Miracle-dz/UniFAR-FTUs huggingface dataset:
A cohort study of mortality predictors and characteristics of patients with combined pulmonary fibrosis and emphysema

Objectives Our purpose was to assess the clinical data, predictors of mortality and acute exacerbation (AE) in combined pulmonary fibrosis and emphysema (CPFE) patients. Design Single-centre retrospective cohort study. Setting Teaching hospital in Japan. Participants We identified 93 CPFE patients with high-resolution computed tomographic (HRCT) through multidisciplinary discussion. Patients who had connective tissue disease, drug-associated interstitial lung disease and occupationally related interstitial lung disease, such as asbestosis and silicosis, were excluded. Interventions There were no interventions. Methods Medical records and HRCT scans from January 2002 through December 2007 were reviewed retrospectively at our hospital. Ninety-three patients had CPFE. Results The mean age of CPFE patients was 74 years. Idiopathic pulmonary fibrosis and non-specific interstitial pneumonia were observed as distinct HRCT patterns. Forty-two patients showed finger clubbing. Mean serum Krebs von den Lungen-6 (KL-6) and per cent predicted forced vital capacity (%FVC) were 1089 IU/l, 63.86%, respectively. Twenty-two patients developed AE during observation period. Baseline KL-6 was a strong predictor of AE (OR=1.0016, p=0.009). Finger clubbing (HR=2.2620, p=0.015) and per cent predicted forced expiratory volume in one second/%FVC more than 1.2 (HR=1.9259, p=0.048) were independent predictors of mortality in CPFE. Conclusions Baseline serum KL-6 was a useful predictor of AE (cut-off =1050, receiver operator characteristic curve: 0.7720), which occurred in 24% (22/93) of the CPFE patients. Finger clubbing and per cent predicted forced expiratory volume in one second/%FVC more than 1.2 were independent predictors of mortality.
Modal Logics of Topological Relations

The eight topological RCC8(or Egenhofer-Franzosa)- relations between spatial regions play a fundamental role in spatial reasoning, spatial and constraint databases, and geographical information systems. In analogy with Halpern and Shoham’s modal logic of time intervals based on the Allen relations, we introduce a family of modal logics equipped with eight modal operators that are interpreted by the RCC8-relations. The semantics is based on region spaces induced by standard topological spaces, in particular the real plane. We investigate the expressive power and computational complexity of the logics obtained in this way. It turns our that, similar to Halpern and Shoham’s logic, the expressive power is rather natural, but the computational behavior is problematic: topological modal logics are usually undecidable and often not even recursively enumerable. This even holds if we restrict ourselves to classes of finite region spaces or to substructures of region spaces induced by topological spaces. We also analyze modal logics based on the set of RCC5relations, with similar results.
Reduction of Cysteine Sulfinic Acid by Sulfiredoxin Is Specific to 2-Cys Peroxiredoxins*

Cysteine residues of certain peroxiredoxins (Prxs) undergo reversible oxidation to sulfinic acid (Cys-SO2H) and the reduction reaction is catalyzed by sulfiredoxin (Srx). Specific Cys residues of various other proteins are also oxidized to sulfinic acid, suggesting that formation of Cys-SO2H might be a novel posttranslational modification that contributes to regulation of protein function. To examine the susceptibility of sulfinic forms of proteins to reduction by Srx, we prepared such forms of all six mammalian Prx isoforms and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Purified sulfiredoxin reduced the sulfinic forms of the four 2-Cys members (Prx I to Prx IV) of the Prx family in vitro, but it did not affect those of Prx V, Prx VI, or GAPDH. Furthermore, Srx bound specifically to the four 2-Cys Prxs in vitro and in cells. Sulfinic forms of Prx I and Prx II, but not of Prx VI or GAPDH, present in H2O2-treated A549 cells were gradually reduced after removal of H2O2; overexpression of Srx increased the rate of the reduction of Prx I and Prx II but did not induce that of Prx VI or GAPDH. These results suggest that reduction of Cys-SO2H by Srx is specific to 2-Cys Prx isoforms. For proteins such as Prx VI and GAPDH, sulfinic acid formation might be an irreversible process that causes protein damage.
Biomimetic Culture Reactor for Whole-Lung Engineering

