Miracle-dz/UniFAR-FTUs huggingface dataset:
ENVIRONMENT‐DEPENDENT ADMIXTURE DYNAMICS IN A TIGER SALAMANDER HYBRID ZONE

Abstract After an estimated five million years of independent evolution, the barred tiger salamander (Ambystoma tigrinum mavortium) was introduced by bait dealers into the native range of the California tiger salamander (A. californiense). Hybridization and backcrossing have been occurring in central California for 50–xs60 years, or an estimated 15–30 generations. We studied genetic and ecological factors influencing admixture of these two divergent gene pools by analyzing frequencies of hybrid genotypes in three kinds of breeding habitats: natural vernal pools, ephemeral man‐made cattle ponds, and perennial man‐made ponds. Perennial ponds tended to have higher frequencies of nonnative alleles than either type of seasonal pond, even in cases where perennial and seasonal ponds are within a few hundred meters. Thus, the hybrid zone has a mosaic structure that depends on pond hydrology or ecology. The presence of some broadly acting constraints on admixture is suggested by linkage disequilibria between physically unlinked molecular markers within ponds. In addition, we found several marker‐specific deviations from Hardy‐Weinberg equilibrium. One marker showed a consistent deficit of heterozygotes across pond types. Another showed heterozygote deficits only in vernal pools. A third was more likely to have heterozygote excess in ephemeral cattle ponds. These patterns indicate that admixture is influenced by complex genotype‐by‐environment interactions.
Particle Swarm Optimization with Powell's Direction Set Method for Remote Sensing Image Registration

Multisensor image registration via mutual information is a powerful approach. However, there are a lot of local maxima in the mutual information surface which prevent optimization methods from finding the global maximum. To solve the problem, the particle swarm optimization(PSO, global optimizer) is used to find a good initial estimation for registration parameters and followed by a refining Powell’s direction set method(PDSM, local optimizer). Experiments with simulated and real multisensor images demonstrate the effectiveness of the proposed optimization method with PSO and PDSM for multisensor image registration.
Treadmill walking in Parkinson's disease patients: Adaptation and generalization effect

We examined the adaptation and generalization effect of one familiarization treadmill walking session on gait in patients with Parkinson's disease (PD) with different degrees of disease severity. Eight moderate PD patients (Hoehn and Yahr stage 2–2.5), eight advanced PD patients (Hoehn and Yahr 3), and eight matched control subjects participated in this study. Subjects first walked overground on a 10‐m walkway at a self‐selected speed (pretreadmill). They then performed a 20‐min treadmill training session, followed by three trials of overground walking (Post1, Post2, Post3). Cadence, step length, speed, and coefficient of variation of stride time (CV) were recorded. During the treadmill session the advanced PD patients significantly decreased their cadence (t = 3.9, P ≤ 0.01) and increased their step length (t = 4.27, P ≤ 0.01) compared with pretreadmill walking. After the treadmill, all subjects walked overground significantly faster (F = 16.51 P ≤ 0.001) and with a larger step length (F = 13.03 P ≤ 0.01) than pretreadmill walking. The present study shows a specific adaptation to walk over the treadmill for the advanced PD patients. Moreover, this confirms the potential therapeutic use of the treadmill for PD gait rehabilitation since a single familiarization session lead to an increase in the step length and thus to the improvement of the main gait impairment in PD. © 2008 Movement Disorder Society
Document clustering with committees

Document clustering is useful in many information retrieval tasks: document browsing, organization and viewing of retrieval results, generation of Yahoo-like hierarchies of documents, etc. The general goal of clustering is to group data elements such that the intra-group similarities are high and the inter-group similarities are low. We present a clustering algorithm called CBC (Clustering By Committee) that is shown to produce higher quality clusters in document clustering tasks as compared to several well known clustering algorithms. It initially discovers a set of tight clusters (high intra-group similarity), called committees, that are well scattered in the similarity space (low inter-group similarity). The union of the committees is but a subset of all elements. The algorithm proceeds by assigning elements to their most similar committee. Evaluating cluster quality has always been a difficult task. We present a new evaluation methodology that is based on the editing distance between output clusters and manually constructed classes (the answer key). This evaluation measure is more intuitive and easier to interpret than previous evaluation measures.
Adaptive variable-length feedback using wireless power transfer for opportunistic beamforming

In the opportunistic beamforming (OBF) scheme, the access point (AP) acquires channel related feedback from the network's terminals and allocates the orthonormal beams to the users with the best link. This paper investigates the OBF scheme in a wireless powered communication network, where multi-antenna terminals with wireless power harvesting capabilities are randomly deployed around the AP. In this context, the terminals adapt the length of their feedback based on the power harvested with the use of rectenna arrays. We study two fundamental architectures for the combination of the rectenna elements, the direct-current combiner and the radio-frequency combiner, as well as a hybrid architecture of these two. By using higher order statistics and stochastic geometry, the beam outage probability is derived in closed form for all considered architectures.
Spatial text processing in relation to spatial abilities and spatial styles

