Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-Time Reverse Transcriptase PCR Assay for Detection of Human Metapneumoviruses from All Known Genetic Lineages

ABSTRACT The discovery of human metapneumovirus and its implications for respiratory tract disease have emphasized the need for a sensitive, specific, and rapid assay to detect this virus in a clinical setting. It recently became clear that human metapneumovirus can be grouped into at least four genetic lineages. Previously described assays for the detection of human metapneumovirus were developed by using limited sequence information and failed to detect viruses from all four genetic lineages with comparable sensitivities. Here we describe the development and evaluation of a real-time reverse transcriptase PCR assay that detects human metapneumovirus from the four known genetic lineages with equal specificities and sensitivities.
Semantic segmentation of modular furniture

This paper proposes an approach for the semantic segmentation and structural parsing of modular furniture items, such as cabinets, wardrobes, and bookshelves, into so called interaction elements. Such a segmentation into functional units is challenging not only due to the visual similarity of the different elements but also because of their often uniformly colored and low-texture appearance. Our method addresses these challenges by merging structural and appearance likelihoods of each element and jointly optimizing over shape, relative location, and class labels using Markov Chain Monte Carlo (MCMC) sampling. We propose a novel concept called rectangle coverings which provides a tight bound on the number of structural elements and hence narrows down the search space. We evaluate our approach's performance on a novel dataset of furniture items and demonstrate its applicability in practice.
Chemical Biology for Understanding Matrix Metalloproteinase Function

The matrix metalloproteinase (MMP) family has long been associated with normal physiological processes such as embryonic implantation, tissue remodeling, organ development, and wound healing, as well as multiple aspects of cancer initiation and progression, osteoarthritis, inflammatory and vascular diseases, and neurodegenerative diseases. The development of chemically designed MMP probes has advanced our understanding of the roles of MMPs in disease in addition to shedding considerable light on the mechanisms of MMP action. The first generation of protease‐activated agents has demonstrated proof of principle as well as providing impetus for in vivo applications. One common problem has been a lack of agent stability at nontargeted tissues and organs due to activation by multiple proteases. The present review considers how chemical biology has impacted the progress made in understanding the roles of MMPs in disease and the basic mechanisms of MMP action.
Analysis of correlation matrices using covariance structure models.

It is often assumed that covariance structure models can be arbitrarily applied to sample correlation matrices as readily as to sample covariance matrices. Although this is true in many cases and leads to an analysis that is mostly correct, it is not permissible for all structures. This article reviews three interrelated problems associated with the analysis of structural models using a matrix of sample correlations. Depending upon the model, applying a covariance structure to a matrix of correlations may (a) modify the model being studied, (b) produce incorrect values of the omnibus test statistic, or (c) yield incorrect standard errors. An important class of models are those that are scale invariant (Browne, 1982), for then Errors a and b cannot occur when a correlation matrix is analyzed. A number of examples based on restricted factor analysis are presented to illustrate the concepts described in the article.
Delayed-dictionary compression for packet networks

This paper considers compression in packet networks. Since data packets may be dropped or arrive reordered, streaming compression algorithms result in a considerable decoding latency. On the other hand, standard stateless packet compression algorithms that compress each packet independently, give a relatively poor compression ratio. We introduce a novel compression algorithm for packet networks: delayed-dictionary compression. By allowing delay in the dictionary construction, the algorithm handles effectively the problems of packet drops and packet reordering, while resulting with a compression quality which is often substantially better than standard stateless packet compression and has a smaller decoding latency than that of streaming compression. We conducted extensive experiments to establish the potential improvement for packet compression techniques, using many data files including the Calgary corpus and the Canterbury corpus. Experimental results of the new delayed-dictionary compression show that its main advantage is in low to medium speed links.
The role of romantic relationships on athletes' performance and well-being.

Guided by the work-family interface literature, this study examined the concept of spillover in a sample of elite athletes. It was conceptualized that there would be potential negativity and interference between athletes’ intense demands of competitive sport and efforts to maintain positive relationships with their partners. Antecedents and consequences of the potential spillover phenomenon were assessed in a sample of 87 elite-level athletes who had either romantic or marital, heterosexual relationships. Findings indicated that while trust, commitment, and communication were not strongly related to spillover, negative transactions were. Moreover, the occurrence of spillover was negatively related to sport satisfaction and positively to depressive symptoms. Finally, it was found that a mechanism by which perceived negative transactions were linked to athletes’ satisfaction and depression was through spillover. Spillover can help explain how personal relationships and sport are likely to contribute to athl.
Neurocognitive Function and Health-Related Quality of Life in Pediatric Korean Survivors of Medulloblastoma

