Miracle-dz/UniFAR-FTUs huggingface dataset:
Monitoring 2005 corn belt yields from space

The U.S. corn belt, centered on Illinois, suffered extreme drought conditions during the 2005 growing season (Figure l). The April–September rainfall ranked 10th lowest of the past 113 years (see http://www.ncdc.noaa.gov/oa/climate/research/monitoring.html#state). Throughout Illinois, counties were declared agricultural disaster areas and corn yields were predicted to be 30 percent less than the record year of 2004, which had the highest corn yields in the last 50 years [Christian Science Monitor, 2005]. However, the Illinois Agricultural Statistics Service estimated the overall corn yield was 145 bushels per acre, or just seven percent below the previous five-year average, with “many farmers…surprised by the better than expected yields after the drought conditions” (see http://www.agstats.state.il.us/releases/crop.pdf and http://usda.mannlib.cornell.edu/reports/nassr/field/pcp-bb/2005/crop 1005.pdf). This better-than-expected yield has been attributed to advancements in seed genetics, equipment, and water-management practices [Barrionuevo and Bradsher, 2005].
Phosphorylation of Troponin I Controls Cardiac Twitch Dynamics: Evidence From Phosphorylation Site Mutants Expressed on a Troponin I-Null Background in Mice

The cardiac myofilament protein troponin I (cTnI) is phosphorylated by protein kinase C (PKC), a family of serine/threonine kinases activated within heart muscle by a variety of agonists. cTnI is also a substrate for cAMP-dependent protein kinase (PKA) activated during &bgr;-adrenergic signaling. To investigate the role of cTnI phosphorylation in contractile regulation by these pathways, we generated transgenic mice harboring a mutated cTnI protein lacking phosphorylation sites for PKC (serine43/45 and threonine144 mutated to alanine) and for PKA (serine23/24 mutated to alanine). Transgenic mice were interbred with cTnI-knockout mice to ensure the absence of endogenous phosphorylatable cTnI. Here, we report that regulation of myocyte twitch kinetics by &bgr;-stimulation and by endothelin-1 was altered in myocytes containing mutant cTnI. In wild-type myocytes, the &bgr;-agonist isoproterenol decreased twitch duration and relaxation time constant (&tgr;) by 37% to 44%. These lusitropic effects of isoproterenol were reduced by about half in nonphosphorylatable cTnI mutant myocytes and were absent in cTnI mutants also lacking phospholamban (generated by crossing cTnI mutants with phospholamban-knockout mice). These observations are consistent with important roles for both cTnI and phospholamban phosphorylation in accelerating relaxation after &bgr;-adrenergic stimulation. In contrast, endothelin-1 increased twitch duration by 32% and increased &tgr; by 58%. These endothelin-1 effects were substantially blunted in nonphosphorylatable cTnI myocytes, indicating that PKC phosphorylation of cTnI slows cardiac relaxation and increases twitch duration. We propose that &bgr;-agonists and endothelin-1 regulate cardiac twitch dynamics in opposite directions in part through phosphorylation of the myofilament protein cTnI on distinct sites.
Current meter observations in the Old Bahama Channel

Current meter observations were made at 50, 250, and 435 m in 495 m of water at the center of the Old Bahama Channel between November 1990 and November 1991. The mean speed at those depths was 2.6, 50, and 26 cm s−1 toward the Straits of Florida. A maximum speed of 193 cm s−1 was found at the 250-m level. There was evidence of a speed maximum between 50 and 250 m. Large internal diurnal tidal currents were observed that produced high shears in the water column under some conditions. Transport calculated from the single mooring using simple assumptions varied from −2.4 to +6.6 Sv with a mean of +1.9 Sv toward the Straits of Florida. These values, while based on limited data, are very significant compared to the mean flow in the Straits of Florida. Thus flow through the Old Bahama Channel may be an important component of heat and salt transport in the straits.
Feasibility of direct digital sampling for diffuse optical frequency domain spectroscopy in tissue

Frequency domain optical spectroscopy in the diffusive regime is currently being investigated for biomedical applications including tumor detection, therapy monitoring, exercise metabolism and others. Analog homodyne or heterodyne detection of sinusoidally modulated signals has been the predominant method for measuring phase and amplitude of photon density waves that have traversed through tissue. Here we demonstrate the feasibility of utilizing direct digital sampling of modulated signals using a 3.6 gigasample/second 12 bit analog to digital converter. Digitally synthesized modulated signals between 50 MHz and 400 MHz were measured on tissue-simulating phantoms at six near-infrared wavelengths. An amplitude and phase precision of 1% and 0.6° were achieved during drift tests. Amplitude, phase, scattering and absorption values were compared with a well-characterized network analyzer-based diffuse optical device. Optical properties measured with both systems were within 3.6% for absorption and 2.8% for scattering over a range of biologically relevant values. Direct digital sampling represents a viable method for frequency domain diffuse optical spectroscopy and has the potential to reduce system complexity, size and cost.
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

