Miracle-dz/UniFAR-FTUs huggingface dataset:
Answering Object Queries over Knowledge Bases with Expressive Underlying Description Logics

Many information sources can be viewed as collections of objects and descriptions about objects. The relationship between objects is often characterized by a set of constraints that semantically encode background knowledge of some domain. The most straightforward and fundamental way to access information in these repositories is to search for objects that satisfy certain selection criteria. This work considers a description logics (DL) based representation of such information sources and object queries, which allows for automated reasoning over the constraints accompanying objects. Formally, a knowledge base K = (T ,A) captures constraints in the terminology (a TBox) T , and objects with their descriptions in the assertions (an ABox) A, using some DL dialect L. In such a setting, object descriptions are L-concepts and object identifiers correspond to individual names occurring in K. Correspondingly, object queries are the well known problem of instance retrieval in the underlying DL knowledge base K, which returns the identifiers of qualifying objects. This work generalizes instance retrieval over knowledge bases to provide users with answers in which both identifiers and descriptions of qualifying objects are given. The proposed query paradigm, called assertion retrieval, is favoured over instance retrieval since it provides more informative answers to users. A more compelling reason is related to performance: assertion retrieval enables a transfer of basic relational database techniques, such as caching and query rewriting, in the context of an assertion retrieval algebra. The main contributions of this work are two-fold: one concerns optimizing the fundamental reasoning task that underlies assertion retrieval, namely, instance checking, and the other establishes a query compilation framework based on the assertion retrieval algebra. The former is necessary because an assertion retrieval query can entail a large volume of instance checking requests in the form of K |= a : C, where a is an individual name and C is a L-concept. This work thus proposes a novel absorption technique, ABox absorption, to improve instance checking. ABox absorption handles knowledge bases that have an expressive underlying dialect L, for instance, that requires disjunctive knowledge. It works particularly well when knowledge bases contain a large number of concrete domain concepts for object descriptions. This work further presents a query compilation framework based on the assertion retrieval algebra to make assertion retrieval more practical. In the framework, a suite of rewriting rules is provided to generate a variety of query plans, with a focus on plans that avoid reasoning w.r. t. the background knowledge bases when sufficient cached results of earlier requests exist. ABox absorption and the query compilation framework have been implemented in a prototypical system, dubbed CARE Assertion Retrieval Engine (CARE).
Overexpression, purification, and late transcription factor activity of the 17-kilodalton protein encoded by the vaccinia virus A1L gene

The A1L, A2L, and G8R open reading frames (ORFs) were previously shown by transfection assays to encode transactivators of late gene expression. We now present evidence that the 17-kDa protein product of the A1L gene can function in vitro as a transcription factor. Simultaneous overexpression of the transactivators was achieved by coinfecting HeLa cells with one recombinant vaccinia virus that encodes the bacteriophage T7 RNA polymerase and three recombinant vaccinia viruses that contain copies of A1L, A2L, and G8R ORFs regulated by T7 promoters. Extracts from the recombinant virus-infected cells exhibited greatly enhanced late in vitro transcription activity and served as a source of factors. The 17-kDa product of the A1L ORF represented approximately 8% of the ammonium sulfate-precipitated cell protein and copurified with a late transcription factor activity. The transcription factor activity could be specifically immunodepleted with immobilized antibody to the bacterially expressed A1L-encoded protein, providing additional evidence for its identity and role. A sequence encoding six consecutive histidines was added to the A1L ORF, which was then incorporated into the genome of a baculovirus expression vector. The 17-kDa protein, synthesized in insect cells and purified by binding to an Ni(2+)-chelating affinity column, could replace the vaccinia virus-overexpressed 17-kDa protein in transcription assays. In addition to the 17-kDa product of the A1L gene, which was named vaccinia virus late transcription factor 2, the proteins that stimulate specific transcription of late promoter-regulated templates included the viral multisubunit RNA polymerase, vaccinia virus late transcription factor 1 (the product of the G8R ORF), and at least one other partially purified protein.
Quantification of pleural effusions: sonography versus radiography.

