Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between Oral Health and the Risk of Lacunar Infarction in Japanese Adults

Background: Poor oral health is associated with an increased risk of dementia in the elderly. One possible pathway linking these two phenomena is lacunar infarction, a potential cause of dementia. An association between poor oral health and an increased risk of ischaemic stroke has been recognised through the oral infection-inflammation pathway. However, little is known about whether poor oral health is associated with the progression of lacunar infarction. Objective: We examined the association between variables related to oral health and lacunar infarction, as detected by magnetic resonance imaging (MRI). Methods: A total of 110 subjects (52 men, 58 women), aged 27-76 years, who visited our periodontology clinic participated in this study. The subjects underwent dental radiography, periodontal examinations and brain MRI. One experienced specialist in cardiovascular disease and one experienced neurosurgeon determined the number of lacunar infarctions on brain MRI. Periodontologists performed clinical periodontal examinations. Variables related to oral health were determined from the radiographs by an oral radiologist. Information on the subjects' lifestyles and disease histories were obtained using a structured questionnaire and confirmed by clinical records. Adjacent categories logit regression analysis with backward elimination was used to determine variables associated with three groups based on the number of lacunar infarctions. Results: Of the 110 subjects, 61 had lacunar infarctions. Nineteen had multiple (≥7) lesions. Aging (p = 0.0004), increased time spent in physical activity per day (p = 0.042), the presence of hypertension (p = 0.006), the absence of hyperlipidaemia (p = 0.045), the presence of diabetes mellitus (p = 0.025) and low alveolar bone height (p = 0.026) were significantly associated with an increased number of lacunar infarctions in the final regression model. The significance of hyperlipidaemia and alveolar bone height disappeared in an unadjusted model. An increased pocket depth, which indicates current periodontal disease progression, tended to be associated with an increased number of lacunar infarctions (p = 0.058). This tendency did not disappear in an unadjusted model. Conclusion: Our results suggest that lacunar infarction may be associated with current periodontal disease in Japanese adults.
Causal Theories of Action: A Computational Core

We propose a framework for simple causal theories of action, and study the computational complexity in it of various reasoning tasks such as determinism, progression and regression under various assumptions. As it turned out, even the simplest one among them, one-step temporal projection with complete initial state, is intractable. We also briefly consider an extension of the framework to allow truly indeterministic actions, and find that this extension does not increase the complexity of any of the tasks considered here.
Scalable Inference for Logistic-Normal Topic Models

Logistic-normal topic models can effectively discover correlation structures among latent topics. However, their inference remains a challenge because of the non-conjugacy between the logistic-normal prior and multinomial topic mixing proportions. Existing algorithms either make restricting mean-field assumptions or are not scalable to large-scale applications. This paper presents a partially collapsed Gibbs sampling algorithm that approaches the provably correct distribution by exploring the ideas of data augmentation. To improve time efficiency, we further present a parallel implementation that can deal with large-scale applications and learn the correlation structures of thousands of topics from millions of documents. Extensive empirical results demonstrate the promise.
Translate Chinese organization names using examples and web

This paper proposes a new approach for translating Chinese organization names that uses example-based method along with web assistance. It consists of two phases, first, it generates a translation candidate for the input Chinese organization name by an example-based translation method; and secondly, it uses the web to amend this translation candidate so as to finish such tasks: translation candidate reordering, word selection revising, and adjustment of the use of function words. Experimental results show that our method outperforms competing traditional statistical translation method in the task of translating Chinese ONs.
Direct near-field phase measurements of lensed fiber employing a single-mode fiber interferometer

A method of direct measurement of near-field wavefront and intensity distribution of lensed fiber employing a single-mode fiber interferometer is proposed and demonstrated. The wavefront of lensed fiber showed a curved wave with the radius of curvatures from 8 to 32 μm at various locations along the z axis. The wavefront radius of curvatures of laser diode and lensed fiber were in good agreement with each other that the similar curved wavefront distributions between laser and lensed fiber was mode matching, results in high coupling from laser to fiber. Detailed measurements of the near-field phase and intensity distributions of laser and fiber are essential for micro-optic design with better mode matching to achieve efficient coupling.
A Scalable Parallel HITS Algorithm for Page Ranking

The hypertext induced topic search (HITS) algorithm is a method of ranking authority of information sources in a hyperlinked environment HITS uses only topological properties of the hyperlinked network to determine rankings. We present an efficient and scalable implementation of the HITS algorithm that uses MPI as an underlying means of communication. We then analyze the performance on a shared memory supercomputer, and use our results to verify the optimal number of processors needed to rank a large number of pages for the link structure of the total University of Southern Mississippi (usm.edu domain) Web sites
Developmentofa gene knockout systemforRalstonia eutropha H 16 based on thebroad-host-rangevectorexpressingamobile group II intron