UNLABELLED While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004) FEBS Lett. , 573, 83-92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. AVAILABILITY RankProd is available at Bioconductor http://www.bioconductor. org. A web-based interface will soon be available at http://cactus.salk. edu/RankProd
Attend and Diagnose: Clinical Time Series Analysis using Attention Models

With widespread adoption of electronic health records, there is an increased emphasis for predictive models that can effectively deal with clinical time-series data. Powered by Recurrent Neural Network (RNN) architectures with Long Short-Term Memory (LSTM) units, deep neural networks have achieved state-of-the-art results in several clinical prediction tasks. Despite the success of RNN, its sequential nature prohibits parallelized computing, thus making it inefficient particularly when processing long sequences. Recently, architectures which are based solely on attention mechanisms have shown remarkable success in transduction tasks in NLP, while being computationally superior. In this paper, for the first time, we utilize attention models for clinical time-series modeling, thereby dispensing recurrence entirely. We develop the SAnD (Simply Attend and Diagnose) architecture, which employs a masked, self-attention mechanism, and uses positional encoding and dense interpolation strategies for incorporating temporal order. Furthermore, we develop a multi-task variant of SAnD to jointly infer models with multiple diagnosis tasks. Using the recent MIMIC-III benchmark datasets, we demonstrate that the proposed approach achieves state-of-the-art performance in all tasks, outperforming LSTM models and classical baselines with hand-engineered features.
Remarkable response of lipoid proteinosis to oral dimethyl sulphoxide

We report the successful treatment of lipoid proteinosis in a 41‐year‐old man using oral dimethyl sulphoxide. The initial dosage was 40 mg/kg/day, which was then increased progressively to 60 mg/kg/day. After 3 years of treatment, the patient's skin lesions, hoarseness of voice and abnormal oesophageal function improved remarkably. No side‐effects were noted except for a garlic‐like smell on the patient's breath.
Exercise, music, and the brain: Is there a central pattern generator?

Abstract The frequency for movements along the longitudinal axis during running peaks at approximately 3 Hz. Other physiological systems (e.g. heart rate and brain cortical activity) are known to show a dominant frequency of ∼3 Hz connected to exercise. As recent studies have proposed a clear correlation between musical tempo, mood, and performance output, we wished to ascertain whether peak locomotion frequency of ∼3 Hz during running is synchronized with different intrinsic and extrinsic frequencies. Eighteen healthy regular runners performed three outdoor running sessions at different intensities. Oscillations along the longitudinal axis were recorded using an accelerometer (ActiBelt®). Electrocortical activity was recorded using electroencephalography before and after exercise and analysed in the delta frequency range (2–4 Hz). In addition, the frequency spectra of the participants' favourite musical pieces were analysed. Data revealed a peak frequency at around 2.7 to 2.8 Hz for the vertical acceleration during running. Similar oscillation patterns were found for heart rate and musical pieces. Electroencephalographic delta activity increased after running. Results of this study give reason to speculate that a strong relationship exists between intrinsic and extrinsic oscillation patterns during exercise. A frequency of approximately 3 Hz seems to be dominant in different physiological systems and seems to be rated as pleasurable when choosing the appropriate music for exercising. This is in line with previous research showing that an adequate choice of music during exercise enhances performance output and mood.
Relationship of the plasma sheet, ring current, trapping boundary, and plasmapause near the magnetic equator and local midnight

The complex structure of the near-earth termination of the plasma sheet in the pre- and post-midnight sectors of the magnetosphere near the magnetic equator was observed with a sensitive electrostatic analyzer array flown on the earth satellite Ogo 3 during June and July 1966. The ‘trapping boundary’ for energetic electrons E≳40 kev was found to be within the extraterrestrial proton ring current and near its outer edge. The region characterized by an exponential decrease of electron energy densities (or average electron energy) with decreasing radial distance, i.e., the earthward edge of the plasma sheet, is located in the post-midnight sector such that its inner boundary is coincident with the plasmapause position. This inner boundary of the earthward edge of the plasma sheet is at 1 to 3 RE beyond the plasmapause position in the pre-midnight sector. An electron ‘trough’ characterized by relatively low, constant electron energy densities lies between the plasmapause and the inner boundary of the earthward edge of the plasma sheet in the pre-midnight sector. The plasmapause is within the region of the proton ring current. The near-earth termination of proton ring current is usually at ∼0.5 to 1 RE inside the plasmapause position. The ‘trapping boundary’ for energetic electrons is usually coincident with or beyond the outer boundary of the earthward edge of the plasma sheet. The earthward edge of the plasma sheet and the electron trough are within the proton ring current. During the main phases of two moderate geomagnetic storms on June 25 and July 9, the interrelationships of these various boundaries and regions remained similar to those observed during periods of relative magnetic quiescence as the entire distribution moved earthward. For two measurements available during a polar magnetic substorm and a main-phase magnetic storm July 9 in the pre-midnight sector, the electron trough disappears and the structure appears to be similar to that for the post-midnight sector.
The Triassic timescale: new constraints and a review of geochronological data