The present study examined how people's spatial abilities and spatial preferences for representing environmental information influence the ways in which they represent information from spatial descriptions. Spatial individual differences can have a central role in sustaining the mental representation deriving from survey and route descriptions. A group of 48 undergraduates listened to survey and route spatial descriptions and performed a sentence verification task on their content. They were then administered two spatial tasks, the Mental Rotation Test (MRT) and the Minnesota Paper Form Board (MPFB), plus a self-rating scale on sense of direction and spatial representation. The results showed that spatial abilities influenced the recall of survey and route texts differently. The MPFB and the MRT positively predicted the accuracy of answers on the survey text, which was negatively predicted by a preference for a route representation. Preference for a survey representation was positively associated with the accuracy of answers on the route text. Taken together, these results support the existence of a relationship between spatial abilities, spatial styles, and the processing of spatial language that depends on whether a route or a survey perspective is adopted.
Regulation of p53 is critical for vertebrate limb regeneration

Significance Our work establishes that endogenous regulation of the activity of the tumor-suppressor p53 is a critical component in vertebrate limb regeneration and is required for the process to occur. We show that down-regulation of p53 is required for cell cycle reentry of postmitotic differentiated cells, the critical step in the formation of the progenitors for the process of regeneration. We propose that the absence of tumor-suppressors that stabilize p53 and the presence of dominant-negative isoforms, permit regeneration by negative regulation of p53. This research sheds light onto previously unknown molecular mechanisms critical for limb regeneration and offers a new perspective on the functions of the tumour suppressor p53. Extensive regeneration of the vertebrate body plan is found in salamander and fish species. In these organisms, regeneration takes place through reprogramming of differentiated cells, proliferation, and subsequent redifferentiation of adult tissues. Such plasticity is rarely found in adult mammalian tissues, and this has been proposed as the basis of their inability to regenerate complex structures. Despite their importance, the mechanisms underlying the regulation of the differentiated state during regeneration remain unclear. Here, we analyzed the role of the tumor-suppressor p53 during salamander limb regeneration. The activity of p53 initially decreases and then returns to baseline. Its down-regulation is required for formation of the blastema, and its up-regulation is necessary for the redifferentiation phase. Importantly, we show that a decrease in the level of p53 activity is critical for cell cycle reentry of postmitotic, differentiated cells, whereas an increase is required for muscle differentiation. In addition, we have uncovered a potential mechanism for the regulation of p53 during limb regeneration, based on its competitive inhibition by ΔNp73. Our results suggest that the regulation of p53 activity is a pivotal mechanism that controls the plasticity of the differentiated state during regeneration.
Immunocytochemistry versus molecular fingerprinting of metastases

Examination of cytological samples of cancer to suggest a possible primary site of origin is one of the commonest and most difficult tasks of diagnostic cytopathologists. Currently, both cytomorphology and immunocytochemistry are the main approaches to this diagnostic dilemma. We report the application of microsatellite analysis in cytological samples in a patient with a primary colonic tumour and two subsequent lung nodules, which were suspected on CT scans of the chest, and compared the findings with those obtained with conventional immunocytochemistry. The molecular results were in agreement with the radiological impression and conflicted with the immunocytochemistry. We conclude that immunocytochemical and molecular biology approaches to the diagnosis of tumours may give rise to contradictory results.
A SIMPLIFIED LIQUID CULTURE MEDIUM FOR THE GROWTH OF HEMOPHILUS PERTUSSIS

Hornibrook (1939) described a liquid medium for the propagation of Hemophilus pertussis having a casein hydrolyzate base to which were added various salts, starch, cysteine, and nicotinic acid and which was capable of growing recently isolated strains. Because of the potential advantages of such a medium, it has been studied by many investigators. Their work has confirmed Hornibrook's original observations but it has also revealed several disadvantages in the medium. Modifications of the original formula stated to prevent precipitation, simplify preparation, decrease the granularity of growth, and increase the final bacterial count have been suggested by Verwey and Sage (1945), Wilson (1945), Farrell and Taylor (1945), and Cohen and Wheeler (1946). It is the purpose of this report to describe further the medium that has been developed in our laboratory and to define the cultural conditions that seem optimal for the growth of H. pertussis in this medium. Some observations concerning the antigenic properties of the liquid medium cultures are included.
Variable selection by RIVAL