The neurocognitive function and quality of life of 58 Korean survivors of childhood medulloblastoma were assessed after surgery, cranial radiation and chemotherapy. All patients were evaluated with a battery of neurocognitive function tests and the Pediatric Functional Assessment of Cancer Therapy-Brain Tumor Survivors, which consists of self-report questionnaires on quality of life. The mean full-scale intelligence quotient (IQ), verbal IQ, and performance IQ scores were 90.2, 97.1, and 84.16, respectively. The mean memory quotient (MQ) score was 86.78, which was within 1 standard deviation of the average score of 100. Processing speed, attention, and executive function showed mild to moderate deficits. Intelligence, memory, executive function, visuospatial function, and simple motor function were significantly lower in the patients diagnosed before 8 years of age compared with those diagnosed after 8. The cognitive deficits in the patients diagnosed at younger ages might be related to earlier exposure to craniospinal irradiation and chemotherapy. The patient and parent proxy evaluations of attention, fine motor function, and quality of life did not differ. We found significant neurocognitive changes in a wide range of neurocognitive functional domains in Korean survivors of childhood medulloblastoma. Long-term follow-up studies of survivors of childhood medulloblastoma beginning at the time of their first diagnosis are required to better understand the deficits exhibited by survivors of childhood medulloblastoma, so that intervention strategies and treatment refinements that reduce the long-term neurocognitive decline can be developed.
ON THE OXYGEN ISOTOPIC COMPOSITION OF THE SOLAR SYSTEM

The 18O/17O ratio of the solar system is 5.2 while that of the interstellar medium (ISM) and young stellar objects is ∼4. This difference cannot be explained by pollution of the Sun's natal molecular cloud by 18O-rich supernova ejecta because (1) the necessary B-star progenitors live longer than the duration of star formation in molecular clouds, (2) the delivery of ejecta gas is too inefficient and the amount of dust in supernova ejecta is too small compared to the required pollution (2% of total mass or ∼20% of oxygen), and (3) the predicted amounts of concomitant short-lived radionuclides (SLRs) conflicts with the abundances of 26Al and 41Ca in the early solar system. Proposals for the introduction of 18O-rich material must also be consistent with any explanation for the origin of the observed slope-one relationship between 17O/16O and 18O/16O in the high-temperature components of primitive meteorites. The difference in 18O/17O ratios can be explained by enrichment of the ISM by the 17O-rich winds of asymptotic giant branch (AGB) stars, the sequestration of comparatively 18O-rich gas from star-forming regions into long-lived, low-mass stars, and a monotonic decrease in the 18O/17O ratio of interstellar gas. At plausible rates of star formation and gas infall, Galactic chemical evolution does not follow a slope-one line in a three-isotope plot, but instead moves along a steeper trajectory toward an 17O-rich state. Evolution of the ISM and star-forming gas by AGB winds also explains the difference in the carbon isotope ratios of the solar system and ISM.
Glosser: Enhanced Feedback for Student Writing Tasks

We describe Glosser, a system that supports students in writing essays by 1) scaffolding their reflection with trigger questions, and 2) using text mining techniques to provide content clues that can help answer those questions. A comparison with other computer generated feedback and scorings systems is provided to explain the novelty of the approach. We evaluate the system with Wiki pages produced by postgraduate students as part of their assessment.
The Relationship Between Gluteal Muscle Activation and Throwing Kinematics in Baseball and Softball Catchers

Abstract Plummer HA and Oliver GD. The relationship between gluteal muscle activation and throwing kinematics in baseball and softball catchers. J Strength Cond Res 28(1): 87–96, 2014—The purpose of this study was to determine the relationship between gluteal muscle activation and pelvis and trunk kinematics when catchers throw to second base. Forty-two baseball and softball catchers (14.74 ± 4.07 years; 161.85 ± 15.24 cm; 63.38 ± 19.98 kg) participated in this study. Muscle activity of the bilateral gluteus maximus and medius as well as pelvis and trunk kinematics throughout the throwing motion were analyzed. It was discovered that at foot contact, there were 2 significant inverse relationships between stride leg gluteus maximus activity and pelvis axial rotation (r = −0.31, r2 = 0.10, p = 0.05), and between trunk axial rotation and pelvis lateral flexion (r = −0.34, r2 = 0.12, p = 0.03). In addition, at foot contact, a significant positive relationship between the drive leg (throwing arm side) and trunk flexion (r = 0.33, r2 = 0.11, p = 0.04) was present. The results of this study provide evidence of gluteal activation both concentrically and eccentrically, in attempt to control the pelvis and trunk during the throwing motion of catchers. The gluteal muscles play a direct role in maintaining the stability of the pelvis, and catchers should incorporate strengthening of the entire lumbopelvic-hip complex into their training regimen. Incorporating concentric and eccentric gluteal exercises will help to improve musculoskeletal core stability, thereby assisting in upper extremity injury prevention.
A physically faithful multigrid method for fast cloth simulation

