Miracle-dz/UniFAR-FTUs huggingface dataset:
Shape of the chest wall in the prone and supine anesthetized dog.

The shape of the passive chest wall of six anesthetized dogs was determined at total lung capacity (TLC) and functional residual capacity (FRC) in the prone and supine body positions by use of volumetric-computed tomographic images. The transverse cross-sectional areas of the rib cage, mediastinum, and diaphragm were calculated every 1.6 mm along the length of the thorax. The changes in the volume and the axial distribution of transverse area of the three chest wall components with lung volume and body position were evaluated. The decrease of the transverse area within the rib cage between TLC and FRC, as a fraction of the area at TLC, was uniform from the apex of the thorax to the base. The volume of the mediastinum increased slightly between TLC and FRC (14% of its TLC volume supine and 20% prone), squeezing the lung between it and the rib cage. In the transverse plane, the heart was positioned in the midthorax and moved little between TLC and FRC. The shape, position, and displacement of the diaphragm were described by contour plots. In both postures, the diaphragm was flatter at FRC than at TLC, because of larger displacements in the dorsal than in the ventral region of the diaphragm. Rotation from the prone to supine body position produced a lever motion of the diaphragm, displacing the dorsal portion of the diaphragm cephalad and the ventral portion caudad. In five of the six dogs, bilateral isovolume pneumothorax was induced in the supine body position while intrathoracic gas volume was held constant. (ABSTRACT TRUNCATED AT 250 WORDS)
Detection of Extended-Spectrum β-Lactamase and Klebsiella pneumoniae Carbapenemase Genes Directly from Blood Cultures by Use of a Nucleic Acid Microarray

ABSTRACT The growing crisis of multidrug-resistant (MDR) Gram-negative bacteria requires that current technologies permit the rapid detection of extended-spectrum β-lactamase (bla ESBL) and Klebsiella pneumoniae carbapenemase (bla KPC) genes. In the present study, we assessed the performance characteristics of a commercially available nucleic acid microarray system for the detection of bla ESBL and bla KPC genes directly from positive blood cultures. Using blood cultures (BCs) that contained Gram-negative bacilli identified by Gram staining, we isolated bacterial DNA using spin columns (BC-C) and rapid water lysis (BC-W). Twenty ESBL/KPC-positive and 20 ESBL/KPC-negative blood culture samples, as well as 20 non-lactose-fermenting organisms, were tested. The 20 isolates that were ESBL positive by phenotypic testing were also evaluated on solid medium (SM), and the DNA was extracted by use of a spin column (SM-C). The resulting 140 DNA extractions were assessed for DNA quantity and quality using 260/280-nm absorbance ratios, and DNA microarray analysis was performed in a blinded fashion. Microarray and phenotypic results were concordant for 98.3% of BC-W, 90% of BC-C, and 95% of SM-C samples. Compared to phenotypic testing, the sensitivity and specificity for BC-C samples were 88.9% and 100%, respectively, and for BC-W samples, the sensitivity and specificity were 94.4% and 100%, respectively. BC-W samples yielded the highest concordance with phenotypic results. Nucleic acid microarrays offer promise in the identification of bla ESBL and bla KPC genes directly from blood cultures, thereby reducing the time to identification of these important pathogens.
The $n$th-Order Bias Optimality for Multichain Markov Decision Processes

In this paper, we propose a new approach to the theory of finite multichain Markov decision processes (MDPs) with different performance optimization criteria. We first propose the concept of nth-order bias; then, using the average reward and bias difference formulas derived in this paper, we develop an optimization theory for finite MDPs that covers a complete spectrum from average optimality, bias optimality, to all high-order bias optimality, in a unified way. The approach is simple, direct, natural, and intuitive; it depends neither on Laurent series expansion nor on discounted MDPs. We also propose one-phase policy iteration algorithms for bias and high-order bias optimal policies, which are more efficient than the two-phase algorithms in the literature. Furthermore, we derive high-order bias optimality equations. This research is a part of our effort in developing sensitivity-based learning and optimization theory.
Parsing with the Shortest Derivation