PURPOSE To develop a practical method of estimating the volume of pleural effusions with sonography. MATERIALS AND METHODS Fifty-one patients underwent sonography of the pleural space while supine. Sonographic results and results of lateral decubitus radiography were compared with actual effusion volumes. The maximum thickness of the pleural fluid layer was measured with both modalities, while actual effusion volume was determined by means of complete drainage. RESULTS Sonographic measurements correlated statistically significantly better with actual effusion volume (r = .80) than did radiographic measurements (r = .58) (P < or = .05). With sonographic measurement, an effusion width of 20 mm had a mean volume of 380 mL +/- 130 (standard deviation), while one of 40 mm had a mean volume of 1,000 mL +/- 330. Prediction error with sonographic measurement (mean, 224 mL) was statistically significantly less (P < or = .002) than that with radiographic measurement (mean, 465 mL). CONCLUSION In quantification of pleural effusions, the sonographic measurement method presented is preferable to radiographic measurement.
ASSOCIATION OF MORAXELLA OVIS WITH KERATOCONJUNCTIVITIS IN MULE DEER AND MOOSE IN WYOMING

Six cases of infectious keratoconjunctivitis (IKC) in mule deer (Odocoileus hemionus) and moose (Alces alces) in Wyoming (USA) were investigated during fall and winter of 1995 and 1996. Excessive lacrimation, mucopurulent conjunctivitis, keratitis, and corneal opacity were observed in mule deer. Moose had severe mucopurulent conjunctivitis, keratitis, and corneal ulceration. Hemolytic, non-piliated Moraxella ovis was isolated from two mule deer and two moose. We attempted to reproduce IKC in three mule deer fawns using an isolate of M. ovis from a clinically affected mule deer. These fawns did not develop clinical signs of infection and the bacterium was not reisolated from inoculated deer. Inoculated deer may not have developed clinical signs because deer were not exposed to ultraviolet light or mechanical insult before inoculation. In addition, the isolate used for inoculation may have lost virulence factors through passage, or M. ovis may not have been the primary pathogen responsible for clinical disease in the natural cases of IKC we investigated. The etiology of IKC in free-ranging wild ruminants remains poorly understood.
The effects of platelet gel–released supernatant on human fibroblasts

In recent years, interest in the topical use of platelet gel (PG) to stimulate wound healing has rapidly extended into various clinical applications and specialized fields. Many recent in vitro and in vivo studies have attempted to explain the biological mechanisms involved in PG‐induced tissue regeneration/reparation. However, it remains unclear which parameters should be used in clinical applications to obtain satisfactory results in the healing of wounds. Toward this end, the present study focused on understanding the relationship between platelet concentrations and the cellular parameters of the cell types, i.e., fibroblasts, involved in wound healing. Normal human dermal fibroblasts were treated with PG‐released supernatant at various concentrations in different assays (proliferation, migration, invasion, and in vitro scratch wound closure) to identify the most effective concentration to promote the fibroblasts' activities. Different concentrations of platelets per microliter in PG have different levels of efficacy in inducing fibroblast activity. The most effective concentration was obtained from PG at a concentration of approximately 0.5–1.5 × 106 plt/μL; higher concentrations were less effective. This study shows that excessively high concentrations of platelets per microliter have an inhibitory effect on the wound healing processes and are, therefore, counterproductive.
Hepatocyte Selection Medium

does not contain hazardous reagents or introduce genetic material. Our results show that hiPS cells die after three days of culture in HSM. Prior to performing the experiments, we compared the hiPS cell viability in media containing crude or dialyzed KSR or combination of insulin (10 μM), dexamethasone (10 μM) and aprotitin (5000 U/ml) (IDA) Unexpectedly, the KSR dialysis and IDA had no effect on hiPS cell survival. As expected, primary human hepatocytes survived in HSM as well as in HCM, which is the recommended medium for their culture. HSM can be used in clinical practices in situations when hepatocytes differentiated from human iPS cells are transplanted to patients suffering from liver failure.
Hematein Inhibits Atherosclerosis by Inhibition of Reactive Oxygen Generation and NF-&kgr;B–Dependent Inflammatory Mediators in Hyperlipidemic Mice