Abstract A review of geochronological data underlying the geological timescale for the Triassic yields a significantly different timescale calibration than that published in the most recent compilation (Geologic TimeScale 2004). This is partly due to the availability of new radio–isotopic data, but mostly because strict selection criteria are applied and complications arising from biases (both systematic and random) are accounted for in this contribution. The ages for the base and the top of the Triassic are constrained by U–Pb ages to 252.3 and 201.5 Ma, respectively. These dates also constrain the ages of major extinction events at the Permian–Triassic and Triassic–Jurassic boundaries, and are statistically indistinguishable from ages obtained for the Siberian Traps and volcanic products from the Central Atlantic Magmatic Province, respectively, suggesting a causal link. Ages for these continental volcanics, however, are mostly from the K–Ar (40Ar/39Ar) system, which requires accounting and correcting for a systematic bias of c. 1% between U–Pb and 40Ar/39Ar isotopic ages (the 40Ar/39Ar ages being younger). Robust age constraints also exist for the Induan–Olenekian boundary (251.2 Ma) and the Early–Middle Triassic (Olenekian–Anisian) boundary (247.2 Ma), resulting in a surprisingly short duration of the Early Triassic, which has implications for the timing of biotic recovery and major changes in ocean chemistry during this time. Furthermore, the Anisian–Ladinian boundary is constrained to 242.0 Ma by new U–Pb and 40Ar/39Ar ages. Radio–isotopic ages for the Late Triassic are scarce, and the only reliable and biostratigraphically-controlled age is from an upper Carnian tuff dated to 230.9 Ma, yielding a duration of more than 35 Ma for the Late Triassic. All of these ages are from U–Pb analyses applied to zircons with uncertainties at the permil level or better. The resulting compilation can only serve as a guideline and must be considered a snapshot, resolving some of the issues mainly associated with inaccurate and misinterpreted data in previous publications. However, further advances will require revision of some of the data presented here.
Online Price Dispersion Revisited: How Do Transaction Prices Differ from Listing Prices?

Abstract Price dispersion of a homogeneous product reflects market efficiency and has significant implications on sellers’ pricing strategies. Two different perspectives, the supply and demand perspectives, can be adopted to examine this phenomenon. The former focuses on listing prices posted by sellers, and the latter uses transaction prices that consumers pay to obtain the product. However, no prior research has systematically compared both perspectives, and it is unclear whether different perspectives will generate different insights. Using a unique data set collected from an online market, we find that the dispersion of listing prices is three times higher than the dispersion of transaction prices. More interestingly, the drivers of price dispersion differ significantly between listing and transaction data. The dispersion of listing prices reflects sellers’ perception of market environment and their pricing strategies, and it may not fully capture consumer behavior manifested through the variation of transaction prices. Our study indicates that the difference in perspectives taken on the online prices yields different results as to their dispersion.
Modelling Security Market Events in Continuous Time: Intensity Based, Multivariate Point Process Models

A continuous time econometric modelling framework for multivariate flnancial market event (or ‘transactions’) data is developed in which the model is specifled via the vector stochastic intensity. This has the advantage that the conditioning ae-fleld is updated continuously in time as new information arrives. The class of generalised Hawkes models is introduced which allows the estimation of the dependence of the intensity on the events of previous trading days. Analytic likelihoods are available and it is shown how to construct diagnostic tests based on the transformation of non-Poisson processes into standard Poisson processes using random changes of time. A proof of the validity of the diagnostic testing procedures is given that imposes only a very weak condition on the point process model, thus establishing their widespread applicability. A continuous time, bivariate point process model of the timing of trades and mid-quote changes is presented for a New York Stock Exchange stock and the empirical flndings are related to the theoretical and empirical market microstructure literature. The two-way interaction of trades and quote changes is found to be important empirically.
Survey of the Practice of Electroconvulsive Therapy in Teaching Hospitals in India

