Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the physical state of one Arctic polar stratospheric

During the Arctic Airborne Stratospheric Expe- dition, simultaneous measurements of aerosol size distribution and NOy (HNO 3 + NO + NO 2 + 2.N20 5) were made along ER-2 flight paths. The flow characteristics of the NOy instrument allow us to derive the condensed NOy amount (assumed to be HNO3) present during polar stratospheric cloud (PSC) events. Analysis of the January 24 th flight indicates that this condensed HNO 3 amount does not agree well with the aerosol volume if the observed PSCs are composed of solid nitric acid trihydrate (NAT), as is generally assumed. However, the composition agrees well with that predicted for liquid H2SO4/I-INO3/I-I2 ¸ solution droplets using a new Aerosol Physical Chemistry Model (APCM). The agreement corresponds in detail to variations in temperature and humidity. The weight percentages of H2SO 4, HNO 3, and H20 derived from the measurements all correspond to those predicted for ternary, liquid solutions.
Fast minimum spanning tree for large graphs on the GPU

Graphics Processor Units are used for many general purpose processing due to high compute power available on them. Regular, data-parallel algorithms map well to the SIMD architecture of current GPU. Irregular algorithms on discrete structures like graphs are harder to map to them. Efficient data-mapping primitives can play crucial role in mapping such algorithms onto the GPU. In this paper, we present a minimum spanning tree algorithm on Nvidia GPUs under CUDA, as a recursive formulation of Borůvka's approach for undirected graphs. We implement it using scalable primitives such as scan, segmented scan and split. The irregular steps of supervertex formation and recursive graph construction are mapped to primitives like split to categories involving vertex ids and edge weights. We obtain 30 to 50 times speedup over the CPU implementation on most graphs and 3 to 10 times speedup over our previous GPU implementation. We construct the minimum spanning tree on a 5 million node and 30 million edge graph in under 1 second on one quarter of the Tesla S1070 GPU.
Mercuric iodide medical imagers for low-exposure radiography and fluoroscopy

Photoconductive polycrystalline mercuric iodide deposited on flat panel thin film transistor (TFT) arrays is being developed for direct digital X-ray detectors that can perform both radiographic and fluoroscopic medical imaging. The mercuric iodide is either vacuum deposited by Physical Vapor Deposition (PVD) or coated onto the array by a wet Particle-In-Binder (PIB) process. The PVD deposition technology has been scaled up to the 20 cm x 25 cm size required in common medical imaging applications. A TFT array with a pixel pitch of 127 microns is used for these imagers. Arrays of 10 cm x 10 cm size have been used to evaluate performance of mercuric iodide imagers. Radiographic and fluoroscopic images of diagnostic quality at up to 15 pulses per second were demonstrated. As we previously reported, the resolution is limited to the TFT array Nyquist frequency of ~3.9 lp/mm (127 micron pixel pitch). Detective Quantum Efficiency (DQE) has been measured as a function of spatial frequency for these imagers. The DQE is lower than the theoretically calculated value due to some additional noise sources of the electronics and the array. We will retest the DQE after eliminating these noise sources. Reliability and stress testing was also began for polycrystalline mercuric iodide PVD and PIB detectors. These are simplified detectors based upon a stripe electrode or circular electrode structure. The detectors were stressed under various voltage bias, temperature and time conditions. The effects of the stress tests on the detector dark current and sensitivity were determined.
Facial feedback affects valence judgments of dynamic and static emotional expressions