The paper considers variable selection problem and proposes an algorithm called the RIVAL (Removing Irrelevant Variables Amidst Lasso Iterations). For a given and fixed length of data points, the algorithm recursively updates the weights so that the ability of the algorithm in detecting zero coefficients is substantially improved. Theoretical convergence is established supported by numerical simulation results.
On the Role of Melanoma-Specific CD8+ T-Cell Immunity in Disease Progression of Advanced-Stage Melanoma Patients

Cytotoxic T-cell immunity directed against melanosomal differentiation antigens is arguably the best-studied and most prevalent form of tumor-specific T-cell immunity in humans. Despite this, the role of T-cell responses directed against melanosomal antigens in disease progression has not been elucidated. To address this issue, we have related the presence of circulating melanoma-specific T cells with disease progression and survival in a large cohort of patients with advanced-stage melanoma who had not received prior treatment. In 42 (68%) of 62 patients, melanoma-specific T cells were detected, sometimes in surprisingly large numbers. Disease progression during treatment was more frequent in patients with circulating melanoma-specific T cells, and mean survival of patients with circulating melanoma-specific T cells was equal to the survival of patients without melanoma-specific T cells. These data suggest that the induction of melanosomal differentiation antigen-specific T-cell reactivity in advanced stage melanoma is a late event most likely due to antigen load and spreading and is not accompanied by a clinically significant antitumor effect. These melanoma-specific T cells may be functionally distinct from T cells raised during spontaneous regression or up vaccination.
OrthoMADS: A Deterministic MADS Instance with Orthogonal Directions

The purpose of this paper is to introduce a new way of choosing directions for the mesh adaptive direct search (Mads) class of algorithms. The advantages of this new OrthoMads instantiation of Mads are that the polling directions are chosen deterministically, ensuring that the results of a given run are repeatable, and that they are orthogonal to each other, which yields convex cones of missed directions at each iteration that are minimal in a reasonable measure. Convergence results for OrthoMads follow directly from those already published for Mads, and they hold deterministically, rather than with probability one, as is the case for LtMads, the first Mads instance. The initial numerical results are quite good for both smooth and nonsmooth and constrained and unconstrained problems considered here.
Distributed LT Codes

This paper proposes a novel distributed encoding procedure to realize codes that resemble LT codes (rateless codes for erasure correction) in both structure and performance. For the case of two sources communicating with a single sink via a common relay, this technique separately encodes k/2 symbols of information onto slightly more than k code symbols at each source. These two codewords are then selectively XOR-ed at the relay, such that the result can be decoded by the sink to recover all k information symbols. It is shown that, for the case of four sources communicating to a single sink, the use of a similar distributed LT code leads to a 50% reduction in overhead at the sink, compared to the use of four individual LT codes
Steady state reliability of maximum power point tracking algorithms used with a thermoelectric generator

A thermoelectric generator (TEG) with its near linear V-I characteristic makes its operation distinct from a photovoltaic (PV) cell. However, when maximum power point tracking (MPPT) is implemented in TEG power electronic systems, the established knowledge and wisdom surrounding PV oriented MPPT systems is often applied directly without consideration of the TEG's characteristics. Unsuitable MPPT algorithms generate large operating point variations thus deteriorating the steady state performance of the TEG. Therefore an algorithm that can reliably deliver power with low steady state error over a range of operating conditions is desired. This paper compares three common MPPT methods (perturb and observe, power gradient tracking and fractional open-circuit voltage / short-circuit current), in terms of their steady state performance and reliability, when used with a 4.2 V, 3.4 A (for matched load at ΔT = 270°C) TEG module. Experimental results are reported that confirm better and more reliable steady state performance of the fractional open-circuit voltage / short-circuit current method compared to the perturb and observe and power gradient tracking algorithms.
Telomerase activity detected by silver staining TRAP-silver staining , a highly sensitive assay for measuring telomerase activity in tumor tissue and cell lines

Measurement of telomerase activity in clinically obtained tumor samples may provide important information for use as both a diagnostic marker and a prognostic indicator for patient outcome. In order to evaluate telomerase activity in tumor tissue without radiolabeling the product, we developed a simple telomeric repeat amplification protocol-silver-staining assay that is less time-consuming, is safe and requires minimal equipment. In addition, we determined the sensitivity of the silverstaining method by using extracts of telomerase-positive thyroid carcinoma cell lines which were serially diluted from 5,000 to 10 cells. Telomerase activity was also assayed in 19 thyroid tumors, 2 normal controls and 27 bone marrow aspirates. The results indicate that the technique permits the detection of telomerase activity from 5000 to as few as 10 cells. We propose that it could be immediately applicable in many laboratories due to the minimal amount of equipment required. Correspondence
Task-based information retrieval: Structuring undergraduate history essays for better course evaluation using essay-type visualizations

