Miracle-dz/UniFAR-FTUs huggingface dataset:
Coral-model comparison highlighting the role of salinity in long-term trends

Diane M. ThoMpson1, T.R. aulT1, M.n. evans2,1, J.e. Cole1,3, J. eMile-Geay4, a.n. leGRanDe5 Department of Geosciences, University of Arizona, Tucson, USA; thompsod@email.arizona. edu Department of Geology and Earth System Science Interdisciplinary Center, University of Maryland, College Park, USA; Department of Atmospheric Sciences, University of Arizona, Tucson; USA; Department of Earth Sciences, University of Southern California, Los Angeles, USA; NASA Goddard Institute for Space Studies and Center for Climate Systems Research, Columbia University, New York, USA
Small Molecule Therapeutics Combined MET Inhibition and Topoisomerase I Inhibition Block Cell Growth of Small Cell Lung Cancer

Small cell lung cancer (SCLC) is a devastating disease, and current therapies have not greatly improved the 5-year survival rates. Topoisomerase (Top) inhibition is a treatment modality for SCLC; however, the response is short lived. Consequently, our research has focused on improving SCLC therapeutics through the identification of novel targets. Previously, we identified MNNG HOS transforming gene (MET) to be overexpressed and functional in SCLC. Herein, we investigated the therapeutic potential of combinatorial targeting of MET using SU11274 and Top1 using 7-ethyl-10-hydroxycamptothecin (SN-38). MET and TOP1 gene copynumbers andprotein expressionwere determined in 29patientswith limited (n1⁄4 11) and extensive (n 1⁄4 18) disease. MET gene copy number was significantly increased (>6 copies) in extensive disease compared with limited disease (P 1⁄4 0.015). Similar TOP1 gene copy numbers were detected in limited and extensive disease. Immunohistochemical staining revealed a significantly higher Top1 nuclear expression in extensive (0.93) versus limited (0.15) disease (P 1⁄4 0.04). Interestingly, a significant positive correlation was detected betweenMET gene copy number and Top1 nuclear expression (r 1⁄4 0.5). In vitro stimulation of H82 cells revealed hepatocyte growth factor (HGF)–induced nuclear colocalization of p-MET and Top1. Furthermore, activation of the HGF/MET axis enhanced Top1 activity, which was abrogated by SU11274. Combination of SN-38 with SU11274 dramatically decreased SCLC growth as compared with either drug alone. Collectively, these findings suggest that the combinatorial inhibition of MET and Top1 is a potentially efficacious treatment strategy for SCLC. Mol Cancer Ther; 13(3); 1–9. 2013 AACR.
Automated manifold surgery: constructing geometrically accurate and topologically correct models of the human cerebral cortex

Highly accurate surface models of the cerebral cortex are becoming increasingly important as tools in the investigation of the functional organization of the human brain. The construction of such models is difficult using current neuroimaging technology due to the high degree of cortical folding. Even single voxel mis-classifications can result in erroneous connections being created between adjacent banks of a sulcus, resulting in a topologically inaccurate model. These topological defects cause the cortical model to no longer be homeomorphic to a sheet, preventing the accurate inflation, flattening, or spherical morphing of the reconstructed cortex. Surface deformation techniques can guarantee the topological correctness of a model, but are time-consuming and may result in geometrically inaccurate models. In order to address this need the authors have developed a technique for taking a model of the cortex, detecting and fixing the topological defects while leaving that majority of the model intact, resulting in a surface that is both geometrically accurate and topologically correct.
Supporting collaborative interpretation in distributed Groupware