Common wisdom has it that the bias of stochastic grammars in favor of shorter derivations of a sentence is harmful and should be redressed. We show that the common wisdom is wrong for stochastic grammars that use elementary trees instead of context-free rules, such as Stochastic Tree-Substitution Grammars used by Data-Oriented Parsing models. For such grammars a non-probabilistic metric based on the shortest derivation outperforms a probabilistic metric on the ATIS and OVIS corpora, while it obtains competitive results on the Wall Street Journal (WSJ) corpus. This paper also contains the first published experiments with DOP on the WSJ.
Sensorless rotor temperature estimation of permanent magnet synchronous motor under load conditions

The work proposes a method for estimating the magnet temperature in permanent magnet synchronous machines (PMSM's) under load conditions. The method implies an intermittent injection of a voltage pulse in the positive and negative d-axis of the motor. Thus, the difference of the resulting d-current responses depends on the machine operating point which is defined by the d-current, the q-current and the actual magnetization level of the permanent magnets. Since the magnetization of the magnets depends on the temperature, different d-current slopes reflect different temperature levels of the magnets. By applying a voltage pulse in the positive and negative d-axis of the motor, symmetry of the induced voltages can be achieved in a manner that the difference of the current responses from the positive and negative pulse is to a great extent speed independent.
Solving linear arithmetic constraints for user interface applications

Linear equality and inequality constraints arise naturally in specifying many aspects of user interfaces, such as requiring that onewindowbe to the left of another, requiring that a pane occupy the leftmost 1/3 of a window, or preferring that an object be contained within a rectangle if possible. Current constraint solvers designed for UI applications cannot efficiently handle simultaneous linear equations and inequalities. This is amajor limitation. We describe incremental algorithms based on the dual simplex and active set methods that can solve such systems of constraints efficiently.
Stereoscopic Surface Interpolation Supports Lightness Constancy

The human visual system has a remarkable ability to construct surface representations from sparse stereoscopic, as well as texture and motion, information. In impoverished displays where few points are used to define regions in depth, the brain often interpolates depth estimates across intervening blank regions to create a compelling sense of a solid surface. The set of experiments described here examined stereoscopic interpolation using a novel technique based on lightness constancy. The effectiveness of this method is notable because it stands as the only technique to date that unequivocally examines the perception of interpolated surfaces, and not surfaces inferred subjectively from depth information in the stimulus. Further, these data support the growing evidence that a primary function of the stereoscopic system is to define three-dimensional surface structure.
Nitric Oxide Inhibits Rhinovirus-Induced Cytokine Production and Viral Replication in a Human Respiratory Epithelial Cell Line

ABSTRACT To better understand the early biochemical events that occur in human rhinovirus (HRV) infections, we examined the kinetics and mechanisms of interleukin-8 (IL-8) and IL-6 production from infected epithelial cells. Several HRV strains caused IL-8 and IL-6 production, but HRV-16 induced maximal IL-8 and IL-6 mRNA expression and protein production more rapidly than did HRV-14, despite similar rates of replication of the two viral strains. Viral induction of cytokine mRNA does not require new protein synthesis, since it was unaffected by cycloheximide treatment. The potent glucocorticoid budesonide did not affect viral replication or cytokine mRNA induction but modestly inhibited cytokine protein production. Interestingly, the nitric oxide donor 3-(2-hydroxy-2-nitroso-1-propylhydrazino)-1-propanamine (NONOate) inhibited both rhinovirus replication and cytokine production in a dose-dependent fashion without reducing levels of cytokine mRNA. The NONOate effects were due to release of nitric oxide, because NONOate that had been depleted of its nitric oxide content had no effect. Thus, nitric oxide may play an important anti-inflammatory and antiviral role in colds and nitric oxide donors may represent a novel therapeutic approach.
A Model for Evaluation of Interactive Information Retrieval