Abstract Decellularized organs are now established as promising scaffolds for whole-organ regeneration. For this work to reach therapeutic practice, techniques and apparatus are necessary for doing human-scale clinically applicable organ cultures. We have designed and constructed a bioreactor system capable of accommodating whole human or porcine lungs, and we describe in this study relevant technical details, means of assembly and operation, and validation. The reactor has an artificial diaphragm that mimics the conditions found in the chest cavity in vivo, driving hydraulically regulated negative pressure ventilation and custom-built pulsatile perfusion apparatus capable of driving pressure-regulated or volume-regulated vascular flow. Both forms of mechanical actuation can be tuned to match specific physiologic profiles. The organ is sealed in an elastic artificial pleura that mounts to a support architecture. This pleura reduces the fluid volume required for organ culture, maintains the organ's position during mechanical conditioning, and creates a sterile barrier allowing disassembly and maintenance outside of a biosafety cabinet. The combination of fluid suspension, negative-pressure ventilation, and physiologic perfusion allows the described system to provide a biomimetic mechanical environment not found in existing technologies and especially suited to whole-organ regeneration. In this study, we explain the design and operation of this apparatus and present data validating intended functions.
Photosystem II Photosynthetic Unit Sizes from Fluorescence Induction in Leaves : CORRELATION TO PHOTOSYNTHETIC CAPACITY.

The use of fluorescence induction measurements in leaves infiltrated with 3-(3,4-dichlorophenyl)-1,1-dimethylurea has been evaluated as a routine method for estimation of the concentration of the reaction centers of photosystem II relative to total chlorophyll in a wide variety of plant species. The procedure is based on a simple theory that takes into account the attenuation of light in passing through the leaf and the linear dependence of the fluorescence induction time from different parts of the leaf on the inverse of the local light intensity. A formula to calculate the reaction center concentration of photosystem II was obtained. The effect of the light attenuation is accounted for by a correction factor which could become practically insignificant by an optimal choice of the excitation and emission wavelengths and the geometry of the photodetector with respect to the sample. Estimation of quantum yields for primary photochemistry and influence of light scattering were considered. The results demonstrate the effect of the above factors under various circumstances and are in agreement, to a first approximation, with the theory.THE UTILITY OF THE METHOD IS DEMONSTRATED BY A DETAILED STUDY OF FOUR DESERT PLANT SPECIES: estimation of reaction center concentrations of both photosystem I (by estimation of P700) and photosystem II (by the fluorescence induction method) were made and were compared to the rates of CO(2) fixation. There was a good quantitative correlation between the photosynthetic rates and the concentration of photosystem II reaction centers (expressed as per chlorophyll or per unit area of the leaf), but no such correlation was found with photosystem I reaction centers.The ratio of total chlorophyll per reaction centers II varied in the range of about 200 to 800 in different species, but there was no variation of this parameter in any single species.
Robust Optimization-Based Coronary Artery Labeling From X-Ray Angiograms

In this paper, we present an efficient robust labeling method for coronary arteries from X-ray angiograms based on energy optimization. The fundamental goal of this research is to facilitate the analysis and diagnosis of interventional surgery in the most efficient way, and such effort could also improve the performance during doctor training, and surgery simulation and planning. Compared to the prior state-of-the-art, our method is much more robust to resist noises and is tolerant to even incomplete data because of the “built-in” nature of global optimization. We start with a fully parallelized algorithm based on Hessian matrix to extract the tubular structure from the X-ray angiograms as vessel candidates. Then, instead of using the candidates directly, we use the grow cut (Vezhnevets and V. Konouchine, Growcut: Interactive multi-label N-D image segmentation by cellular automata, in Proc. of Graphicon, 2005, pp. 150-156.) method, which is similar to graph cut (Boykov et al. , Fast approximate energy minimization via graph cuts, IEEE Trans. Pattern Anal. Mach. Intell. , vol. 23, no. 11, pp. 1222-1239, Nov. 2001.)but with better performance to extract the precise vessel structure from the images. Next, we use the fast marching method with second derivatives and cross neighbors to extract the accurate skeleton segments. After that, we propose an efficient method based on iterative closest point (Z. Zhang, Iterative point matching for registration of free-form curves and surfaces, Int J. Comput. Vis., vol. 13, no. 2, pp. 119-152, 1994.) to organize the skeleton segments by treating the continuity and similarity as extra constraints. Finally, we formulate the vessel labeling problem as an energy optimization problem and solve it using belief propagation. We also demonstrate several typical applications including flow velocity estimation, heart beat estimation, and vessel diameter estimation to show its practical uses in clinical diagnosis and treatment. Our experiments exhibit the correctness and robustness, as well as the high performance of our algorithm. We envision that our system would be of high utility for diagnosis and therapy to treat vessel-related diseases in a clinical setting in the near future.
Defining the Normal Bacterial Flora of the Oral Cavity

