Miracle-dz/UniFAR-FTUs huggingface dataset:
The Genetic Basis of Thermal Reaction Norm Evolution in Lab and Natural Phage Populations

Two major goals of laboratory evolution experiments are to integrate from genotype to phenotype to fitness, and to understand the genetic basis of adaptation in natural populations. Here we demonstrate that both goals are possible by re-examining the outcome of a previous laboratory evolution experiment in which the bacteriophage G4 was adapted to high temperatures. We quantified the evolutionary changes in the thermal reaction norms—the curves that describe the effect of temperature on the growth rate of the phages—and decomposed the changes into modes of biological interest. Our analysis indicated that changes in optimal temperature accounted for almost half of the evolutionary changes in thermal reaction norm shape, and made the largest contribution toward adaptation at high temperatures. Genome sequencing allowed us to associate reaction norm shape changes with particular nucleotide mutations, and several of the identified mutations were found to be polymorphic in natural populations. Growth rate measures of natural phage that differed at a site that contributed substantially to adaptation in the lab indicated that this mutation also underlies thermal reaction norm shape variation in nature. In combination, our results suggest that laboratory evolution experiments may successfully predict the genetic bases of evolutionary responses to temperature in nature. The implications of this work for viral evolution arise from the fact that shifts in the thermal optimum are characterized by tradeoffs in performance between high and low temperatures. Optimum shifts, if characteristic of viral adaptation to novel temperatures, would ensure the success of vaccine development strategies that adapt viruses to low temperatures in an attempt to reduce virulence at higher (body) temperatures.
Efficient Output Kernel Learning for Multiple Tasks

The paradigm of multi-task learning is that one can achieve better generalization by learning tasks jointly and thus exploiting the similarity between the tasks rather than learning them independently of each other. While previously the relationship between tasks had to be user-defined in the form of an output kernel, recent approaches jointly learn the tasks and the output kernel. As the output kernel is a positive semidefinite matrix, the resulting optimization problems are not scalable in the number of tasks as an eigendecomposition is required in each step. Using the theory of positive semidefinite kernels we show in this paper that for a certain class of regularizers on the output kernel, the constraint of being positive semidefinite can be dropped as it is automatically satisfied for the relaxed problem. This leads to an unconstrained dual problem which can be solved efficiently. Experiments on several multi-task and multi-class data sets illustrate the efficacy of our approach in terms of computational efficiency as well as generalization performance.
Data Compression of Multiresolution Surfaces

In this paper we introduce a new compressed representation for multiresolution models (MRM) of triangulated surfaces of 3D-objects. Associated with the representation we present compression and decompression algorithms. Our representation allows us to extract the surface at variable resolution in time linear in the output size. It applies to MRMs generated by different simplification algorithms like local vertex deletion or edge and triangle collapse. The time required to transmit models over communication lines and the space needed to store the MRMs is significantly reduced.
L5 Root Compression Caused by Degenerative Spinal Stenosis of the L1‐L2 and L2‐L3 Spaces

Study Design. A severe bilateral L5 root lesion associated with spinal stenosis at L1‐L2 and L2‐L3 is described. Objective. To describe clinical findings and the difficulty in obtaining a correct diagnosis of L5 Root Compression. Summary of Background Data. The disorder reported in this study has not been reported previously. Only one similar case has been described in the literature: an L5 root compression at L1‐L2 caused by disc herniation. Methods. Diagnosis was obtained by using computed tomography scanning, magnetic resonance imaging, and computed tomography myelography. The findings at L5‐S1 were minimal to justify the patient's clinical symptoms, but a detailed study of the upper levels revealed spinal stenosis at L1‐L2 and L2‐L3, which could have been causing L5 and S1 root compression. A decompressive laminectomy and partial facetectomy in both levels were performed. Results. The patient's pain and claudication disappeared, and clinical symptoms associated with the right L5 root improved. The left L5 root deficit remained stable. Conclusion. An unusual case of L5 root compression caused by degenerative stenosis of L1‐L2 and L2‐L3 is described.
Intensive induction chemotherapy followed by myeloablative chemotherapy with autologous hematopoietic progenitor cell rescue for young children newly‐diagnosed with central nervous system atypical teratoid/rhabdoid tumors: The head start III experience

Atypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system (CNS) is a rare embryonal neoplasm of early childhood with dismal outcome and no current uniformly accepted treatment. Given its highly aggressive nature and predilection for dissemination at diagnosis, intensive multimodal therapy is required.
Packing Triangles in Weighted Graphs