Collaborative interpretationoccurs when a group interprets and transforms a diverse set of information fragments into a coherent set of meaningful descriptions. This activity is characterized byemergence, where the participants' shared understanding develops gradually as they interact with each other and the source material. Our goal is to support collaborative interpretation by small, distributed groups. To achieve this, we first observed how face-to-face groups perform collaborative interpretation in a particular work context. We then synthesized design principles from two relevant areas: the key behaviors of people engaged in activities where emergence occurs, and how distributed groups work together over visual surfaces. We built and evaluated a system that supports a specific collaborative interpretation task. This system provides a large workspace and several objects that encourages emergence in interpretation. People manipulatecardsthat contain the raw information fragments. They reduce complexity by placing duplicate cards intopiles. They suggest groupings as they manipulate the spatial layout of cards and piles. They enrich spatial layouts throughnotes, textandfreehand annotations. They record their understanding of their final groupings asreportscontaining coherent descriptions.
Led Astray by Hemoglobin A1c

Hemoglobin A1c (A1c) is used frequently to diagnose and treat diabetes mellitus. Therefore, it is important be aware of factors that may interfere with the accuracy of A1c measurements. This is a case of a rare hemoglobin variant that falsely elevated a nondiabetic patient’s A1c level and led to a misdiagnosis of diabetes. A 67-year-old male presented to endocrine clinic for further management after he was diagnosed with diabetes based on an elevated A1c of 10.7%, which is approximately equivalent to an average blood glucose of 260 mg/dL. Multiple repeat A1c levels remained >10%, but his home fasting and random glucose monitoring ranged from 92 to 130 mg/dL. Hemoglobin electrophoresis and subsequent genetic analysis diagnosed the patient with hemoglobin Wayne, a rare hemoglobin variant. This variant falsely elevates A1c levels when A1c is measured using cation-exchange high-performance liquid chromatography. When the boronate affinity method was applied instead, the patient’s A1c level was actually 4.7%. Though hemoglobin Wayne is clinically silent, this patient was erroneously diagnosed with diabetes and started on an antiglycemic medication. Due to this misdiagnosis, the patient was at risk of escalation in his “diabetes management” and hypoglycemia. Therefore, it is important that providers are aware of factors that may result in hemoglobin A1c inaccuracy including hemoglobin variants.
An active search strategy for efficient object class detection

Object class detectors typically apply a window classifier to all the windows in a large set, either in a sliding window manner or using object proposals. In this paper, we develop an active search strategy that sequentially chooses the next window to evaluate based on all the information gathered before. This results in a substantial reduction in the number of classifier evaluations and in a more elegant approach in general. Our search strategy is guided by two forces. First, we exploit context as the statistical relation between the appearance of a window and its location relative to the object, as observed in the training set. This enables to jump across distant regions in the image (e.g. observing a sky region suggests that cars might be far below) and is done efficiently in a Random Forest framework. Second, we exploit the score of the classifier to attract the search to promising areas surrounding a highly scored window, and to keep away from areas near low scored ones. Our search strategy can be applied on top of any classifier as it treats it as a black-box. In experiments with R-CNN on the challenging SUN2012 dataset, our method matches the detection accuracy of evaluating all windows independently, while evaluating 9× fewer windows.
Dynamic Clamp: Insights From State-of-the-Art Experimentation.

Mutations in KCNH2 (hERG) underlie the long-QT2 syndrome. Most long-QT2 mutations produce a trafficking defect resulting in a decrease in n, the number of functional channels on the cell surface. Some mutations can also alter gating characteristics. The short-QT syndrome generally relates to shifts in the voltage dependence of inactivation to more depolarized potentials results in less inward rectification at physiological potentials and a larger time-dependent current at the expense of the magnitude of the repolarizing tail current. Article see p 1265 Altomare et al1 provide conceptual advances in understanding the relative contributions of changes in gating features and gmax to action potential duration (APD) and its temporal variance. They should be congratulated for their innovative experimental approach and the interesting results. The insights that they provide seem to have clinical relevance. Altomare et al1 substituted the innate guinea pig rectifier K+ current ( I Kr) with injection of a modeled and programmable I Kr. This approach allows an assessment of the impact of programmable changes in the characteristics of I Kr on temporal variance on APD in the context of an otherwise native guinea pig cardiac action potential. This also allows requisite changes in cycle length elicited by a command potential in action potential clamp mode. They examined temporal variability in repolarization.1 Poincare plots allowed an assessment of the dynamics of the beat-to-beat variability of APD. Two metrics of beat-to-beat variability were computed: …
Primary care clinician antibiotic prescribing decisions in consultations for children with RTIs: a qualitative interview study

