Miracle-dz/UniFAR-FTUs huggingface dataset:
Agricultural landscape simplification and insecticide use in the Midwestern United States

Agronomic intensification has transformed many agricultural landscapes into expansive monocultures with little natural habitat. A pervasive concern is that such landscape simplification results in an increase in insect pest pressure, and thus an increased need for insecticides. We tested this hypothesis across a range of cropping systems in the Midwestern United States, using remotely sensed land cover data, data from a national census of farm management practices, and data from a regional crop pest monitoring network. We found that, independent of several other factors, the proportion of harvested cropland treated with insecticides increased with the proportion and patch size of cropland and decreased with the proportion of seminatural habitat in a county. We also found a positive relationship between the proportion of harvested cropland treated with insecticides and crop pest abundance, and a positive relationship between crop pest abundance and the proportion cropland in a county. These results provide broad correlative support for the hypothesized link between landscape simplification, pest pressure, and insecticide use. Using regression coefficients from our analysis, we estimate that, across the seven-state region in 2007, landscape simplification was associated with insecticide application to 1.4 million hectares and an increase in direct costs totaling between $34 and $103 million. Both the direct and indirect environmental costs of landscape simplification should be considered in design of land use policy that balances multiple ecosystem goods and services.
Marine Ecosystem Responses to Cenozoic Global Change

The future impacts of anthropogenic global change on marine ecosystems are highly uncertain, but insights can be gained from past intervals of high atmospheric carbon dioxide partial pressure. The long-term geological record reveals an early Cenozoic warm climate that supported smaller polar ecosystems, few coral-algal reefs, expanded shallow-water platforms, longer food chains with less energy for top predators, and a less oxygenated ocean than today. The closest analogs for our likely future are climate transients, 10,000 to 200,000 years in duration, that occurred during the long early Cenozoic interval of elevated warmth. Although the future ocean will begin to resemble the past greenhouse world, it will retain elements of the present “icehouse” world long into the future. Changing temperatures and ocean acidification, together with rising sea level and shifts in ocean productivity, will keep marine ecosystems in a state of continuous change for 100,000 years.
Does Separation of Powers Promote Stability and Moderation?

It is often asserted that separation of legislative powers tends to make legislation both more moderate (because concessions to all veto players are needed to secure enactment) and less frequent (because sufficient concessions are sometimes infeasible). The formal analysis in this article shows this claim to be incomplete and sometimes incorrect. Although greater separation of powers makes legislation more difficult to enact, it also makes legislation, once enacted, more difficult to repeal. Attenuating the threat of repeal means that when one faction has sufficient power to push through extreme policies, it is more likely to do so than would be the case if legislative power were more concentrated. These two effects cut in opposite directions, and it is difficult to say, as a general matter, which will predominate. Indeed, increasing the fragmentation of legislative power may sometimes increase both the expected frequency and the expected extremism of legislative enactments.
Gene Expression of Parathyroid Tumors

Parathyroid tumors are heterogeneous, and diagnosis is often difficult using histologic and clinical features. We have undertaken expression profiling of 53 hereditary and sporadic parathyroid tumors to better define the molecular genetics of parathyroid tumors. A class discovery approach identified three distinct groups: (1) predominantly hyperplasia cluster, (2) HRPT2/carcinoma cluster consisting of sporadic carcinomas and benign and malignant tumors from Hyperparathyroidism-Jaw Tumor Syndrome patients, and (3) adenoma cluster consisting mainly of primary adenoma and MEN 1 tumors. Gene sets able to distinguish between the groups were identified and may serve as diagnostic biomarkers. We demonstrated, by both gene and protein expression, that Histone 1 Family 2, amyloid β precursor protein, and E-cadherin are useful markers for parathyroid carcinoma and suggest that the presence of a HRPT2 mutation, whether germ-line or somatic, strongly influences the expression pattern of these 3 genes. Cluster 2, characterized by HRPT2 mutations, was the most striking, suggesting that parathyroid tumors with somatic HRPT2 mutation or tumors developing on a background of germ-line HRPT2 mutation follow pathways distinct from those involved in mutant MEN 1-related parathyroid tumors. Furthermore, our findings likely preclude an adenoma to carcinoma progression model for parathyroid tumorigenesis outside of the presence of either a germ-line or somatic HRPT2 mutation. These findings provide insights into the molecular pathways involved in parathyroid tumorigenesis and will contribute to a better understanding, diagnosis, and treatment of parathyroid tumors.
MMSE precoder for unitary space-time codes in correlated time-varying channels