1.INTRODUCTION Research in information retrieval (IR) has expanded to take a broader perspective of the information seeking process to explicitly include users, tasks, and contexts in a dynamic setting rather than treating information search as static or as a sequence of unrelated events. The traditional Cranfield/TREC IR system evaluation paradigm, using document relevance as a criterion, and evaluating single search results, is not appropriate for many circumstances considered in current research. Several alternatives to relevance have been proposed, including utility, and satisfaction. We suggest an evaluation model and methodology grounded in the nature of information seeking and centered on usefulness. We believe this model has broad applicability in current IR research.
Anion channels in the sea urchin sperm plasma membrane

Ionic fluxes in sea urchin sperm plasma membrane regulate cell motility and the acrosome reaction (AR). Although cationic channels mediate some of the ionic movements, little is known about anion channels in these cells. The fusion of sperm plasma membranes into lipid bilayers allowed identification of a 150 pS anion channel. This anion channel was enriched from detergent‐solubilized sperm plasma membranes using a wheat germ agglutinin Sepharose column. Vesicles formed from this preparation were fused into black lipid membranes (BLM), yielding single channel anion‐selective activity with the properties of those found in the sperm membranes. The following anion selectivity sequence was found: NO3− > CNS− > Br− > CI−. This anion channel has a high open probability at the holding potentials tested, it is partially blocked by 4,4′‐diisothiocyano‐2,2′ ‐stilbendisulfonic acid (DIDS), and it often displays substates. The sperm AR was also inhibited by DIDS. © 1993 Wiley‐Liss, Inc.
Polygenic selection underlies evolution of human brain structure and behavioral traits

Seemingly paradoxical characteristics of psychiatric disorders, including moderate to high prevalence, reduced fecundity, and high heritability have motivated explanations for the persistence of common risk alleles for severe psychiatric phenotypes throughout human evolution. Proposed mechanisms include balancing selection, drift, and weak polygenic adaptation acting either directly, or indirectly through selection on correlated traits. While many mechanisms have been proposed, few have been empirically tested. Leveraging publicly available data of unprecedented sample size, we studied twenty-five traits (i.e., ten neuropsychiatric disorders, three personality traits, total intracranial volume, seven subcortical brain structure volume traits, and four complex traits without neuropsychiatric associations) for evidence of several different signatures of selection over a range of evolutionary time scales. Consistent with the largely polygenic architecture of neuropsychiatric traits, we found no enrichment of trait-associated single-nucleotide polymorphisms (SNPs) in regions of the genome that underwent classical selective sweeps (i.e., events which would have driven selected alleles to near fixation). However, we discovered that SNPs associated with some, but not all, behaviors and brain structure volumes are enriched in genomic regions under selection since divergence from Neanderthals ~600,000 years ago, and show further evidence for signatures of ancient and recent polygenic adaptation. Individual subcortical brain structure volumes demonstrate genome-wide evidence in support of a mosaic theory of brain evolution while total intracranial volume and height appear to share evolutionary constraints consistent with concerted evolution. We further characterized the biological processes potentially targeted by selection, through expression Quantitative Trait Locus (eQTL) and Gene Ontology (GO) enrichment analyses and found evidence for the role of regulatory functions among selected SNPs in immune and brain tissues. Taken together, our results suggest that alleles associated with neuropsychiatric, behavioral, and brain volume phenotypes have experienced both ancient and recent polygenic adaptation in human evolution, acting through neurodevelopmental and immune-mediated pathways.
A Statistical Comparison of Three Root Cause Analysis Tools

Dr. Mark Doggett is a post-doctoral fellow andinstructor at Colorado State University and is anadjunct faculty member at Aims Community Col-lege. He is currently working on grants for theNational Science Foundation in medical technol-ogy and the Department of Education in careerand technical education. He also teaches coursesin process control, leadership, and project man-agement. His research interests are decision-mak-ing and problem-solving strategies, technicalmanagement, theory of constraints, and opera-tions system design.
Dynamic MRA With Four-Dimensional Time-Resolved Angiography Using Keyhole at 3 Tesla in Head and Neck Vascular Lesions