The ability to judge others' emotions is required for the establishment and maintenance of smooth interactions in a community. Several lines of evidence suggest that the attribution of meaning to a face is influenced by the facial actions produced by an observer during the observation of a face. However, empirical studies testing causal relationships between observers' facial actions and emotion judgments have reported mixed findings. This issue was investigated by measuring emotion judgments in terms of valence and arousal dimensions while comparing dynamic vs. static presentations of facial expressions. We presented pictures and videos of facial expressions of anger and happiness. Participants (N = 36) were asked to differentiate between the gender of faces by activating the corrugator supercilii muscle (brow lowering) and zygomaticus major muscle (cheek raising). They were also asked to evaluate the internal states of the stimuli using the affect grid while maintaining the facial action until they finished responding. The cheek raising condition increased the attributed valence scores compared with the brow-lowering condition. This effect of facial actions was observed for static as well as for dynamic facial expressions. These data suggest that facial feedback mechanisms contribute to the judgment of the valence of emotional facial expressions.
Identification of transcription factor binding sites with variable-order Bayesian networks

MOTIVATION We propose a new class of variable-order Bayesian network (VOBN) models for the identification of transcription factor binding sites (TFBSs). The proposed models generalize the widely used position weight matrix (PWM) models, Markov models and Bayesian network models. In contrast to these models, where for each position a fixed subset of the remaining positions is used to model dependencies, in VOBN models, these subsets may vary based on the specific nucleotides observed, which are called the context. This flexibility turns out to be of advantage for the classification and analysis of TFBSs, as statistical dependencies between nucleotides in different TFBS positions (not necessarily adjacent) may be taken into account efficiently--in a position-specific and context-specific manner. RESULTS We apply the VOBN model to a set of 238 experimentally verified sigma-70 binding sites in Escherichia coli. We find that the VOBN model can distinguish these 238 sites from a set of 472 intergenic 'non-promoter' sequences with a higher accuracy than fixed-order Markov models or Bayesian trees. We use a replicated stratified-holdout experiment having a fixed true-negative rate of 99.9%. We find that for a foreground inhomogeneous VOBN model of order 1 and a background homogeneous variable-order Markov (VOM) model of order 5, the obtained mean true-positive (TP) rate is 47.56%. In comparison, the best TP rate for the conventional models is 44.39%, obtained from a foreground PWM model and a background 2nd-order Markov model. As the standard deviation of the estimated TP rate is approximately 0.01%, this improvement is highly significant.
Occurrence and Dissipation of the Antibiotics Sulfamethoxazole, Sulfadiazine, Trimethoprim, and Enrofloxacin in the Mekong Delta, Vietnam

The Mekong Delta in Vietnam has seen a rapid development and intensification of aquaculture in the last decades, with a corresponding widespread use of antibiotics. This study provides information on current antibiotic use in freshwater aquaculture, as well as on resulting antibiotic concentrations in the aquatic environment of the Mekong Delta. Two major production steps, fish hatcheries and mature fish cultivation, were surveyed (50 fish farm interviews) for antibiotic use. Different water sources, including surface water, groundwater and piped water (164 water samples) were systematically screened for antibiotic residues. To better understand antibiotic fate under tropical conditions, the dissipation behavior of selected antibiotics in the aquatic environment was investigated for the first time in mesocosm experiments. None of the investigated antibiotics were detected in groundwater and piped water samples. Surface water, which is still often used for drinking and domestic purposes by local populations, contained median concentrations of 21 ng L-1 sulfamethoxazole (SMX), 4 ng L-1 sulfadiazine (SDZ), 17 ng L-1 trimethoprim (TRIM), and 12 ng L-1 enrofloxacin (ENRO). These concentrations were lower than the predicted no effect concentrations (PNECs) and minimum inhibitory concentrations (MICs), suggesting limited antibiotic-related risk to aquatic ecosystems in the monitored systems. The dissipation half-lives of the studied antibiotics ranged from <1 to 44 days, depending on the availability of sunlight and sediment. Among the studied antibiotics TRIM was the most persistent in water systems. TRIM was not susceptible to photodegradation, while the dissipation of ENRO and SDZ was influenced by photolysis. The recorded dissipation models gave good predictions of the occurrence and concentrations of TRIM, ENRO and SDZ in surface water. In summary, the currently measured concentrations of the investigated antibiotics are unlikely to cause immediate risks to the aquatic environment, yet the persistence of these antibiotics is of concern and might lead to chronic exposure of aquatic organisms as well as humans.
Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector

The adult phenotype of mosquitoes depends on the types of bacteria encountered environmentally during development. Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector.
Supersymmetric giant graviton solutions in AdS(3)

We parametrize all classical probe brane configurations that preserve four supersymmetries in (a) the extremal D1-D5 geometry, (b) the extremal D1-D5-P geometry, (c) the smooth D1-D5 solutions proposed by Lunin and Mathur, and (d) global ${\mathrm{AdS}}_{3}\ifmmode\times\else\texttimes\fi{}{S}_{3}\ifmmode\times\else\texttimes\fi{}{T}^{4}/K3$. These configurations consist of D1 branes, D5 branes, and bound states of D5 and D1 branes with the property that a particular Killing vector is tangent to the brane world volume at each point. We show that the supersymmetric sector of the D5-brane world volume theory may be analyzed in an effective $1+1$ dimensional framework that places it on the same footing as D1 branes. In global AdS and the corresponding Lunin-Mathur solution, the solutions we describe are ``bound'' to the center of AdS for generic parameters and cannot escape to infinity. We show that these probes only exist on the submanifold of moduli space where the background ${B}_{NS}$ field and theta angle vanish. We quantize these probes in the near-horizon region of the extremal D1-D5 geometry and obtain the theory of long strings discussed by Seiberg and Witten.
Using cellular fitness to map the structure and function of a major facilitator superfamily effluxer

The major facilitator superfamily (MFS) effluxers are prominent mediators of antimicrobial resistance. The biochemical characterization of MFS proteins is hindered by their complex membrane environment that makes in vitro biochemical analysis challenging. Since the physicochemical properties of proteins drive the fitness of an organism, we posed the question of whether we could reverse that relationship and derive meaningful biochemical parameters for a single protein simply from fitness changes it confers under varying strengths of selection. Here, we present a physiological model that uses cellular fitness as a proxy to predict the biochemical properties of the MFS tetracycline efflux pump, TetB, and a family of single amino acid variants. We determined two lumped biochemical parameters roughly describing Km and Vmax for TetB and variants. Including in vivo protein levels into our model allowed for more specified prediction of pump parameters relating to substrate binding affinity and pumping efficiency for TetB and variants. We further demonstrated the general utility of our model by solely using fitness to assay a library of tet(B) variants and estimate their biochemical properties.
A Mixed Finite Element Approximation for Equilibrium Equations

This paper describes a numerical solution for plane elasticity problem. It includes algorithms for discretization by mixed finite element methods. The discrete scheme allows the utilization of Brezzi-Douglas-Fortin-Marini (BDFM2) for the stress tensor and piecewise linear elements for the displacement. The numerical results are compared with some previously published works or with others coming from commercial code like ABAQUS.
Invasive Pneumococcal Disease in Infants Aged 0–60 Days in the United States in the 13-Valent Pneumococcal Conjugate Vaccine Era

We identified 53 infants aged 0-60 days with invasive pneumococcal disease (IPD) at 8 children's hospitals in the United States (2005-2015). After the introduction of 13-valent pneumococcal conjugate vaccine (PCV13), IPD caused by PCV13 serotypes decreased ~30% providing some evidence of indirect protection. However, approximately 60% of IPD was still caused by PCV13 serotypes.
The histopathology of 103 consecutive colonoscopy biopsies from 82 symptomatic patients with acquired immunodeficiency syndrome: original and look-back diagnoses.