This letter addresses the problem of the design of a precoder for multiple transmit antenna communication systems with spatially and temporally correlated fading channels. By using the asymptotic (high signal-to-noise ratio) mean-square error of the channel estimates, the letter derives a precoder for unitary space-time codes that can exploit the spatiotemporal correlation in the time-varying fading channels. Simulation results illustrate that significant performance gains can be achieved by using the new precoder.
Nonlinear Optimal Control Design Considering a Class of System Constraints With Validation on a Magnetic Levitation System

In this letter, based on the theory developed, a nonlinear optimal controller is designed via stable manifold theory making use of Lagrange multipliers to take into account a class of system constraints. A feature of this method is that a discontinuous Hamiltonian system has to be solved. The existence and uniqueness of solutions of the Hamiltonian system are proven in this letter with a discussion on the stability of the designed controller. The effectiveness of the method is experimentally validated on a Quanser magnetic levitation system. The result shows that the designed nonlinear controller is able to handle the acceleration constraints with better control performance compared with the linear optimal one.
Analysis of chattering in continuous sliding-mode controllers

An analysis of two most popular continuous sliding-mode algorithms: The power-fractional sliding-mode algorithm and a second-order sliding-mode algorithm known as the super-twisting is carried out in the frequency domain with the use of the describing function method. It is shown that in the presence of an actuator, the transient process converges to a periodic motion. Parameters of this periodic motion are analyzed. A few examples are considered to illustrate the obtained results.
Using Provenance for Repeatability

We present Provenance-To-Use (PTU), a tool that minimizes computation time during repeatability testing. Authors can use PTU to build a package that includes their software program and a provenance trace of an initial reference execution. Testers can select a subset of the package's processes for a partial deterministic replay---based, for example, on their compute, memory and I/O utilization as measured during the reference execution. Using the provenance trace, PTU guarantees that events are processed in the same order using the same data from one execution to the next. We show the efficiency of PTU for conducting repeatability testing of workflow-based scientific programs.
Cellular adaptation to hypoxia: O2‐sensing protein hydroxylases, hypoxia‐inducible transcription factors, and O2‐regulated gene expression

Although it was known for a long time that oxygen deprivation leads to the transcriptional induction of the gene encoding erythropoietin, the molecular mechanisms behind this process remained enigmatic. The cloning of the hypoxia‐inducible factors (HIFs), the finding that HIF‐1 regulates the expression of many more genes apart from erythropoietin, and the elucidation of the oxygen‐dependent mechanisms degrading the HIF a subunits recently led to the spectacular discovery of the molecular principles of oxygen sensing. This review aims to summarize our current knowledge of oxygen‐regulated gene expression. —Wenger, R. H. Cellular adaptation to hypoxia: O2‐sensing protein hydroxylases, hypoxia‐inducible transcription factors, and O2‐regulated gene expression. FASEB J. 16, 1151–1162 (2002)
A survey of preoperative blood tests in primary open-angle glaucoma patients versus cataract surgery patients.