Background Respiratory tract infections (RTIs) are a major primary care challenge in children because they are common and costly, there is uncertainty regarding their diagnosis, prognosis, and management, and the overuse of antibiotics leads to illness medicalisation and bacterial resistance. Aim To investigate healthcare professional (HCP) diagnostic and antibiotic prescribing decisions for children with RTIs. Design and setting Semi-structured interviews conducted with 22 GPs and six nurses. HCPs were recruited from six general practices and one walk-in centre, serving a mix of deprived and affluent areas. Method Interviews were audiorecorded, transcribed, imported into NVivo 9, and analysed thematically. Results HCPs varied in the symptom and clinical examination findings used to identify children they thought might benefit from antibiotics. Their diagnostic reasoning and assessment of perceived clinical need for antibiotics used a dual process, combining an initial rapid assessment with subsequent detailed deductive reasoning. HCPs reported confidence diagnosing and managing most minor and severe RTIs. However, residual prognostic uncertainty, particularly for the intermediate illness severity group, frequently led to antibiotic prescribing to mitigate the perceived risk of subsequent illness deterioration. Some HCPs perceived a need for more paediatrics training to aid treatment decisions. The study also identified a number of non-clinical factors influencing prescribing. Conclusion Prognostic uncertainty remains an important driver of HCPs’ antibiotic prescribing. Experience and training in recognising severe RTIs, together with more evidence to help HCPs identify the children at risk of future illness deterioration, may support HCPs’ identification of the children most and least likely to benefit from antibiotics.
Graph Selection with GGMselect

Applications on inference of biological networks have raised a strong interest in the problem of graph estimation in high-dimensional Gaussian graphical models. To handle this problem, we propose a two-stage procedure which first builds a family of candidate graphs from the data, and then selects one graph among this family according to a dedicated criterion. This estimation procedure is shown to be consistent in a high-dimensional setting, and its risk is controlled by a non-asymptotic oracle-like inequality. The procedure is tested on a real data set concerning gene expression data, and its performances are assessed on the basis of a large numerical study.The procedure is implemented in the R-package GGMselect available on the CRAN.
Determination of chemical oxygen demand (COD) using ultrasound digestion and oxidation-reduction potential-based titration

A new method for determining wastewater chemical oxygen demand (COD) using ultrasonic digestion and titration based on oxidation reduction potential (ORP) was developed. COD values of potassium hydrogen phthalate solution obtained by ultrasonic digestion were well matched with those obtained using Standard Methods. When applied to determine COD of real wastewater collected from a local treatment plant, results from the new method were within 80% to 90% of those obtained using Standard Methods. Nonetheless, the proposed strategy has the potential to be implemented into an online COD analyzing system.
ICD reciprocity calibration for distributed large-scale MIMO systems with BD precoding

Time division duplexing (TDD) operation is usually used for distributed large-scale multiple-input multiple-output (MIMO) systems to perform the downlink precoding by the uplink channel estimation due to the channel reciprocity. However, the channel reciprocity is often disabled by the non-symmetric transceiver radio frequency (RF) circuits at both sides of the link. This paper is focused on the reciprocity calibration for the distributed large-scale MIMO systems where both access points (APs) and user equipments (UEs) have multiple antennas. Theoretical analysis show that RF mismatches at the UEs still bring the inter-stream interference (ISI) and lead to a significant performance loss, although with the perfect partial calibration. Then, to avoid eigenvalue decomposition (EVD) operation of the total least squares (TLS) method, an iterative algorithm named as iterative coordinate descent (ICD) method is proposed to perform the full calibration, which significantly reduces the complexity and essentially achieves the performance of the TLS method.
Statistics and Brain Mapping