Tuza conjectured that for every graph $G$ the maximum size $\nu$ of a set of edge-disjoint triangles and minimum size $\tau$ of a set of edges meeting all triangles satisfy $\tau \leq 2\nu$. We consider an edge-weighted version of this conjecture, which amounts to packing and covering triangles in multigraphs. Several known results about the original problem are shown to be true in this context, and some are improved. In particular, we answer a question of Krivelevich, who proved that $\tau \leq 2\nu^*$ (where $\nu^*$ is the fractional version of $\nu$) and asked whether this is tight. We prove that $\tau \leq 2\nu^*-\frac{1}{\sqrt{6}}\sqrt{\nu^*}$ and show that this bound is essentially best possible.
A random walk based algorithm for structural test case generation

Structural testing is a significant and expensive process in software development. By converting test data generation into an optimization problem, search-based software testing is one of the key technologies of automated test case generation. Motivated by the success of random walk in solving the satisfiability problem (SAT), we proposed a random walk based algorithm (WalkTest) to solve structural test case generation problem. WalkTest provides a framework, which iteratively calls random walk operator to search the optimal solutions. In order to improve search efficiency, we sorted the test goals with the costs of solutions completely instead of traditional dependence analysis from control flow graph. Experimental results on the condition-decision coverage demonstrated that WalkTest achieves better performance than existing algorithms (random test and tabu search) in terms of running time and coverage rate.
Comparison of Properties between General Purpose Stainless Steel Wire and Commercial Orthodontic Stainless Steel Wire

In Thailand, commercial orthodontic stainless steel wires are imported from overseas and expensive. However, lower cost general purpose stainless steel wires, the same type and number as commercial orthodontic stainless steel wires may be used for orthodontic purposes. Objective: This study aimed to determine the physical, mechanical and chemical properties of general purpose stainless steel wire compared with commercial orthodontic stainless steel wires. Materials and Method: Two commercial orthodontic stainless steel wires (Ormco and Highland) and general purpose stainless steel wire (SUS 304H) were evaluated. The physical and mechanical properties were studied according to ISO 15841:2006 and corrosion resistance was studied according to ISO 10271:2001. Surface characteristics and composition were studied by scanning electron microscope (SEM) and electron probe micro analyzer, respectively. Results: The experiment indicated that SUS 304H had the diameter and mechanical properties in the range of orthodontic stainless steel wires. The surface characteristics SUS 304H were similar from observation by SEM magnifications but SUS 304H had lower corrosion resistance due to lower nickel content. The composition confirmed that the three samples wires were genuine type 304. Conclusion: SUS 304H properties are comparable to commercial orthodontic wire properties.
Health care utilization in dementia patients with psychiatric comorbidity.

PURPOSE The purpose of this research was to determine if differences in service use exist between dementia patients with and without psychiatric comorbidity. DESIGN AND METHODS A retrospective cohort study was conducted on all Veterans Affairs (VA) beneficiaries seen at the Houston Veterans Affairs Medical Center with a VA Outpatient Clinic File diagnosis of dementia in 1997. The primary dependent measure was amount of Houston VA health service use from study entry until the end of fiscal year 1999 or until death. RESULTS Of the 864 dementia patients in the identified cohort, two thirds had a comorbid psychiatric diagnosis. Examination of 2-year health service use revealed that, after adjusting for demographic and medical comorbidity differences, dementia patients with psychiatric comorbidity had increased medical and psychiatric inpatient days of care and more psychiatric outpatient visits compared with patients without psychiatric comorbidity. IMPLICATIONS Further understanding of the current health service use of dementia patients with psychiatric comorbidity may help to establish a framework for considering change in the current system of care. A coordinated system of care with interdisciplinary teamwork may provide both cost-effective and optimal treatment for dementia patients.
A Randomized Prospective Controlled Study of the Metabolism and Hepatotoxicity of Halothane in Humans