Conventional MRA provides inadequate visualization of the dynamic features of blood flow in vascular lesions of the head and neck. Four-dimensional time-resolved angiography using keyhole (4D-TRAK) is a new technique of performing contrast-enhanced MRA. By combining parallel imaging with sensitivity encoding (SENSE) with the keyhole imaging technique and a high field strength (3 T) magnet, we have been able to obtain detailed hemodynamic information similar to that obtained via catheter angiography with digital subtraction (DSA), but without the risks associated with ionizing radiation exposure, iodizing contrast agents, or catheterization itself.
Smad3 Couples Pak1 With the Antihypertrophic Pathway Through the E3 Ubiquitin Ligase, Fbxo32

Pathological cardiac hypertrophy is regarded as a critical intermediate step toward the development of heart failure. Many signal transduction cascades are demonstrated to dictate the induction and progression of pathological hypertrophy; however, our understanding in regulatory mechanisms responsible for the suppression of hypertrophy remains limited. In this study, we showed that exacerbated hypertrophy induced by pressure overload in cardiac-deleted Pak1 mice was attributable to a failure to upregulate the antihypertrophic E3 ligase, Fbxo32, responsible for targeting proteins for the ubiquitin-degradation pathway. Under pressure overload, cardiac overexpression of constitutively active Pak1 mice manifested strong resilience against pathological hypertrophic remodeling. Mechanistic studies demonstrated that subsequent to Pak1 activation, the binding of Smad3 on a critical singular AGAC-286-binding site on the FBXO32 promoter was crucial for its transcriptional regulation. Pharmacological upregulation of Fbxo32 by Berberine ameliorated hypertrophic remodeling and improved cardiac performance in cardiac-deficient Pak1 mice under pressure overload. Our findings discover Smad3 and Fbxo32 as novel downstream components of the Pak1-dependent signaling pathway for the suppression of hypertrophy. This discovery opens a new venue for opportunities to identify novel targets for the management of cardiac hypertrophy.
Clustering of scientific journals

A cluster analysis procedure is described in which 288 journals in the disciplines of physics, chemistry and molecular biology are grouped into clusters. Most of the clusters are easily identified as subdisciplinary subject areas. The data source was the cross citing amongst the journals derived from the Journal Citation Index (JCI), a file derived in turn from the Science Citation Index (SCI)®. The JCI consists of journal by journal tabulation of citings to and from each journal processed in the SCI. Two‐step citation maps linking the clusters are presented for each discipline. Within the disciplines the clusters of journals form fully transitive hierarchies with very few relational conflicts.
Defining and Implementing Commutativity Conditions for Parallel Execution

Irregular applications, which manipulate complex, pointer-based data structures, are a promising target for parallelization. Recent studies have shown that these programs exhibit a kind of parallelism called amorphous data-parallelism. Prior approaches to parallelizing these applications, such as thread-level speculation and transactional memory, often obscure parallelism because they do not distinguish between the concrete representation of a data structure and its semantic state; they conflate metadata and data. Exploiting the semantic commutativity of methods in complex data structures is a promising approach to exposing more parallelism. Prior work has shown that abstract locks can be used to capture a subset of commutativity properties, however, abstract locks cannot uncover the parallelism in some complex data structures, such as kd-trees and union-find structures. In this paper, we propose a more flexible implementation of commutativity properties, called gatekeepers, which capture more complex commutativity conditions and thus expose more parallelism. We provide a formal definition of semantic commutativity and define conditions under which abstract locking can be applied and those under which gatekeeping is necessary. We present a quantitative study demonstrating the benefits of abstract locking and gatekeeping in amorphous data-parallel programs. We also present an efficient implementation of gatekeeping, which we evaluate on a real-world application.
Spatial Analysis of The Correlation Between Hot Spot Distribution and Land Cover Type in Sumatra, Indonesia