ABSTRACT More than 700 bacterial species or phylotypes, of which over 50% have not been cultivated, have been detected in the oral cavity. Our purposes were (i) to utilize culture-independent molecular techniques to extend our knowledge on the breadth of bacterial diversity in the healthy human oral cavity, including not-yet-cultivated bacteria species, and (ii) to determine the site and subject specificity of bacterial colonization. Nine sites from five clinically healthy subjects were analyzed. Sites included tongue dorsum, lateral sides of tongue, buccal epithelium, hard palate, soft palate, supragingival plaque of tooth surfaces, subgingival plaque, maxillary anterior vestibule, and tonsils. 16S rRNA genes from sample DNA were amplified, cloned, and transformed into Escherichia coli. Sequences of 16S rRNA genes were used to determine species identity or closest relatives. In 2,589 clones, 141 predominant species were detected, of which over 60% have not been cultivated. Thirteen new phylotypes were identified. Species common to all sites belonged to the genera Gemella, Granulicatella, Streptococcus, and Veillonella. While some species were subject specific and detected in most sites, other species were site specific. Most sites possessed 20 to 30 different predominant species, and the number of predominant species from all nine sites per individual ranged from 34 to 72. Species typically associated with periodontitis and caries were not detected. There is a distinctive predominant bacterial flora of the healthy oral cavity that is highly diverse and site and subject specific. It is important to fully define the human microflora of the healthy oral cavity before we can understand the role of bacteria in oral disease.
Case Study on Vehicle-Based Virtual Segment Architecture -- On Application, Field Experiment, and Simulation

Various information delivery schemes based on store-carry-forward routing with extensions have been studied as part of efforts to support non-real-time communications in sparse or intermittent networks. However, communication service schemes that cover large areas based solely on store-carry-forward technology have previously been considered impractical because the delay time for message delivery increases in proportion to the size of the service area. Therefore, in an effort to extend the communication service area of such networks, while providing controllable performance in a cost-effective manner, the authors previously proposed a Virtual Segment (VS) concept in which global communications are provided through a combination of a store-carry-forward service provided by vehicles traveling on roadways along with broadband wireless/wired network devices connected to the Internet. A prototype system has been developed for proof-of-concept implementation. In the present paper, we report a case study evaluation of the VS concept and introduce a sample RSS distribution application of the prototype system. Following a field experiment to validate the system concept, and to obtain realistic data reflecting the geographical features of the segment, a simulation using information obtained from the field experiment was conducted to evaluate the VS concept from realistic and quantitative viewpoints.
Fractures of the odontoid process of the axis.

1. Fifty-one cases of fracture of the odontoid have been analysed. Forty were reported by other surgeons; eleven were new cases first reported by us. 2. Fracture of the odontoid in young children is an epiphysial separation. It occurs up to the age of seven years. As in epiphysial separations elsewhere, it unites readily, and remodelling occurs when reduction has been incomplete, so that normal anatomy is restored. 3. In adults forward displacement is twice as common as backward displacement. 4. Immediate paralysis is commoner if backward displacement occurs, but late neurological disorders are seen only after fractures with forward displacement. 5. Failure of bony healing is not dangerous if treatment has resulted in firm fibrous union, for there is neither excessive abnormal mobility nor progressive subluxation, either of which could injure the spinal cord or medulla. Neurological disorders developing after the fracture are the result of mobility from inadequate early treatment. It is the results of inadequate early treatment which have given this fracture a sinister reputation. 6. The fracture should be reduced by skeletal traction through a skull caliper. The reduction should be maintained for six weeks by continuous traction, and this should be followed by a period of six weeks in a plaster. 7. The increasing definition of the fracture-line seen in the radiographs of some patients indicates non-union.
The Effects of Hydrocolloid and Emulsifier Usage on Chemical Composition and Sensory Quality of Turkish Cheese Dessert: Hosmerim

Hosmerim (cheese dessert) is a traditional Turkish dessert which is manufactured from unsalted fresh cheese, sugar, egg, cream or butter and flour (instead of flour, semolina or starch can also be used). In this research the effects of critical process parameters such as different hydrocolloid or emulsifier agents levels on some compositional and structural characteristics of cheese dessert were investigated. For lecithin, inulin and agar agar of the hosmerim samples, three different levels were adjusted (0.5, 1, 2%). According to the results, some compositional and structural properties of experimental samples, determined for both parameters (lecithin, inulin, agar agar) are as follows, respectively: dry matter (%): 52.07-59.34, 52.45-58.03, 54.53-59.07; total sugar (%): 23.45-25.01, 20.18-23.67, 20.66-23.04; protein (%): 6.46-7.01, 6.54-6.89, 6.77-6.86; titratable acidity (%): 0.21-0.23, 0.22-0.23, 0.21-0.22; ash (%): 0.87-0.91, 0.86-0.92, 0.86-0.92; hardness (loadgram): 42.37-50.91, 42.96-53.11, 51.42-56.04; firmness 42.36-101.6, 42.36-102.5, 52.47-125.09; springiness 0.237-0.335, 0.163-0.257, 0.165-0.198; gumminess 1.08-1.11, 2.12-2.34, 2.45-2.58. Textural and sensorial properties (such as colour, odour, taste, appearance) were affected significantly by these ingredients (P < 0.01). Inulin was found to be the most suitable one among those tested. This ingredient can be used for either its nutritional advantages or technological properties, but it is often applied to offer a dual benefit: an improved organoleptic quality and a better-balanced nutritional composition.
InGaN blue light-emitting diodes with optimized n-GaN layer