The scientific aim of brain mapping is to investigate which regions of the brain are used when a subject is involved in a particular task, such as cognitive tasks, sensory stimuli, or memory challenges, or how brain function differs between different groups of subjects, such as normals and schizophrenics. A second aim is the study of how brain anatomy differs between different groups of subjects. There are three different types of images for measuring brain function: cerebral blood flow (CBF) measured by positron emission tomography (PET) (Raichle, 1994), blood oxygenation level dependent (BOLD) response, measured by functional magnetic resonance imaging (fMRI) (Lange & Zeger, 1997), and neurotransmitter kinetics measured by dynamic PET (Dagher et al., 1998). There are three different types of images for measuring changes in shape of brain structures, such as the cortex: binary structure masks (1=inside, 0=outside) from segmented MRI scans; normal displacements of the structure surface; and vector deformations required to warp the structure to an atlas (standard structure). On the surface, this looks like a standard statistical problem of relating dependent variables Y(t) (function, anatomy) to explanatory variables X (tasks, groups). The novelty is that the dependent variables are 3D images with a value at each voxel t ∈ S ⊂ 3. Usually S is the entire brain or part of it, or, in the case of surface normal displacements, the 2D manifold of the surface of the structure. The most widely used tool is the linear model which is applied separately to each voxel t: Y(t) = Xβ(t) + (t) (Friston et al., 1995). The errors (t) may be correlated for images taken on the same subject, either because of random effects, or because of temporal correlation, particularly for PET kinetics and fMRI data, where images are aquired every few seconds. This methodology has been found to be sufficiently flexible to treat image data from all the above six sources; the only slight generalisation required is a multivariate linear model for the three components of the vector deformations data (Cao & Worsley, 1999), logistic regression for binary structure masks (Taylor et al., 1998), and nonlinear models for PET kinetics (Dagher et al., 1998). Lange & Zeger (1997) have developed a more sophisticated model for fMRI data that incorporates spatial as well as temporal information. In most laboratories worldwide, this is done using the SPM (Statistical Parametric Mapping) software package (see Friston et al., 1995). …
Influence of Rice Husk - Mulch on Soil Water Balance Components under Sorghum and Millet Crops in Maiduguri, Semi Arid Northeast Nigeria

A 2 x 3 factorial experiment was conducted at two sites in Maiduguri, Borno State during the 2009 cropping season. The objective was to evaluate the influence of rice husk-mulch on soil water balance components under sorghum and millet crops. The treatments comprised of two test crops (sorghum and millet) and three rates of application (0, 10 and 15 t ha-1) of rice husk mulch, fitted in a split-plot design. The test crops were assigned to the main plot, while the mulch application rates were assigned to the sub-plot. The treatments were replicated three times. The components of soil water balance determined were annual rainfall, moisture storage within sorghum and millet root zone, drainage below crop root zone and seasonal crop evapotranspiration. Profile moisture content was measured weekly with the aid of a neutron probe installed at a depth of 2.0 m using access tubes. Also, soil (0 – 30 cm depth) moisture content was determined gravimetrically on weekly basis. Rainfall was measured using a manual rain gauge installed at each of the two sites. Findings in this study indicated that, under the prevailing circumstances, annual rainfall was lower than the amount observed over a ten-year period in Maiduguri. Consequently, soil moisture storage, drainage and seasonal crop evapotranspiration generally declined. An average of over 90 % of this low annual rainfall was lost as seasonal crop evapotranspiration. Sorghum plots stored higher moisture within the root zone, had higher drainage and lower seasonal evapotranspiration than millet plots. Moisture storage and drainage increased with increasing mulch application rate, while, seasonal crop evapotranspiration decreased with it.
Predicting the thermal protective performance of heat-protective fabrics from basic properties