We present an efficient multigrid algorithm that is adequate to solve a heavy linear system given in cloth simulation. Although a multigrid solver has been successfully employed to the Poisson problems, it is hard to apply the solver to complicated cloth deformations due to its lack of physical meaning in level construction. We address this problem by developing a physically faithful technique ensuring the conservation of all physical quantities across levels. The performance of our approach is demonstrated on a number of garment simulations implemented by the state of the art techniques: the implicit integration, the triangle‐based in‐plane energy model, and the curvature‐based bending energy model. Our multigrid algorithm is about four times faster than the preconditioned Conjugate Gradient method for a garment with 20K particles. Copyright © 2008 John Wiley & Sons, Ltd.
Avian Resistance to Campylobacter jejuni Colonization Is Associated with an Intestinal Immunogene Expression Signature Identified by mRNA Sequencing

Campylobacter jejuni is the most common cause of human bacterial gastroenteritis and is associated with several post-infectious manifestations, including onset of the autoimmune neuropathy Guillain-Barré syndrome, causing significant morbidity and mortality. Poorly-cooked chicken meat is the most frequent source of infection as C. jejuni colonizes the avian intestine in a commensal relationship. However, not all chickens are equally colonized and resistance seems to be genetically determined. We hypothesize that differences in immune response may contribute to variation in colonization levels between susceptible and resistant birds. Using high-throughput sequencing in an avian infection model, we investigate gene expression associated with resistance or susceptibility to colonization of the gastrointestinal tract with C. jejuni and find that gut related immune mechanisms are critical for regulating colonization. Amongst a single population of 300 4-week old chickens, there was clear segregation in levels of C. jejuni colonization 48 hours post-exposure. RNAseq analysis of caecal tissue from 14 C. jejuni-susceptible and 14 C. jejuni-resistant birds generated over 363 million short mRNA sequences which were investigated to identify 219 differentially expressed genes. Significantly higher expression of genes involved in the innate immune response, cytokine signaling, B cell and T cell activation and immunoglobulin production, as well as the renin-angiotensin system was observed in resistant birds, suggesting an early active immune response to C. jejuni. Lower expression of these genes in colonized birds suggests suppression or inhibition of a clearing immune response thus facilitating commensal colonization and generating vectors for zoonotic transmission. This study describes biological processes regulating C. jejuni colonization of the avian intestine and gives insight into the differential immune mechanisms incited in response to commensal bacteria in general within vertebrate populations. The results reported here illustrate how an exaggerated immune response may be elicited in a subset of the population, which alters host-microbe interactions and inhibits the commensal state, therefore having wider relevance with regard to inflammatory and autoimmune disease.
Query expansion and query translation as logical inference

A number of studies have examined the problems of query expansion in monolingual Information Retrieval (IR), and query translation for crosslanguage IR. However, no link has been made between them. This article first shows that query translation is a special case of query expansion. There is also another set of studies on inferential IR. Again, there is no relationship established with query translation or query expansion. The second claim of this article is that logical inference is a general form that covers query expansion and query translation. This analysis provides a unified view of different subareas of IR. We further develop the inferential IR approach in two particular contexts: using fuzzy logic and probability theory. The evaluation formulas obtained are shown to strongly correspond to those used in other IR models. This indicates that inference is indeed the core of advanced IR.
Engineering formal metatheory

Machine-checked proofs of properties of programming languages have become acritical need, both for increased confidence in large and complex designsand as a foundation for technologies such as proof-carrying code. However, constructing these proofs remains a black art, involving many choices in the formulation of definitions and theorems that make a huge cumulative difference in the difficulty of carrying out large formal developments. There presentation and manipulation of terms with variable binding is a key issue. We propose a novel style for formalizing metatheory, combining locally nameless representation of terms and cofinite quantification of free variable names in inductivedefinitions of relations on terms (typing, reduction, .). The key technical insight is that our use of cofinite quantification obviates the need for reasoning about equivariance (the fact that free names can be renamed in derivations); in particular, the structural induction principles of relations defined using cofinite quantification are strong enough for metatheoretic reasoning, and need not be explicitly strengthened. Strong inversion principles follow (automatically, in Coq) from the induction principles. Although many of the underlying ingredients of our technique have been used before, their combination here yields a significant improvement over other methodologies using first-order representations, leading to developments that are faithful to informal practice, yet require noexternal tool support and little infrastructure within the proof assistant. We have carried out several large developments in this style using the Coq proof assistant and have made them publicly available. Our developments include type soundness for System F sub; and core ML (with references, exceptions, datatypes, recursion, and patterns) and subject reduction for the Calculus of Constructions. Not only do these developments demonstrate the comprehensiveness of our approach; they have also been optimized for clarity and robustness, making them good templates for future extension.
Vector Lane Threading