OBJECTIVE To compare the primary diagnoses assigned by general surgical pathologists on a series of 103 consecutive colon biopsies from individuals infected with human immunodeficiency virus (HIV) with diagnoses rendered by a pathologist with extensive experience in gastrointestinal pathology in HIV/acquired immunodeficiency syndrome. DESIGN New sections were cut from paraffin blocks of 103 consecutive colon biopsies taken during colonoscopies of 82 different HIV-infected patients; all new sections were stained with hematoxylin-eosin. These individuals either had negative stool studies or had failed to respond to therapy and had chronic large bowel symptoms, such as frequent small volume-type diarrhea, tenesmus, and/or bright red blood per rectum. Immunohistochemistry for cytomegalovirus (CMV) was performed on 18 of 22 specimens originally diagnosed with CMV colitis. RESULTS The initial study yielded 70 (68%) negative or nonspecific diagnoses, 22 (21%) cases of CMV colitis, 5 (5%) Cryptosporidium diagnoses, 2 cases each of adenomatous polyps and Kaposi sarcoma, and 1 case each of spirochetosis and squamous cell carcinoma of the anorectum. Review of the recuts yielded 64 (62%) negative or nonspecific diagnoses, 12 (12%) new adenovirus infections (3 combined with CMV), and 11 (11%) lone CMV infections. Three attaching and effacing bacterial infections were diagnosed, 1 with adenovirus coinfection. A total of 4 spirochetosis cases were found on review. Seven (7%) of the biopsies showed at least 1 coinfection. Nine biopsies had features suggestive of inflammatory bowel disease. CONCLUSIONS Colonoscopy with biopsy after negative stool studies or failure to respond to therapy yielded a high proportion of negative or nonspecific diagnoses. Adenovirus and enteropathogenic bacterial infections had been totally overlooked on initial examination. It takes particular experience to evaluate gastrointestinal biopsies from HIV-infected patients.
Effect of medetomidine-butorphanol and dexmedetomidine-butorphanol combinations on intraocular pressure in healthy dogs.

OBJECTIVE To assess the effects of intravenous (IV) medetomidine-butorphanol and IV dexmedetomidine-butorphanol on intraocular pressure (IOP). STUDY DESIGN Prospective, randomized, blinded clinical study. ANIMALS Forty healthy dogs. Mean ± SD body mass 37.6 ± 6.6 kg and age 1.9 ± 1.3 years. METHODS Dogs were allocated randomly to receive an IV combination of dexmedetomidine, 0.3 mg m(-2), combined with butorphanol, 6 mg m(-2), (group DEX) or medetomidine 0.3 mg m(-2), combined with butorphanol 6 mg m(-2), (group MED). IOP and pulse (PR) and respiratory (f(R) ) rates were measured prior to (baseline) and at 10 (T10), 20 (T20), 30 (T30) and 40 (T40) minutes after drug administration. Oxygen saturation of hemoglobin (SpO(2)) was monitored following sedation. Data were analyzed by anova followed by Dunnett's tests for multiple comparisons. Changes were considered significant when p < 0.05. RESULTS Following drug administration, PR and f(R) were decreased significantly at all time points but did not differ significantly between groups. Baseline IOP in mmHg was 14 ± 2 for DEX and 13 ± 2 for MED. With both treatments, at T10, IOP increased significantly (p < 0.001), reaching 20 ± 3 and 17 ± 2 for DEX and MED respectively. This value for DEX was significantly higher than for MED. There were no significant differences in IOP values between groups at any other time points. At T30 and T40, IOP in both groups was below baseline (DEX, 12 ± 2 and 11 ± 2: MED 12 ± 2 and 11 ± 2) and this was statistically significant, for DEX. CONCLUSIONS AND CLINICAL RELEVANCE At the documented doses, both sedative combinations induced a transient increase and subsequent decrease of IOP relative to baseline, which must be taken into consideration when planning sedation of animals in which marked changes in IOP would be undesirable.
Automatic Evaluation of Students’ Answers using Syntactically Enhanced LSA