Hematein, a natural compound, is a known anti-inflammatory and antiatherogenic agent in the rabbit model. The authors investigated the effects of this compound on atherogenesis and possible mechanisms of the actions in the hyperlipidemic mice. Low-density lipoprotein receptor–deficient (Ldlr−/−) mice fed a high-cholesterol diet alone for 8 weeks developed the fatty streak lesion in the aortic sinus, whereas this lesion was significantly reduced by hematein treatment without a change in plasma lipid levels compared with control mice. Hematein treatment reduced plasma levels of lipid peroxide and superoxide generation in LPS-stimulated peritoneal macrophage. Hematein treatment inhibited NF-&kgr;B-DNA binding activity in peritoneal macrophages from Ldlr−/− mice and the activation of NF-&kgr;B in RAW264.7 macrophages. This compound suppressed plasma nitrite/nitrate levels in Ldlr−/− mice and NO production and iNOS expression in LPS+IFN&ggr;-stimulated peritoneal macrophages. Hematein treatment also suppressed the activity of iNOS promoters in RAW264.7 macrophages, and reduced the plasma levels of TNF-&agr; and IL-1&bgr; and the production of these cytokines in LPS+IFN&ggr;-stimulated peritoneal macrophages. These results suggest that hematein inhibits atherosclerotic lesion formation, possibly by reducing proinflammatory mediators through a decrease in reactive oxygen species generation and NF-&kgr;B activation.
Conducted EMI Reduction in Power Converters by Means of Periodic Switching Frequency Modulation

Spread spectrum clock generation techniques were originally developed to reduce electromagnetic interference (EMI) in communications and microprocessor systems working in the range of hundreds of megahertz. Nowadays, the switching frequency of power converters has been increasing up to values that make worthy the application of such switching frequency modulation techniques to reduce EMI emissions in power converters. Although random modulations have been applied before to power converters, periodic patterns can provide some advantages. First, theoretical principles of frequency modulation using three periodic patterns for the modulating function are presented. The influence of some important modulation parameters on the EMI reduction is analyzed and some considerations about the EMI filters design are also presented. The effectiveness of such methods in terms of EMI reduction is demonstrated theoretically and confirmed with experimental results obtained from tests carried out on two converters. The first one is a 2.5 W buck converter that can be switched up to 1 MHz and the second one is a 600 W boost converter switching at 40 kHz. In both cases, attenuations obtained in conducted EMI are evaluated. Finally, special attention has been paid to input current and output voltage ripple in order to evaluate possible undesired side-effects produced by this technique.
Memory Efficient de novo Assembly Algorithm using Disk Streaming of K-mers

Sequencing the whole genome of various species has many applications, not only in understanding biological systems, but also in medicine, pharmacy, and agriculture. In recent years, the emergence of high-throughput next generation sequencing technologies has dramatically reduced the time and costs for whole genome sequencing. These new technologies provide ultrahigh throughput with a lower per-unit data cost. However, the data are generated from very short fragments of DNA. Thus, it is very important to develop algorithms for merging these fragments. One method of merging these fragments without using a reference dataset is called de novo assembly. Many algorithms for de novo assembly have been proposed in recent years. Velvet and SOAPdenovo2 are well-known assembly algorithms, which have good performance in terms of memory and time consumption. However, memory consumption increases dramatically when the size of input fragments is larger. Therefore, it is necessary to develop an alternative algorithm with low memory usage. In this paper, we propose an algorithm for de novo assembly with lower memory. In the proposed method, memory-efficient DSK (disk streaming of k-mers) to count k-mers is adopted. Moreover, the amount of memory usage for constructing de bruijn graph is reduced by not keeping edge information in the graph. In our experiment using human chromosome 14, the average maximum memory consumption of the proposed method was approximately 7. 5â8.8% of that of the popular assemblers.
Beta-glucan functions as an adjuvant for monoclonal antibody immunotherapy by recruiting tumoricidal granulocytes as killer cells.