Developmentofa gene knockout systemforRalstonia eutropha H16based on thebroad-host-rangevectorexpressingamobile group II intron Jong Myoung Park, Yu-Sin Jang, Tae Yong Kim & Sang Yup Lee Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, Daejeon, Korea; BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon, Korea; Bioinformatics Research Center, KAIST, Daejeon, Korea; and Department of Bio and Brain Engineering, KAIST, Daejeon, Korea
Relationship between stearoyl-CoA desaturase 1 gene expression, relative protein abundance, and its fatty acid products in bovine tissues

Stearoyl-CoA desaturase 1 (SCD1) greatly contributes to the unsaturated fatty acids present in milk and meat of cattle. The SCD1 enzyme introduces a double bond into certain saturated fatty acyl-CoAs producing monounsaturated fatty acids (MUFA). The SCD1 enzyme also has been shown to be active in the bovine mammary gland converting t11 18 : 1 (vaccenic acid) to c9 t11 conjugated linoleic acid (CLA). The objective of this study was to determine any association between the gene expression of SCD1 and occurrence of its products (c9 14 : 1, c9 16 : 1, c9 18 : 1, and c9 t11 18 : 2) in various bovine tissues. Tissue samples were obtained from lactating Holstein cows (n=28) at slaughter, frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted and converted to complementary DNA for quantitative real time polymerase chain reaction (PCR) analysis of the SCD1 gene. Extracted lipid was converted to fatty acid methyl esters and analysed by GC. Tissues varied in expression of SCD1 gene with mammary, cardiac, intestinal adipose, and skeletal muscle expressing greater copy number as compared with lung, large intestine, small intestine and liver (371, 369, 328, 286, 257, 145, 73, and 21 copies/ng RNA, respectively). Tissues with high mRNA expression of SCD1 contained greater SCD1 protein whereas detection of SCD1 protein in tissues with low SCD1 mRNA expression was very faint or absent. Across tissues, the desaturase indices for c9 18 : 1 (r=0·24) and sum of SCD products (r=0·20) were positively correlated with SCD1 gene expression (P<0·01 for both). Within each tissue, the relationship between SCD1 gene expression and the desaturase indices varied. No correlation was detected between SCD1 expression and desaturase indices in the liver, large and small intestines, lung, cardiac or skeletal muscles. Positive correlations, however, were detected between SCD1 expression and the desaturase indices in intestinal adipose tissue (P<0·02 for all) except 14 : 1, whereas only c9 18 : 1, c9 t11 18 : 2 and sum of all desaturase indices were positively correlated with SCD1 expression in mammary tissue (P⩽0·03). Overall, the relationship between SCD1 gene expression and occurrence of its products seems to be tissue specific.
Speed scaling to manage energy and temperature

Speed scaling is a power management technique that involves dynamically changing the speed of a processor. We study policies for setting the speed of the processor for both of the goals of minimizing the energy used and the maximum temperature attained. The theoretical study of speed scaling policies to manage energy was initiated in a seminal paper by Yao et al. [1995], and we adopt their setting. We assume that the power required to run at speed s is P(s) = sα for some constant α > 1. We assume a collection of tasks, each with a release time, a deadline, and an arbitrary amount of work that must be done between the release time and the deadline. Yao et al. [1995] gave an offline greedy algorithm YDS to compute the minimum energy schedule. They further proposed two online algorithms Average Rate (AVR) and Optimal Available (OA), and showed that AVR is 2α − 1 αα-competitive with respect to energy. We provide a tight αα bound on the competitive ratio of OA with respect to energy. We initiate the study of speed scaling to manage temperature. We assume that the environment has a fixed ambient temperature and that the device cools according to Newton's law of cooling. We observe that the maximum temperature can be approximated within a factor of two by the maximum energy used over any interval of length 1/b, where b is the cooling parameter of the device. We define a speed scaling policy to be cooling-oblivious if it is simultaneously constant-competitive with respect to temperature for all cooling parameters. We then observe that cooling-oblivious algorithms are also constant-competitive with respect to energy, maximum speed and maximum power. We show that YDS is a cooling-oblivious algorithm. In contrast, we show that the online algorithms OA and AVR are not cooling-oblivious. We then propose a new online algorithm that we call BKP. We show that BKP is cooling-oblivious. We further show that BKP is e-competitive with respect to the maximum speed, and that no deterministic online algorithm can have a better competitive ratio. BKP also has a lower competitive ratio for energy than OA for α ≥5. Finally, we show that the optimal temperature schedule can be computed offline in polynomial-time using the Ellipsoid algorithm.
The Second International Timetabling Competition (ITC-2007): Curriculum-based Course Timetabling (Track 3) — preliminary presentation —