PURPOSE To investigate biomarker differences in routine preoperative blood tests performed on primary open-angle glaucoma (POAG) case and control patients presenting for anterior segment eye surgery. METHODS POAG cases and age-related cataract surgery patients (controls) who underwent anterior segment surgery at Massachusetts Eye and Ear from January 2009 through March 2012 were identified by retrospective record review. Patients with diabetes mellitus, secondary glaucoma, and cataract due to trauma or steroid exposure were excluded. Data on demographic features, preoperative ophthalmological and medical diagnosis, blood pressure, anthropometric measures, basic metabolic panel, and complete blood count were extracted from the medical records. Univariate differences in lab values between POAG cases and controls were assessed using unpaired t tests. Multivariate logistic regression analysis was completed to determine the independent associations of biomarkers with POAG. RESULTS A total of 150 cases and 150 age-related controls were included. In multivariate analysis, higher AG was inversely associated with POAG (odds ratio [OR] = 0.90; 95% confidence interval [CI], 0.80-1.00), and higher Cl- level was positively associated with POAG (OR = 1.15; 95% CI, 1.02-1.29). The lower AG in POAG patients could be explained by higher IgG levels as the available data in post hoc analysis showed a nonsignificant trend toward higher IgG in cases compared to controls (17 vs 23; 1142 ± 284 mg/dl vs 1028 ± 291 mg/dl; P = 0.22). Furthermore, in multivariable analysis, a higher red blood cell count was also associated with POAG (OR = 1.91; 95% CI, 1.11-3.28). CONCLUSIONS Patients with POAG presenting for anterior segment surgery had a lower AG compared to age-related cataract surgery patients. The etiology of this reduced gap is unclear but the possible contribution of IgG warrants further exploration. The etiology of higher red blood cell counts in POAG cases is unknown and deserves further exploration.
Large scale evaluation of corpus-based synthesizers: results and lessons from the blizzard challenge 2005

The Blizzard Challenge 2005 was a large scale international evaluation of various corpus-based speech synthesis systems using common datasets. Six sites from around the world, both academic and industrial, participated in this evaluation, the first ever to compare voices built by different systems using the same data. Here we describe results of the evaluation and many of the observations and lessons discovered in carrying it out.
Predictive Power Conservation based on the Idle Time Pattern from Disk Access Data

We examined the power consumption of various dynamic disk spindown policies with the goal to save energy for mobile computing. Based on a trace from HP Laboratories, we find that the proposed adaptive 2-competitve algorithm can outperform the share algorithm by 15% or so when the disk spindown cost is low. The relative power performance of different disk spindown techniques are presented and compared. We focus on algorithms that explicitly exploit the burst nature of disk access pattern.
Profiling in Policy and Practice

Analyzing the system of offender profiling, this book takes into consideration the quality and validity of the information on which police base their decisions, assessing the possibilities for detecting deception. The consistencies of a criminal's behaviour are also studied, with a look at the differences between one offender and another. Other questions asked include what form such groups take and the influence they have on trhe criminal's actions, the role of leaders in crimes or the socio-cultural processes of which they are a part. There are also imortant issues about the implications and use of any answers that may emerge from scientific studies of crimes and their investigation.
Analytical Design Method of Brachiation Controller on the Irregular Ladder

In this paper, we present the control method to achieve the continuous brachiation on the irregular ladder. The uniform ladder problem was solved by means of symmetric property previously. However, as for the irregular ladder problem, it's impossible to build the controller based on symmetric property since the motion cannot be designed symmetrically. Therefore, it is necessary to estimate the energy difference caused by symmetry breaking. We apply passive dynamic autonomous control (PDAC), which was proposed previously, to the locomotion action and evaluate the energy difference. Swing motion is adjusted so as to satisfy the desired energy calculated from the energy difference. The validity of proposed method is tested by the experiment of Gorilla Robot III and the irregular ladder brachiation is realized
Importance of Correlation between Gene Expression Levels: Application to the Type I Interferon Signature in Rheumatoid Arthritis