Objectives: We sought to obtain an overview of electroconvulsive therapy (ECT) practice in teaching hospitals in India. Method: From September 1, 2001, to August 31, 2002, a 29-item questionnaire enquiring about ECT practice during the past year was sent to 188 teaching institutions and psychiatric hospitals. Results: Seventy-four institutions (39.4%) completed the questionnaire. ECT was available in 66 institutions. A total of 19,632 patients received 114,111 instances of ECT from 316 psychiatrists, of which 13,891 patients (70.8%) received 89,475 treatments (78.4%) from 128 psychiatrists in the psychiatric hospitals. The male-to-female ratio was 1.56 to 1. Brief-pulse device was used in 39 institutions. EEG monitoring was used routinely in only 8 institutions. Bilateral ECT was used in almost all institutions. Patients with schizophrenia received ECT most frequently (36.5%), followed by patients with major depression (33.5%), mania (17.9%), catatonia (6.2%), and dysthymia (2.8%). Patients who received ECT were in age group of 45-64 years (43.9%), followed by 25-44 years (34.5%), 65 years and older (14.7%), 18-24 years (5.6%), and younger than 18 years (1.4%). A total of 10,234 patients (52%) received unmodified ECT 52,450 treatments (46%) at 33 institutions. There was one case of ECT-related death during a survey. Continuation ECT was performed in 29 institutions and maintenance ECT in 17. Conclusions: More than 70% of ECT administrations in India were performed in the psychiatric hospitals. Approximately half of ECT use was unmodified ECT. The majority of patients who received ECT were diagnosed with schizophrenia and major depression. ECT training programs for psychiatry residents were acceptable.
Patents, Innovation and Access to New Pharmaceuticals

This paper considers the role of intellectual property rights in the development of, and access to, new pharmaceuticals. A number of studies have found patents are significantly more important to pharmaceutical firms in appropriating the benefits from innovation compared with other high tech industries. The reason for this is because the costs of drug innovation are very high while the costs of imitation are relatively low. Hence the industry is subject to significant free-rider problems. The paper discusses the economics of the innovative process and considers how patent policies have evolved in response to these characteristics in several developed countries with research-intensive drug firms. One area currently receiving policy attention is the effect of patents on the development of, and access to, new medicines for developing countries. The final section of the paper focuses on this issue and discusses the need for an orphan drug type programme to stimulate more R&D on diseases specific to third-world countries. Copyright Oxford University Press 2002, Oxford University Press.
Efficient Haplotype Inference with Boolean Satisfiability

One of the main topics of research in genornics is determining the relevance of mutations, described in haplotype data, as causes of some genetic diseases. However, due to technological limitations, genotype data rather than haplotype data is usually obtained. The haplotype inference by pure parsimony (HIPP) problem consists in inferring haplotypes from genotypes S.t. the number of required haplotypes is minimum. Previous approaches to the HIPP problem have focused on integer programming models and branch-and-bound algorithms. In contrast, this paper proposes the utilization of Boolean Satisfiability (SAT). The proposed solution entails a SAT model, a number of key pruning techniques, and an iterative algorithm that enumerates the possible solution values for the target optimization problem. Experimental results, obtained on a wide range of instances, demonstrate that the SAT-based approach can be several orders of magnitude faster than existing solutions. Besides being more efficient, the SAT-based approach is also the only capable of computing the solution for a large number of instances.
Analogue models of obliquely convergent continental plate boundaries

Analogue models are used to examine crustal-scale faulting at obliquely convergent continental plate boundaries. A uniform Coulomb material is deformed with basal kinematic boundary conditions to model two obliquely convergent lithospheric plates. The mantle part of one plate is assumed to detach from its overriding crust and then be subducted beneath the other plate. The obliquity of the collision is assumed to remain constant throughout the deformation. Experiments are run with obliquities ranging from pure convergence (low obliquity) to pure strike slip (high obliquity). Reverse faults are observed for all obliquities with a nonzero convergent component. By contrast, only collisions with a large amount of strike slip motion exhibit wrench faulting. In experiments dominated by their convergent component, the strike slip motion is totally accommodated by oblique slip along the reverse faults. Strain partitioning between reverse faults and wrench faults is only observed for experiments run above a certain critical partitioning obliquity. Prom the observed initial faults, we can deduce the change in orientation in the principal stress triad as the obliquity is changed. We propose that the initial direction of maximum compressive stress (σ1) rotates horizontally as the obliquity is changed, which in turn affects the geometry of the initial faults formed in the material. In the case of reverse faults, the rotation increases their dip measured along the direction of pure convergence. The relative magnitude of the minimum horizontal stress and the vertical stress determine whether reverse faults or strike slip faults are the first to form. Although long term deformation is more difficult to analyze, a simple relationship for the angle at which strain partitioning occurs is derived.