Novel experimental techniques were developed to measure changes in the weight, thickness, density, heat capacity, heat conductivity, and infrared (IR) transmission of protective fabrics occurring during a thermal protective performance (TPP) test. Comparisons are made between polybenzimidazole (PBI), aramid, a PBI/aramid blend fabric, and flame-retardant (FR) cotton fabrics in the 250 g/m 2 (7.5-oz/yd 2 ) weight range. This research analyzes changes in fabric heat transfer properties produced through mechanisms of pyrolysis, char formation, and shrinkage. Fiber character is shown to play a decisive role in determining the direction and extent of change in thermophysical properties. Retention of air volume is found to be critical to prolonged thermal protection performance. Experimental data indicate that air and fiber conduction dominate in intense exposures to a mixture of radiant and convective thermal energy; direct radiant transmission is not an important contributor to the total heat transferred in these exposures. The ability of fabrics to maintain surface fibers is thought to have significant impact in blocking convective heat transmission. The degradation behaviors of different materials are compared and related to their thermal protective performance.
Formulation and make-up of simulate dilute water, low ionic content aqueous solution

This procedure describes the formulation and make-up of Simulated Dilute Water (SOW), a low-ionic-content water to be used for Activity E-20-50, Long-Term Corrosion Studies. This water has an ionic content which is nominally a factor of ten higher than that of representative waters at or near Yucca Mountain. Representative waters were chosen as J-13 well water [Harrar, 1990] and perched water at Yucca Mountain [Glassley, 1996]. J-13 well water is obtained from ground water that is in contact with the Topopah Spring tuff, which is the repository horizon rock. The perched water is located in the Topopah Spring tuff, but below the repository horizon and above the water table. A nominal times ten higher ionic content was chosen to simulate the effect of ionic concentrating due to elevated temperature water flowing through fractures where salts and minerals have been deposited due to evaporation and boiling.
Skeletal program enumeration for rigorous compiler testing

A program can be viewed as a syntactic structure P (syntactic skeleton) parameterized by a collection of identifiers V (variable names). This paper introduces the skeletal program enumeration (SPE) problem: Given a syntactic skeleton P and a set of variables V , enumerate a set of programs P exhibiting all possible variable usage patterns within P. It proposes an effective realization of SPE for systematic, rigorous compiler testing by leveraging three important observations: (1) Programs with different variable usage patterns exhibit diverse control- and data-dependence, and help exploit different compiler optimizations; (2) most real compiler bugs were revealed by small tests (i.e., small-sized P) — this “small-scope” observation opens up SPE for practical compiler validation; and (3) SPE is exhaustive w.r. t. a given syntactic skeleton and variable set, offering a level of guarantee absent from all existing compiler testing techniques. The key challenge of SPE is how to eliminate the enormous amount of equivalent programs w.r. t. α-conversion. Our main technical contribution is a novel algorithm for computing the canonical (and smallest) set of all non-α-equivalent programs. To demonstrate its practical utility, we have applied the SPE technique to test C/C++ compilers using syntactic skeletons derived from their own regression test-suites. Our evaluation results are extremely encouraging. In less than six months, our approach has led to 217 confirmed GCC/Clang bug reports, 119 of which have already been fixed, and the majority are long latent despite extensive prior testing efforts. Our SPE algorithm also provides six orders of magnitude reduction. Moreover, in three weeks, our technique has found 29 CompCert crashing bugs and 42 bugs in two Scala optimizing compilers. These results demonstrate our SPE technique’s generality and further illustrate its effectiveness.
Sparse image coding using an asynchronous spiking neural network

In order to explore coding strategies in the retina, we use a wavelet-like transform which output is sparse, as is observed in biological retinas [4]. This transform is defined in the context of a one-pass feed-forward spiking neural network, and the output is the list of its neurons’ spikes: it is recursively constructed using a greedy matching pursuit scheme which first selects higher contrast energy values. As in [7], we find invariants in the output for some classes of images, allowing to code the absolute contrast value solely by its rank in the spike list. An application to image compression is shown which is comparable to other techniques such as JPEG at low bit compression.