Background The analysis of gene expression data shows that many genes display similarity in their expression profiles suggesting some co-regulation. Here, we investigated the co-expression patterns in gene expression data and proposed a correlation-based research method to stratify individuals. Methodology/Principal Findings Using blood from rheumatoid arthritis (RA) patients, we investigated the gene expression profiles from whole blood using Affymetrix microarray technology. Co-expressed genes were analyzed by a biclustering method, followed by gene ontology analysis of the relevant biclusters. Taking the type I interferon (IFN) pathway as an example, a classification algorithm was developed from the 102 RA patients and extended to 10 systemic lupus erythematosus (SLE) patients and 100 healthy volunteers to further characterize individuals. We developed a correlation-based algorithm referred to as Classification Algorithm Based on a Biological Signature (CABS), an alternative to other approaches focused specifically on the expression levels. This algorithm applied to the expression of 35 IFN-related genes showed that the IFN signature presented a heterogeneous expression between RA, SLE and healthy controls which could reflect the level of global IFN signature activation. Moreover, the monitoring of the IFN-related genes during the anti-TNF treatment identified changes in type I IFN gene activity induced in RA patients. Conclusions In conclusion, we have proposed an original method to analyze genes sharing an expression pattern and a biological function showing that the activation levels of a biological signature could be characterized by its overall state of correlation.
A Convex Formulation for Learning from Crowds

Recently crowdsourcing services are often used to collect a large amount of labeled data for machine learning, since they provide us an easy way to get labels at very low cost and in a short period. The use of crowdsourcing has introduced a new challenge in machine learning, that is, coping with the variable quality of crowd-generated data. Although there have been many recent attempts to address the quality problem of multiple workers, only a few of the existing methods consider the problem of learning classifiers directly from such noisy data. All these methods modeled the true labels as latent variables, which resulted in non-convex optimization problems. In this paper, we propose a convex optimization formulation for learning from crowds without estimating the true labels by introducing personal models of the individual crowd workers. We also devise an efficient iterative method for solving the convex optimization problems by exploiting conditional independence structures in multiple classifiers. We evaluate the proposed method against three competing methods on synthetic data sets and a real crowdsourced data set and demonstrate that the proposed method outperforms the other three methods.
Dock3 regulates BDNF‐TrkB signaling for neurite outgrowth by forming a ternary complex with Elmo and RhoG

Dock3, a new member of the guanine nucleotide exchange factor family, causes cellular morphological changes by activating the small GTPase Rac1. Overexpression of Dock3 in neural cells promotes neurite outgrowth through the formation of a protein complex with Fyn and WAVE downstream of brain‐derived neurotrophic factor (BDNF) signaling. Here, we report a novel Dock3‐mediated BDNF pathway for neurite outgrowth. We show that Dock3 forms a complex with Elmo and activated RhoG downstream of BDNF‐TrkB signaling and induces neurite outgrowth via Rac1 activation in PC12 cells. We also show the importance of Dock3 phosphorylation in Rac1 activation and show two key events that are necessary for efficient Dock3 phosphorylation: membrane recruitment of Dock3 and interaction of Dock3 with Elmo. These results suggest that Dock3 plays important roles downstream of BDNF signaling in the central nervous system where it stimulates actin polymerization by multiple pathways.
Dopamine D2-like Receptors Are Expressed in Pancreatic Beta Cells and Mediate Inhibition of Insulin Secretion*

Dopamine signaling is mediated by five cloned receptors, grouped into D1-like (D1 and D5) and D2-like (D2, D3 and D4) families. We identified by reverse transcription-PCR the presence of dopamine receptors from both families in INS-1E insulin-secreting cells as well as in rodent and human isolated islets. D2 receptor expression was confirmed by immunodetection revealing localization on insulin secretory granules of INS-1E and primary rodent and human beta cells. We then tested potential effects mediated by the identified receptors on beta cell function. Dopamine (10 μm) and the D2-like receptor agonist quinpirole (5 μm) inhibited glucose-stimulated insulin secretion tested in several models, i.e. INS-1E beta cells, fluorescence-activated cell-sorted primary rat beta cells, and pancreatic islets of rat, mouse, and human origin. Insulin exocytosis is controlled by metabolism coupled to cytosolic calcium changes. Measurements of glucose-induced mitochondrial hyperpolarization and ATP generation showed that dopamine and D2-like agonists did not inhibit glucose metabolism. On the other hand, dopamine decreased cell membrane depolarization as well as cytosolic calcium increases evoked by glucose stimulation in INS-1E beta cells. These results show for the first time that dopamine receptors are expressed in pancreatic beta cells. Dopamine inhibited glucose-stimulated insulin secretion, an effect that could be ascribed to D2-like receptors. Regarding the molecular mechanisms implicated in dopamine-mediated inhibition of insulin release, our results point to distal steps in metabolism-secretion coupling. Thus, the role played by dopamine in glucose homeostasis might involve dopamine receptors, expressed in pancreatic beta cells, modulating insulin release.
Automatic Pose Recovery for High-Quality Textures Generation