The tumor-killing mechanisms available to monoclonal antibodies (mAbs; e.g., antagonism of growth factor receptors, antibody-dependent cell-mediated cytotoxicity) limit efficacy. Previous studies suggested that i.v. beta-glucan might function as an adjuvant for antitumor mAbs. beta- Glucan had been shown to function via the iC3b-receptor complement receptor 3 (CR3; CD11b/CD18) thereby enhancing leukocyte killing of tumor cells coated with iC3b via naturally occurring antitumor antibodies. Therapy with beta-glucans was limited by levels of natural antibodies and by tumor escape through elimination of antigen-positive cells. Accordingly, it was hypothesized that beta-glucan responses could be improved by combined administration with antitumor mAbs. Five tumor models were explored in BALB/c or C57Bl/6 mice using tumors that expressed either high levels of naturally occurring antigens (e.g., G(D2) ganglioside) or recombinant human MUC1. In comparison with antitumor mAb or beta-glucan alone, combined treatment with mAb plus beta-glucan produced significantly greater tumor regression in all models that included mammary, s.c. , and hepatic tumors. Tumor-free survival only occurred in models that incorporated stable expression of the target antigen. beta-Glucan enhancement of the mAb tumoricidal response did not occur in mice deficient in either leukocyte CR3 (CD11b(-/-)) or serum C3, confirming the requirement for CR3 on leukocytes and iC3b on tumors. Granulocytes appeared to be primarily responsible for tumoricidal activity, because beta-glucan therapeutic responses did not occur in granulocyte-depleted mice. These data suggest that the therapeutic efficacy of mAbs known to activate complement (e.g., Herceptin, Rituxan, and Erbitux) could be significantly enhanced if they were combined with beta-glucan.
In Vivo Regeneration of Cut Nerves Encased in Silicone Tubes: Growth across a Six‐millimeter Gap

We describe an experimental in vivo system for studying peripheral nerve regeneration, in which the proximal stump of a transected nerve regrows through a transparent silicone chamber toward the distal stump. Physical separation permits examination of the effects of the humoral and/or cellular influences from the distal stump on regenerating fibers before they invade the distal segment itself. A small segment of the rat sciatic nerve was resected, leaving a 6 mm gap which was then encased by a cylindrical silicone chamber. Within the first weeks, a nerve trunk regenerated along the central axis of the chamber bridged the gap between the proximal and distal stumps. When the distal nerve stump was omitted from the distal opening of the chamber, only a thin structure with a few small-caliber fibers extended across the gap. In each instance regenerating nerve appeared as a cord-like structure completely surrounded by clear fluid, a feature which permits easy collection of the extracellular fluid for analysis of its chemical properties and biological activity. This feature also allows in vivo manipulation of the humoral environment in which nerve regeneration occurs.
Identification and Characterization of the Three Chitin-Binding Domains within the Multidomain Chitinase Chi92 fromAeromonas hydrophila JP101