In the extensive research dedicated recently to metal- organic chemical vapor deposition (MOCVD)-grown high- efficiency GaN LED device design, a significant effort has been made to increase the conductivity of p-GaN layers, while n-GaN layers received relatively little attention. We demonstrated, both experimentally and theoretically, that the resistivity of n-GaN layers has a profound effect on blue InGaN LED performance. Optimization of n-GaN epitaxial layers allows the achievement of device series resistances below 15 Ohms and forward voltages as low as 2.9 Volts at 20 mA. We have also shown that contactless measurements of sheet resistivity of the entire LED epitaxial structure closely correlate with the ohmic resistance of the GaN layer measured in the fabricated devices. This provides an excellent non-destructive characterization tool for n-GaN optimization. Insufficient n-GaN conductivity is shown to trigger a distinct degradation mechanism by initiating current crowding in a localized device area. InGaN LED lamps with optimized n-GaN layers had a high external quantum efficiency and a good long-term reliability.
Influence of Substratum Characteristics on the Attachment of a Marine Pseudomonad to Solid Surfaces

The attachment of a marine Pseudomonas sp. to a variety of surfaces was investigated, and the number of bacteria which became attached was related to the surface charge and degree of hydrophobicity of the substratum. Large numbers of bacteria attached to hydrophobic plastics with little or no surface charge [Teflon, polyethylene, polystyrene, poly(ethylene terephthalate)]; moderate numbers attached to hydrophilic metals with a positive (platinum) or neutral (germanium) surface charge; and very few attached to hydrophilic, negatively charged substrata (glass, mica, oxidized plastics). The results suggest that both electrostatic and hydrophobic interactions are involved in bacterial attachment.
Fabrication and properties of porous silicon nitride ceramics via microwave sintering

Abstract Porous silicon nitride ceramics were fabricated without pore formers via microwave sintering. Microwave sintering at different temperatures produced unique microstructures with high porosity. The best porous silicon nitride ceramics were fabricated at 1550°C for 30 min; the resulting product had a bulk density of 1552 g cm−3, an open porosity of 43.9%, and a flexural strength of 43.6 MPa. The mean pore channel size and the dielectric constants of the fabricated porous silicon nitride ceramics ranged from 0.1 μm to 1 μm and 2.9 to 3.4 under different temperatures, respectively.
HVEM and nectin-1 are the major mediators of herpes simplex virus 1 (HSV-1) entry into human conjunctival epithelium.

PURPOSE The human conjunctiva is a natural target for herpes simplex virus (HSV)-1 infection. The goals of this study were to investigate the cellular and molecular mechanisms of HSV-1 entry into human conjunctival epithelial (HCjE) cells. Specific features of entry studied included the method of initial viral binding to cells, pH dependency, and expression and usage of specific HSV-1 entry receptors. METHODS To observe HSV-1 initial binding, live cell imaging was performed on HSV-1-infected HCjE cells. Reporter HSV-1 virions expressing beta-galactosidase were used to determine entry of wild-type HSV-1(KOS) and a mutant, HSV-1(KOS)Rid1, into HCjE cells. HSV-1 replication in HCjE cells was determined by plaque assays. Lysosomotropic agents were used to determine whether viral entry was pH dependent. Reverse transcription (RT)-PCR, flow cytometry, and immunohistochemistry were used to determine the expression of receptors. Receptor-specific siRNAs were used to define the role of individual entry receptors. RESULTS HSV-1 virions attach to filopodia present on HCjE cells and use them to reach the cell body for entry. Cultured HCjE cells demonstrate susceptibility to HSV-1 entry and form plaques confirming viral replication. Blocking vesicular acidification significantly reduces entry, implicating a pH-dependent mode of entry. Multiple assays confirm the expression of entry receptors nectin-1, HVEM, and 3-O-sulfated heparan sulfate (3-OS HS) on the HCjE cell membrane. Knocking down of gD receptors by siRNAs interference implicates nectin-1 and HVEM as the major mediators of entry. CONCLUSIONS HSV-1 entry into HCjE cells is a pH-dependent process that is aided by targeted virus travel on filopodia. HCjE cells express all three major entry receptors, with nectin-1 and HVEM playing the predominant role in mediating entry.
Cytokinin Regulation of Auxin Synthesis in Arabidopsis Involves a Homeostatic Feedback Loop Regulated via Auxin and Cytokinin Signal Transduction[W][OA]

This study demonstrates that auxin and cytokinin regulate each other's biosynthesis, providing an intrinsic mechanism for optimizing the relative intracellular concentrations of both hormones. Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.