Latent semantic analysis (LSA) has been used in several intelligent tutoring systems(ITS's) for assessing students' learning by evaluating their answers to questions in the tutoring domain. It is based on word-document co-occurrence statistics in the training corpus and a dimensionality reduction technique. However, it doesn't consider the word-order or syntactic information, which can improve the knowledge representation and therefore lead to better performance of an ITS. We present here an approach called Syntactically Enhanced LSA (SELSA) which generalizes LSA by considering a word along with its syntactic neighborhood given by the part-of-speech tag of its preceding word, as a unit of knowledge representation. The experimental results on Auto-Tutor task to evaluate students' answers to basic computer science questions by SELSA and its comparison with LSA are presented in terms of several cognitive measures. SELSA is able to correctly evaluate a few more answers than LSA but is having less correlation with human evaluators than LSA has. It also provides better discrimination of syntactic-semantic knowledge representation than LSA.
Age and Semantic Inhibition Measured by the Hayling Task: A Meta-Analysis

Objective Cognitive aging is commonly associated with a decrease in executive functioning (EF). A specific component of EF, semantic inhibition, is addressed in the present study, which presents a meta-analytic review of the literature that has evaluated the performance on the Hayling Sentence Completion test in young and older groups of individuals in order to assess the magnitude of the age effect. Method A systematic search involving Web of Science, PsyINFO, PsychARTICLE, and MedLine databases and Google Scholar was performed. A total of 11 studies were included in this meta-analysis, encompassing a total of 887 participants; 440 young and 447 older adults. The effect sizes for group differences on four measures of the Hayling test, latency responses and error scores on the Automatic and Inhibition sections of the test were calculated using the Comprehensive Meta-Analysis software package. Results The results revealed large age effects for response latencies in both the Automatic (Hedges' g = 0.81) and Inhibitory conditions (Hedges' g = 0.98), though the latter two effect sizes did not differ from each other. In contrast, analysis of errors revealed a significant difference between the small effect seen in the Automatic condition (Hedges' g = 0.13) relative to the moderate effect seen in the Inhibition condition (Hedges' g = 0.55). Conclusions These results may be important for a better understanding of the inhibitory functioning in elderly individuals, although they should be interpreted with caution because of the limited number of studies in the literature to date.
Individualized Angiotensin‐Converting Enzyme (ACE)‐Inhibitor Therapy in Stable Coronary Artery Disease Based on Clinical and Pharmacogenetic Determinants: The PERindopril GENEtic (PERGENE) Risk Model

Background Patients with stable coronary artery disease (CAD) constitute a heterogeneous group in which the treatment benefits by angiotensin‐converting enzyme (ACE)‐inhibitor therapy vary between individuals. Our objective was to integrate clinical and pharmacogenetic determinants in an ultimate combined risk prediction model. Methods and Results Clinical, genetic, and outcomes data were used from 8726 stable CAD patients participating in the EUROPA/PERGENE trial of perindopril versus placebo. Multivariable analysis of phenotype data resulted in a clinical risk score (range, 0–21 points). Three single‐nucleotide polymorphisms (rs275651 and rs5182 in the angiotensin‐II type I‐receptor gene and rs12050217 in the bradykinin type I‐receptor gene) were used to construct a pharmacogenetic risk score (PGXscore; range, 0–6 points). Seven hundred eighty‐five patients (9.0%) experienced the primary endpoint of cardiovascular mortality, nonfatal myocardial infarction or resuscitated cardiac arrest, during 4.2 years of follow‐up. Absolute risk reductions ranged from 1.2% to 7.5% in the 73.5% of patients with PGXscore of 0 to 2. As a consequence, estimated annual numbers needed to treat ranged from as low as 29 (clinical risk score ≥10 and PGXscore of 0) to 521 (clinical risk score ≤6 and PGXscore of 2). Furthermore, our data suggest that long‐term perindopril prescription in patients with a PGXscore of 0 to 2 is cost‐effective. Conclusions Both baseline clinical phenotype, as well as genotype determine the efficacy of widely prescribed ACE inhibition in stable CAD. Integration of clinical and pharmacogenetic determinants in a combined risk prediction model demonstrated a very wide range of gradients of absolute treatment benefit.