This paper proposes new techniques to generate high quality textures for urban building models by automatic camera calibration and pose recovery. The camera pose is decomposed into an orientation and a translation, an edge error model and knowledge-based filters are used to estimate correct vanishing points with heavy trees occlusion, and the vanishing points are used for the camera calibration and orientation estimation. We propose new techniques to estimate the camera orientation with infinite vanishing points and translation with under-constraints. The final textures are generated using color calibration and blending with the recovered pose. A number of textures for outdoor buildings are automatically generated, which shows the effectiveness of our algorithms
Multi-camera visual odometry for skid steered field robot

Position estimation using wheel odometric systems tends to give rather poor performances for an outdoor four-wheel skid steered mobile robot. Therefore autonomous control of these vehicles is extremely challenging in outdoor environments. This paper describes an outdoor localization system based on visual odometry for skid steered vehicle using forward faced camera and a downward faced camera. Optical flow field data is statistically analyzed to correctly estimate the position of the robot. Kalman Filtering is used to fuse data from two cameras for optimum performance. Also real-time Instantaneous Center of Rotation (ICR) detection using optical flow field data is proposed to calculate the heading angle. Two consumer grade cameras were used and algorithm was tested using open source image processing libraries. The proposed system yielded an acceptable positioning accuracy on short runs in typical outdoor terrains.
Matrix Metalloproteinase‐3 Genotype Contributes to Age‐Related Aortic Stiffening Through Modulation of Gene and Protein Expression

Abstract —Matrix metalloproteinases (MMPs) include most major constituents of the arterial wall as substrates. A common promotor polymorphism (5A/6A) is associated with differences in MMP‐3 (stromelysin‐1) activity, and associations with certain forms of vascular disease have been shown. This study investigated whether the MMP‐3 5A/6A promoter polymorphism contributes to age‐related large artery stiffening. MMP‐3 5A/6A genotype was determined in 203 (135 male) low cardiovascular risk, unmedicated individuals who were divided prospectively into two groups (30 to 60 years, n=126; ≥61 years, n=77). Noninvasive large artery stiffness was measured as ascending aortic input impedance from brachial blood pressure, carotid tonometry, and Doppler ascending aortic blood flow. In the older group, homozygotes had higher aortic input (P<0.01) and characteristic (P<0.01) impedance, ie, higher stiffness, than heterozygotes after correction for the effects of age, gender, and mean arterial pressure. There was no such difference in the younger group. Gene expression was subsequently investigated in dermal biopsies in randomly selected older men from the same cohort with real‐time PCR (n=40). In 5A homozygotes, gene expression was 4‐fold higher (P<0.05), and in 6A homozygotes, 2‐fold lower (P<0.05) compared with the heterozygotes. Differences in gene expression were associated with corresponding significant changes in MMP‐3 protein levels. Concordance between dermal and aortic gene and protein expression was shown in a separate cohort of postmortem aortic samples (n=7). We conclude that MMP‐3 genotype may be an important determinant of vascular remodeling and age‐related arterial stiffening, with the heterozygote having the optimal balance between matrix accumulation and deposition. (Circ Res. 2003;92:1254–1261.)