates were used to develop an animal model that closely mimics human Mycobacterium tuberculosis infection. Cynomolgus macaques were infected with low doses of virulent M. tuberculosis via bronchoscopic instillation into the lung. All monkeys were successfully infected, based on tuberculin skin test conversion and peripheral immune responses to M. tuberculosis antigens. Progression of infection in the 17 monkeys studied was variable. Active-chronic infection, observed in 50 to 60% of monkeys, was characterized by clear signs of infection or disease on serial thoracic radiographs and in other tests and was typified by eventual progression to advanced disease. Approximately 40% of monkeys did not progress to disease in the 15 to 20 months of study, although they were clearly infected initially. These monkeys had clinical characteristics of latent tuberculosis in humans. Low-dose infection of cynomolgus macaques appears to represent the full spectrum of human M. tuberculosis infection and will be an excellent model for the study of pathogenesis and immunology of this infection. In addition, this model will provide an opportunity to study the latent M. tuberculosis infection observed in ∼90% of all infected humans.
Experimental study of two event-based PI controllers in a solar distributed collector field

In this work we focus on the study of limit cycles that appear in a control scheme which is based on the use of a PI controller with an event-based send-on-delta sampling (SOD), which can be used to sample either the process variable or the control variable. We use an algorithm to calculate the limit cycles properties and then we compare the results obtained in simulations with experiments performed on a real plant, a distributed solar collector field at the Solar Platform of Almería (PSA, Spain). The process is identified as a first order plus time delay (FOPTD). Practical issues, such as the implementation of an anti-windup mechanism and a bumpless transfer between the manual and automatic mode are also addressed.
Tensor-based item recommendation using probabilistic ranking in social tagging systems

A common problem with the use of tensor modeling in generating quality recommendations for large datasets is scalability. In this paper, we propose the Tensor-based Recommendation using Probabilistic Ranking method that generates the reconstructed tensor using block-striped parallel matrix multiplication and then probabilistically calculates the preferences of user to rank the recommended items. Empirical analysis on two real-world datasets shows that the proposed method is scalable for large tensor datasets and is able to outperform the benchmarking methods in terms of accuracy.
Simulations of the trend and annual cycle in stratospheric CO2

The distribution and evolution of stratospheric CO2 in response to the observed annual cycle, interannual variations, and long-term trends in tropospheric CO2 is simulated with the GISS 23 layer stratospheric general circulation model. Carbon dioxide is a tracer of stratospheric transport which has essentially no local sources or sinks but still displays gradients due to the forcing at the surface. Consequently, observations of stratospheric CO2, until recently limited to a few flask samples, but now included as high frequency in situ sampling in aircraft campaigns, provide a test of tracer transport in stratospheric simulations independent of model chemistry. In our model, CO2 enters the stratosphere primarily through the tropical tropopause, where air parcels are effectively labeled in time by their CO2 values (although not uniquely because of the cycles in tropospheric concentration). Parcels of differing ages are subsequently mixed in the stratosphere. Only when the growth is purely linear can the CO2 offset in a parcel relative to the troposphere be interpreted as the average time since stratospheric air was last in contact with the troposphere, i.e., the “age” of the stratosphere. Our model is in qualitative agreement with multiyear averages of balloon soundings at northern mid- and high latitudes; the stratosphere at 30 km at mid-latitudes is about 4 years (6 ppm of CO2) behind the troposphere. We predict significant propagation of the CO2 annual cycle into the lower stratosphere, an effect which must be accounted for when interpreting observations. While the annual cycle is negligible above the lower stratosphere, interannual oscillations, such as those associated with El Ninos, can propagate well into the middle stratosphere as positive offsets from the linear trend lasting significantly longer than their duration in the troposphere.
Persistent Browser Cache Poisoning

Caching web content increases the performance on both the client side (by avoiding unnecessary requests) and the server side (by reducing bandwidth and I/O load). To this end, the HTTP protocol uses expiration and validation mechanisms to ensure that stale content is updated when necessary. It performs the corresponding integrity checks, however, only on the server side. Worse, current browsers lack proper cross-domain cache authentication. We exploit this absence of security checks, and show that an attacker who accesses the network through the same shared medium as the victim can modify cacheable content in the victim’s browser without attracting the notice of the victim. This attack is particularly effective against web applications that offload a large part of stable functionality to the client’s cache. To demonstrate the feasibility of the attack, we implement air-poison, a proof-of-concept tool designed to be used in wireless networks that answers HTTP requests for JavaScript documents by prepending a malicious payload of the attacker’s choice. Each time the victim loads the document, regardless of the security origin context, the malicious script executes and establishes a bidirectional JavaScript communication channel to a host controlled by the attacker. The systematic study of the severity of this threat is an interesting future avenue of research.
Robust global disturbance rejection of spacecraft rendezvous system via gain scheduling

The paper proposed a nonlinear continuous static gain scheduled controller for the spacecraft circular orbit rendezvous system with input saturation, input-additive uncertainties and external disturbances by combining the parametric Lyapunov equation-based low gain feedback design method and gain scheduling technique. The relative models are established based on C-W equation. To apply the proposed gain scheduling approaches, only a scalar nonlinearity equation is required to be solved. Especially, the simulations have carried out directly on the nonlinearity model of the spacecraft rendezvous instead of a linearized one show the effectiveness of the proposed approach.
A general framework for improving query processing performance on multi-level memory hierarchies

We propose a general framework for improving the query processing performance on multi-level memory hierarchies. Our motivation is that (1) the memory hierarchy is an important performance factor for query processing, (2) both the memory hierarchy and database systems are becoming increasingly complex and diverse, and (3) increasing the amount of tuning does not always improve the performance. Therefore, we categorize multiple levels of memory performance tuning and quantify their performance impacts. As a case study, we use this framework to improve the in-memory performance of storage models, B+-trees, nested-loop joins and hash joins. Our empirical evaluation verifies the usefulness of the proposed framework.
Modeling and evaluation of control flow prediction schemes using complete system simulation and Java workloads

Program control flow transfer (branch) prediction is considered to be a performance hurdle and a key design issue for current and future microprocessors. Branch prediction schemes with high prediction accuracy have been proposed to support longer processor pipelines with higher frequency clocks. In the previously published literature, the design and evaluation of branch predictors have been based heavily on the simulation of only user instructions from scientific and commercial workloads written in programming languages such as C or C++. To complement the existing research, the paper presents a case study of the modeling and evaluation of advanced branch predictors using full-system simulation of Java workloads running on a commercial operating system. The contributions of the paper are: (1) the presentation of a full system simulation framework to model, simulate and evaluate the performance of a set of advanced prediction schemes on emerging Java workloads; (2) an analysis of the performance and design complexity of advanced branch predictors in the presence of full system code; (3) an accurate modeling of user/kernel branch aliasing on a wide range of branch predictors.