In a randomized prospective controlled study in humans, the metabolism and hepatic effects of a single administration of halothane were compared with enflurane and meperidine. Pre- and postoperative antipyrine pharmacokinetics, intraoperative indocyanine green clearance, liver histology, and postoperative liver function tests were determined in 24 patients undergoing abdominal surgery who were randomly allocated to receive either halothane (0.5%, group I), enflurane (0.8%, group II), or meperidine (group III) as a supplement to a common basal anesthetic regimen consisting of thiopental, nitrous oxideloxygen/muscle relaxant. In addition, end-tidal concentrations of the volatile reductive metabolites of halothane, chlorodifluoroethylene (CDF), and chlorotrifluoroethane (CTF) were determined in group I patients and serum and urinary inorganic fluoride were determined in both group I and II patients. Indocyanine green clearance was measured before anesthesia (stage I), during basal anesthesia (stage II), in the presence of surgical stimuli (stage III), and after introduction of the selected anesthetic agent (stage IV). CDF and CTF were detectable within 20 min of the start of halothane anesthesia in every patient receiving halothane. Peak serum fluoride concentrations occurred at 2 and 24 hr in the enflurane and halothane groups, respectively, whereas urinary fluoride excretion was elevated postanesthesia in the enflurane group only. There was no difference between the pre- and postoperative disposition of antipyrine in group II or III, but after anesthesia, antipyrine clearance was significantly decreased (P < 0.02) and plasma half-life increased (P < 0.05) in group I patients (halothane). Concentrations of serum alanine aminotransferase (ALT) and bilirubin were significantly elevated (P < 0.05) postoperatively in groups I and II but unchanged from preoperative values in group III patients. Three of the 24 liver biopsies taken at the end of stage IV showed several foci of acute liver cell necrosis; of these, two patients were from group I and one from group II. There were no significant differences in liver cell morphology (P > 0.5) in biopsies taken at the end of stage IV compared with biopsies at the end of stage III, from groups I and II. The results of this study show that reductive metabolism of halothane occurs routinely in patients undergoing halothane anesthesia under conditions of normoxia. This may be the cause of the changes in antipyrine clearance after halothane anesthesia.
Influence of Superplasticizers on Workability of Concrete

This paper outlines the theoretical foundations governing the rheological properties of concrete. The rheological equation for fresh concrete is given as a modification of Bingham's equation. The shear resistance of the concrete mix is explained in terms of two constants—yield value and plastic viscosity. The complex nature of the yield value is described. It is pointed out that there are three different zones of rheological behavior of fresh concrete, which arise as a result of the relation between shear stress and yield value of the mix. This paper also describes an experimental study that measures the effects of superplasticizer, water-to-cement (w/c) ratio, condensed silica fume (CSF) and elapsed time on the rheological parameters for fresh concrete. The rheological tests were carried out on a ROD1E rotational rheometer. In total, 102 flow curves were obtained from which the yield values g and the plastic viscosities h for a wide range of concrete mixes were determined. The results showed that superpl.
The connection between BRG1, CTCF and topoisomerases at TAD boundaries

ABSTRACT The eukaryotic genome is partitioned into topologically associating domains (TADs). Despite recent advances characterizing TADs and TAD boundaries, the organization of these structures is an important dimension of genome architecture and function that is not well understood. Recently, we demonstrated that knockdown of BRG1, an ATPase driving the chromatin remodeling activity of mammalian SWI/SNF enzymes, globally alters long-range genomic interactions and results in a reduction of TAD boundary strength. We provided evidence suggesting that this effect may be due to BRG1 affecting nucleosome occupancy around CTCF sites present at TAD boundaries. In this review, we elaborate on our findings and speculate that BRG1 may contribute to the regulation of the structural and functional properties of chromatin at TAD boundaries by affecting the function or the recruitment of CTCF and DNA topoisomerase complexes.
Early activity is feasible and safe in respiratory failure patients*

Objective: To determine whether early activity is feasible and safe in respiratory failure patients. Design: Prospective cohort study. Setting: From June 1, 2003, through December 31, 2003, we assessed safety and feasibility of early activity in all consecutive respiratory failure patients who required mechanical ventilation for >4 days admitted to our respiratory intensive care unit (RICU). A majority of patients were treated in another intensive care unit (ICU) before RICU admission. We excluded patients who required mechanical ventilation for ≤4 days. Patients: Eight‐bed RICU at LDS Hospital. Interventions: We assessed patients for early activity as part of routine respiratory ICU care. We prospectively recorded activity events and adverse events. We defined three activity events as sit on bed, sit in chair, and ambulate. We defined six activity‐related adverse events as fall to knees, tube removal, systolic blood pressure >200 mm Hg, systolic blood pressure <90 mm Hg, oxygen desaturation <80%, and extubation. Measurements and Main Results: During the study period, we conducted a total of 1,449 activity events in 103 patients. The activity events included 233 (16%) sit on bed, 454 (31%) sit in chair, and 762 (53%) ambulate. In patients with an endotracheal tube in place, there were a total of 593 activity events, of which 249 (42%) were ambulation. There were <1% activity‐related adverse events, including fall to the knees without injury, feeding tube removal, systolic blood pressure >200 mm Hg, systolic blood pressure <90 mm Hg, and desaturation <80%. No patient was extubated during activity. Conclusions: We conclude that early activity is feasible and safe in respiratory failure patients. A majority of survivors (69%) were able to ambulate >100 feet at RICU discharge. Early activity is a candidate therapy to prevent or treat the neuromuscular complications of critical illness.
Efficient VLSI implementations of fast multiplierless approximated DCT using parameterized hardware modules for silicon intellectual property design