When domain novices are in C.C. Kuhlthau's (1993) Stage 3, the exploration stage of researching an assignment, they often do not know their information need; this causes them to go back to Stage 2, the topic-selection stage, when they are selecting keywords to formulate their query to an Information Retrieval (IR) system. Our hypothesis is that instead of going backward, they should be going forward toward a goal state--the performance of the task for which they are seeking the information. If they can somehow construct their goal state into a query, this forward-looking query better operationalizes their information need than does a topic-based query. For domain novice undergraduates seeking information for a course essay, we define their task as selecting a high-impact essay structure which will put the student's learning on display for the course instructor who will evaluate the essay. We report a study of first-year history undergraduate students which tested the use and effectiveness of "essay type" as a task-focused query-formulation device. We randomly assigned 78 history undergraduates to an intervention group and a control group. The dependent variable was essay quality, based on (a) an evaluation of the student's essay by a research team member, and (b) the marks given to the student's essay by the course instructor. We found that conscious or formal consideration of essay type is inconclusive as a basis of a task-focused query-formulation device for IR.
Abnormal Development of Forebrain Midline Glia and Commissural Projections in Nfia Knock-Out Mice

Nuclear factor I (NFI) genes are expressed in multiple organs throughout development (Chaudhry et al., 1997; for review, seeGronostajski, 2000). All four NFI genes are expressed in embryonic mouse brain, with Nfia, Nfib, andNfix being expressed highly in developing cortex (Chaudhry et al., 1997). Disruption of the Nfia gene causes agenesis of the corpus callosum (ACC), hydrocephalus, and reduced GFAP expression (das Neves et al., 1999). Three midline structures, the glial wedge, glia within the indusium griseum, and the glial sling are involved in development of the corpus callosum (Silver et al., 1982; Silver and Ogawa, 1983; Shu and Richards, 2001). BecauseNfia−/−mice show glial abnormalities and ACC, we asked whether defects in midline glial structures occur inNfia− / − mice. NFI-A protein is expressed in all three midline populations. InNfia− / − , mice sling cells are generated but migrate abnormally into the septum and do not form a sling. Glia within the indusium griseum and the glial wedge are greatly reduced or absent and consequently Slit2 expression is also reduced. Although callosal axons approach the midline, they fail to cross and extend aberrantly into the septum. The hippocampal commissure is absent or reduced, whereas the ipsilaterally projecting perforating axons (Hankin and Silver, 1988; Shu et al., 2001) appear relatively normal. These results support an essential role for midline glia in callosum development and a role for Nfia in the formation of midline glial structures.
Loose L 1/2 regularised sparse representation for face recognition

Sparse representation (or sparse coding) has been applied to deal with frontal face recognition. Two representative methods are the sparse representation-based classification (SRC) and the collaborative representation-based classification (CRC), in which the query face image is represented by a sparse linear combination of all the training samples. The difference between SRC and CRC is that the L 1-norm constraint of coding is employed in the former to guarantee the sparse property, while the L 2-norm constraint is utilised in the latter. In this paper, we propose a novel loose L 1/2 regularised sparse representation (SR) for face recognition, named L 1/2 classification (LHC), which is inspired by L 1/2 regularisation. Additionally, an iterative Tikhonov regularisation (ITR) is proposed to solve LHC efficiently compared with the original algorithm. Using ITR, the balance between the collaborative representation (CR) and the SR can be tuned by the iterations. Attributed to the sparser L 1/2 regularisation and the iterative solution mechanism, a better performance can be achieved by LHC. Extensive experiments on three benchmark face databases demonstrated that LHC is more effective than the state-of-the-art SR-based methods in dealing with frontal face recognition.
Fully CMOS-Compatible 1T1R Integration of Vertical Nanopillar GAA Transistor and Oxide-Based RRAM Cell for High-Density Nonvolatile Memory Application

A fully CMOS-compatible vertical nanopillar gate-all-around transistor integrated with a transition-oxide-based resistive random access memory cell to realize 4F2 footprint has been demonstrated and systematically characterized. The nanopillar transistor exhibits excellent transfer characteristics with diameter scaled down to a few tens of nanometer. Three types of resistive switching behavior have been observed in the fabricated one-transistor one-resistor cell, namely, preforming ultralow-current switching, unipolar switching, and bipolar switching after forming process. A reset current of only 200 pA has been observed in the preforming ultralow-current switching, while for the unipolar and bipolar switching modes after forming process, good memory performance and operation parameter uniformity are demonstrated. Furthermore, reset current is found to decrease with reducing nanopillar transistor design diameter, which is beneficial for circuit power consumption consideration.
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