Based on land cover data of 2015, Sumatra is dominated by shrubs, bushes, plantations with hardwoods, and plantations. It is the island with the largest peat distribution in Indonesia. Peatland forest map provided by Ministry of Environment and Forestry in 2015 represent that the total area of peatland in Sumatra is about 9.6 million hectares, mostly located in Riau, Jambi, and South Sumatra Province. Fire incidents can be indicated through hot spots distribution data. The data used is the distribution of hot spot of Sumatra in 2005–2016. The purpose of this study was to analyze the pattern of hot spot distribution and its relations with land cover changes. Overlay results indicate that 31.75% fires occur in shrubs and bushes, 20.87% in plantations with hardwoods, 16.60% in other natural cleared areas, 14.55% in forest crops, and the rest spreads in lowland crops, dry season crops, and swamp / peat forests. The highest hot spots are in 2005 and 2015 due to the El Nino effect that causes prolonged drought. Available land cover data indicates a change during 1990 through 2011. Most of peat land turn into plantation between 1990 to 2000. The result of overlay of hot spot distribution with land cover data from 2006–2015 shows that forest fires mostly occur in industrial plantation forest. This can be seen from the land cover classification where previously a plantation forest, then it is burned into a field and become an industrial plantation forest. Nevertheless, this analysis still need to be validated through ground truth to check the actual land cover and land use in field.
New Insights and Methods For Predicting Face-To-Face Contacts

The prediction of new links in social networks is a challeng- ing task. In this paper, we focus on predicting links in net- works of face-to-face spatial proximity by using information from online social networks, such as co-authorship networks in DBLP, and a number of node level attributes. First, we analyze influence factors for the link prediction task. Then, we propose a novel method that combines information from different networks and node level attributes for the pre- diction task: We introduce an unsupervised link prediction method based on rooted random walks, and show that it out- performs state-of-the-art unsupervised link prediction meth- ods. We present an evaluation using three real-world datasets. Furthermore, we discuss the impact of our results and of the insights we glean in the field of link prediction and human contact behavior.
Simulating artificial life using Boltzmann machines

This work describes a concept neural architecture and an expandable software library we created to simulate autonomous biologically inspired agents (biots) in a changing environment. The concept and the software developed are based on a set of restrictive rules. First, whenever there is a decision to be taken, the method more alike to biological systems is to be chosen. Second, we made it a big point that biots were individual beings capable of learning by their own experiences, not instances of a single algorithm. Third, the biots are supposed to know as little as possible about their location in the testing ground, methods of reaching the goal or any measurement of progress. We call that the "no hints" rule. Finally, a rule that is in a way related to the previous rules; in hope of future hardware implementations, we try to keep the model physically realistic and implementable in hardware. This is not always quite possible due to certain simplifications.
Quantification of artificial surfaces impact on Urban Heat Island of Novi Sad (Vojvodina, Serbia)

Introduction It is crucial in land cover and climate change research to systematically describe the environment in order to detect its changes, human-related causes and responses. Earth’s land surface and its changes are central in most of the biophysical processes of global environmental change. Therefore, land change is qualified as a forcing function within the global environmental change (Grugia et al., 2010, Jansen and Di Gregorio, 2002; Turner, 2002; Turner, 2006). Land cover has been defined by the attributes of the Earth’s land surface and immediate subsurface, including biota, soil, topography, surface and groundwater, and human (mainly built-up) structure (Lambin et al., 2006). This paper analyse land cover patches and urban temperature intensity of the City of Novi Sad (Vojvodina, Serbia). The main purpose of the analyses is to quantify land cover patches within zones of annual mean urban heat island (UHI) temperature intensity of Novi Sad. Quantified land cover patches are bringing most useful information about state of UHI that is impacted by human influences.
Fast inter-layer mode decision in Scalable Video Coding

The recently developed video encoding standard Scalable Video Coding (SVC) is designed as the extension of H.264/AVC. By employing new techniques such as hierarchal layer encoding, SVC could produce bit streams with different frame rates, bit rates and spatial resolutions; but meanwhile, the computational complexity of video encoder is also increased, which makes optimization of SVC encoding a necessity. In this paper, a novel algorithm is proposed, which utilizes the encoding mode of Base Layer (BL) macroblocks (MBs) to initialize the potential optimal candidate encoding mode list for Enhancement Layer (EL) MBs, by mapping encoding modes onto a Two-Dimensional (2D) map. Experimental results demonstrate that, the proposed algorithm could achieve significantly better and more robust time saving than two recent works while maintaining the video performances.