Multi-lane vector processors achieve excellent computational throughput for programs with high data-level parallelism (DLP). However, application phases without significant DLP are unable to fully utilize the datapaths in the vector lanes. In this paper, we propose vector lane threading (VLT), an architectural enhancement that allows idle vector lanes to run short-vector or scalar threads. VLT-enhanced vector hardware can exploit both data-level and thread-level parallelism to achieve higher performance. We investigate implementation alternatives for VLT, focusing mostly on the instruction issue bandwidth requirements. We demonstrate that VLT's area overhead is small. For applications with short vectors, VLT leads to additional speedup of IA to 23 over the base vector design. For scalar threads, VLT outperforms a 2-way CMP design by a factor of two. Overall, VLT allows vector processors to reach high computational throughput for a wider range of parallel programs and become a competitive alternative to CMP systems
Timing driven placement in interaction with netlist transformations

In this paper, we present a new approach that performs timing driven placement for standard cell circuits in interaction with netlist transformations. As netlist transformations are integrated into the placement process, an accurate net delay model is available. This model provides the basis for e ective netlist transformations. In contrast to previous approaches that apply netlist transformations during placement, we are not restricted to local transformations like fanout bu ering or gate resizing. Instead, we exploit global dependencies between the signals in the circuit. Results for benchmark circuits show excellent placement quality. The maximum path delay is reduced up to 33% compared to the initial timing driven placement of the original netlist and up to 18% compared to the results obtained by consecutive optimization of the netlist and timing driven placement of the optimized netlist. This delay reduction is achieved with almost no increase in chip area.
Automatic Selection of Reference Pages in Wikipedia for Improving Targeted Entities Disambiguation

In Targeted Entity Disambiguation setting, we take (i) a set of entity names which belong to the same domain (target entities), (ii) candidate mentions of the given entities which are texts that contain the target entities as input, and then determine which ones are true mentions of “target entity”. For example, given the names of IT companies, including Apple, we determine Apple in a mention denotes an IT company or not. Prior work proposed a graph based model. This model ranks all candidate mentions based on scores which denote the degree of relevancy to target entities. Furthermore, this graph based model could utilize reference pages of target entities. However, human annotators must select reference pages in advance. We propose an automatic method that can select reference pages. We formalize the selection problem of reference pages as an Integer Linear Programming problem. We show that our model works as well as the prior work that manually selected reference pages.
Comparison of the Bactec Peds Plus pediatric blood culture vial with Roche pediatric Septi-Chek for blood cultures from pediatric patients

Equal volumes of blood from 4,112 blood cultures were inoculated into one Bactec Peds Plus bottle and one Roche Septi-Chek bottle. There were no significant differences in the recoveries of bloodstream pathogens. Initial detection occurred earlier with Bactec Peds Plus, while growth on solid media occurred earlier with Roche Septi-Chek.
Robust and Data-Driven Optimization: Modern Decision-Making Under Uncertainty

Traditional models of decision-making under uncertainty assume perfect information, i.e., accurate values for the system parameters and speciflc probability distributions for the random variables. However, such precise knowledge is rarely available in practice, and a strategy based on erroneous inputs might be infeasible or exhibit poor performance when implemented. The purpose of this tutorial is to present a mathematical framework that is well-suited to the limited information available in real-life problems and captures the decision-maker’s attitude towards uncertainty; the proposed approach builds upon recent developments in robust and data-driven optimization. In robust optimization, random variables are modeled as uncertain parameters belonging to a convex uncertainty set and the decision-maker protects the system against the worst case within that set. Data-driven optimization uses observations of the random variables as direct inputs to the mathematical programming problems. The flrst part of the tutorial describes the robust optimization paradigm in detail in single-stage and multi-stage problems. In the second part, we address the issue of constructing uncertainty sets using historical realizations of the random variables and investigate the connection between convex sets, in particular polyhedra, and a speciflc class of risk measures.