ABSTRACT The gene (chi92) encoding the extracellular chitinase of Aeromonas hydrophila JP101 has been cloned and expressed in Escherichia coli. The mature form of Chi92 is an 842-amino-acid (89.830-kDa) modular enzyme comprised of a family 18 catalytic domain, an unknown-function region (the A region), and three chitin-binding domains (ChBDs; Chi92-N, ChBDCI, and ChBDCII). The C-terminally repeated ChBDs, ChBDCI and ChBDCII, were grouped into family V of cellulose-binding domains on the basis of sequence homology. Chitin binding and enzyme activity studies with C-terminally truncated Chi92 derivatives lacking ChBDs demonstrated that the ChBDs are responsible for its adhesion to unprocessed and colloidal chitins. Further adsorption experiments with glutathione S-transferase (GST) fusion proteins (GST-CI and GST-CICII) demonstrated that a single ChBD (ChBDCI) could promote efficient chitin and cellulose binding. In contrast to the two C-terminal ChBDs, the Chi92-N domain is similar to ChiN of Serratia marcescens ChiA, which has been proposed to participate in chitin binding. A truncated derivative of Chi92 that contained only a catalytic domain and Chi92-N still exhibited insoluble-chitin-binding and hydrolytic activities. Thus, it appears that Chi92 contains Chi92-N as the third ChBD in addition to two ChBDs (ChBDCI and ChBDCII).
Guardians of ‘the gift’: the emotional challenges of heart and lung transplant professionals in Denmark

ABSTRACT This paper deals with the emotional challenges encountered by doctors and nurses caring for heart and lung transplant patients. Organ transplantation enables body parts from the dead to become usable in patients with no other life-saving option. These exchanges are not possible without transplant professionals carefully selecting, guiding and interacting with organ recipients before, during and after the transplant. Based on anthropological fieldwork at a Danish heart and lung transplant unit, the paper explores how doctors and nurses experience and handle the emotional challenges of their working life. By focusing on the everyday life of the transplant unit which, contrary to public understanding of transplant miracles, is sometimes characterised by sad cases and devastation, this paper argues that transplant professionals operate in the presence of death. Medically and emotionally they are at risk. They must take the difficult decisions of whether to admit critically ill patients onto the organ waiting list; face the distress of post-transplant sufferings and deaths; and deal with organ recipients who do not behave according to post-transplant recommendations. Drawing on a familiar metaphor for donated organs, it is suggested that transplant doctors and nurses are ‘guardians of the gift’. Attention to the emotional burdens and rewards of this particular position enables new understandings of the practices of transplant medicine, of gift exchange theory, and of the role of emotion in medical practice.
A synchrotron X‐ray study of the changes occurring in the corneal stroma during processing for electron microscopy

Using a high‐intensity synchrotron X‐ray source, the structural changes occurring in the corneal stroma were monitored during each stage of several different processing runs for the transmission electron microscope (TEM) and scanning electron microscope (SEM). The parameters studied were interfibrillar spacing, intermolecular spacing, D‐periodicity and fibril diameter.
The Lateral Scapular Slide Test: A Reliability Study of Males with and without Shoulder Pathology.

BACKGROUND Abnormal scapular movement or malposition is related to shoulder pathology. The lateral scapular slide test (LSST) is used to determine scapular position with the arm abducted in three positions. OBJECTIVE The purpose of this study was to test the reliability of the LSST using a scoliometer. METHODS Thirty-three male subjects (18 to 34 years) participated in this study. Group one (n=15) had shoulder pathology; Group two (n=18) did not have pathology. A test-retest, repeated measures design, with three experienced raters and the three positions of the LSST, was used to test the reliability of the LSST. All measurements in each position were taken bilaterally. RESULTS Pearson Correlations for Position 1 and 2 ranged from . 78 to . 92 whereas position 3 ranged from . 62 to . 81. The ICC (2,2) ranged from . 87 to . 95 for positions 1 and 2. ICC (2,2) ranged from . 70 to.82 for positions 3. Overall ICC (2,3) ranged from . 83 to . 96. The coefficients of determination ranged from . 38 to . 89. The SEM ranged from 3.00 to 8.26 mm, with the largest error found in position 3. DISCUSSION AND CONCLUSION The LSST can be reliable in screening scapular position. Although a large range of error exists in measurements as indicated by the standard error of the measurement, the LSST provides more objective measures than pure observation.