An efficient implementation of discrete cosine transform (DCT) computations are presented based on the so-called shifted discrete Fourier transform (SDFT), a generalization of the conventional DFT (DFT). Due to the simple form of the factorized matrices, the derived architecture can be easily constructed from the cascade of only two types of parameterized hardware modules: butterfly operators and rotators. The butterfly operator performs the conventional butterfly shuffling and addition/subtraction. The rotator that performs plane rotations of two-dimensional (2-D) vectors is designed using carry-save-adder (CSA)-based unfolded pipelined CORDIC architecture where the rotation angles can be approximated with different accuracies using a sequence of bipolar signs. The proposed one-dimensional and 2-D DCT implementations composed of the above two types of parameterized modules can be used as flexible and reusable Silicon Intellectual Property (SIP) for the DCT computation unit to be embedded in system-on-a-chip (SoC) design. The proposed implementations have many features and advantages, including SIP reusability, low complexity, high-throughput, regularity, scalability (easy extension of transform length), and flexibility (approximated DCT with various accuracies).
Tobacco Smoke, Indoor Air Pollution and Tuberculosis: A Systematic Review and Meta-Analysis

Background Tobacco smoking, passive smoking, and indoor air pollution from biomass fuels have been implicated as risk factors for tuberculosis (TB) infection, disease, and death. Tobacco smoking and indoor air pollution are persistent or growing exposures in regions where TB poses a major health risk. We undertook a systematic review and meta-analysis to quantitatively assess the association between these exposures and the risk of infection, disease, and death from TB. Methods and Findings We conducted a systematic review and meta-analysis of observational studies reporting effect estimates and 95% confidence intervals on how tobacco smoking, passive smoke exposure, and indoor air pollution are associated with TB. We identified 33 papers on tobacco smoking and TB, five papers on passive smoking and TB, and five on indoor air pollution and TB. We found substantial evidence that tobacco smoking is positively associated with TB, regardless of the specific TB outcomes. Compared with people who do not smoke, smokers have an increased risk of having a positive tuberculin skin test, of having active TB, and of dying from TB. Although we also found evidence that passive smoking and indoor air pollution increased the risk of TB disease, these associations are less strongly supported by the available evidence. Conclusions There is consistent evidence that tobacco smoking is associated with an increased risk of TB. The finding that passive smoking and biomass fuel combustion also increase TB risk should be substantiated with larger studies in future. TB control programs might benefit from a focus on interventions aimed at reducing tobacco and indoor air pollution exposures, especially among those at high risk for exposure to TB.
Cosmological constraints from the SDSS luminous red galaxies

We measure the large-scale real-space power spectrum P(k) using luminous red galaxies (LRGs) in the Sloan Digital Sky Survey (SDSS) and use this measurement to sharpen constraints on cosmological parameters from the Wilkinson Microwave Anisotropy Probe (WMAP). We employ a matrix-based power spectrum estimation method using Pseudo-Karhunen-Loeve eigenmodes, producing uncorrelated minimum-variance measurements in 20 k-bands of both the clustering power and its anisotropy due to redshift-space distortions, with narrow and well-behaved window functions in the range 0.01h/Mpc 0.1h/Mpc and associated nonlinear complications, yet agree well with more aggressive published analyses where nonlinear modeling is crucial.
Impact of Rheumatoid Arthritis Disease Activity Test on Clinical Practice

Background Variability exists in the assessment of disease activity in rheumatoid arthritis (RA) patients that may affect quality of care. Objectives To measure the impact on quality of care of a Multi-Biomarker Disease Activity (MBDA) test that quantitatively assesses RA disease activity. Methods Board-certified rheumatologists without prior experience with the MBDA test (N = 81) were randomized into an intervention or control group as part of a longitudinal randomized-control study. All physicians were asked to care for three simulated RA patients, using Clinical Performance and Value (CPV™) vignettes, in a before and after design. CPV™ vignettes have been validated to assess the quality of clinical practice and identify variation in care. The vignettes covered all domains of a regular patient visit; scores were determined as a percentage of explicit predefined criteria completed. Three vignettes, representing typical RA cases, were administered each round. In the first round, no physician received information about the MBDA test. In the second round, only physicians in the intervention group were given educational materials about the test and hypothetical test results for each of the simulated patients. The outcome measures were the overall quality of care, disease assessment and treatment. Results The overall quality scores in the intervention group improved by 3 percent (p = 0.02) post-intervention compared with baseline, versus no change in the control group. The greatest benefit in the intervention group was to the quality of disease activity assessment and treatment decisions, which improved by 12 percent (p<0.01) compared with no significant change in the control group. The intervention was associated with more appropriate use of biologic and/or combination DMARDs in the co-morbidity case type (p<0.01). Conclusions Based on these results, use of the MBDA test improved the assessment and treatment decisions for simulated cases of RA and may prove useful for rheumatologists in clinical practice.