Following the success of the First International Timetabling Competition in 2002, the timetabling research community is organising a new competition on this problem (opening August 1st). This new competition will be on three different timetabling problems, and one of the tracks concerns the course timetabling formulation that applies to Italian universities (called Curriculum-based Course Timetabling). The dataset is composed by real-world instances provided by the University of Udine. In this work, we overview the general rules of the competition and we describe in details the problem formulation and the instances proposed for this track.
Agreement on Indication for Systemic Therapy between Biopsied Tissue and Surgical Excision Specimens in Breast Cancer Patients

Purpose In breast cancer therapy, the indication for systemic therapy is typically based on prognostic markers from the surgical excision specimen. If such is unavailable, for instance prior to tumor ablation therapy, the indication for adjuvant systemic therapy may be assessed from pretreatment biopsies. The effect of differences in tumor characteristics between biopsy and excision specimen on agreement in indication for systemic therapy is, however, largely unknown. The aim of this study is to determine the agreement in eligibility for systemic therapy between preoperative and postoperative assessment. Secondly, to identify which patient-, tumor- or lymph node characteristics may influence this agreement. Materials and Methods In this retrospective study, 300 consecutive female patients with primary invasive breast carcinoma on biopsy were included. Indication for systemic therapy was determined separately from biopsied tissue and from excision specimens using national guidelines based on adjuvant! online. Agreement was assessed, and patient-, tumor- and lymph node characteristics affecting agreement analyzed. Results Agreement in tumor characteristics between biopsy and excision specimen varied from high (ER-status: 99%), to lower (tumor grade: 62%, tumor size: 59%, and lymph node status: 67%). Without preoperative sentinel node biopsy (SNB), agreement on systemic therapy exists in 77% of patients (kappa = 0,547). Positive pretreatment indication for systemic therapy was highly indicative of the postoperative indication (PPV = 94%). Negative indication was, however, only indicative in 67% of patients. Conversely, with preoperative SNB, agreement on negative indication was raised to 89%. Agreement was especially high for ER-negative status, tumor grade 3, tumor size >2 cm, lymph node positivity at biopsy and a negative preoperative SNB. Conclusions A positive indication for systemic therapy from biopsy is highly indicative for a positive indication from the excision specimen. When the indication is negative, additional stratification using preoperative SNB raises the agreement. Still, discordance occurs in 1 out of 10 patients.
Histone Deacetylase Activity Represses Gamma Interferon-Inducible HLA-DR Gene Expression following the Establishment of a DNase I-Hypersensitive Chromatin Conformation

ABSTRACT Expression of the retinoblastoma tumor suppressor protein (Rb) is required for gamma interferon (IFN-γ)-inducible major histocompatibility complex class II gene expression and transcriptionally productive HLA-DRA promoter occupancy in several human tumor cell lines. Treatment of these Rb-defective tumor cell lines with histone deacetylase (HDAC) inhibitors rescued IFN-γ-inducible HLA-DRA and -DRB mRNA and cell surface protein expression, demonstrating repression of these genes by endogenous cellular HDAC activity. Additionally, Rb-defective, transcriptionally incompetent tumor cells retained the HLA-DRA promoter DNase I-hypersensitive site. Thus, HDAC-mediated repression of the HLA-DRA promoter occurs following the establishment of an apparent nucleosome-free promoter region and before transcriptionally productive occupancy of the promoter by the required transactivators. Repression of HLA-DRA promoter activation by HDAC activity likely involves a YY1 binding element located in the first exon of the HLA-DRA gene. Chromatin immunoprecipitation experiments localized YY1 to the HLA-DRA gene in Rb-defective tumor cells. Additionally, mutation of the YY1 binding site prevented repression of the promoter by HDAC1 and partially prevented activation of the promoter by trichostatin A. Mutation of the octamer element also significantly reduced the ability of HDAC1 to confer repression of inducible HLA-DRA promoter activation. Treatment of Rb-defective tumor cells with HDAC inhibitors greatly reduced the DNA binding activity of Oct-1, a repressor of inducible HLA-DRA promoter activation. These findings represent the first evidence that HDAC activity can repress IFN-γ-inducible HLA class II gene expression and also demonstrate that HDAC activity can contribute to promoter repression following the establishment of a DNase I-hypersensitive chromatin conformation.
Hypoxia-inducible factor signaling provides protection in Clostridium difficile-induced intestinal injury.

BACKGROUND & AIMS Clostridium difficile is the leading cause of nosocomial infectious diarrhea. Antibiotic resistance and increased virulence of strains have increased the number of C difficile-related deaths worldwide. The innate host response mechanisms to C difficile are not resolved; we propose that hypoxia-inducible factor (HIF-1) has an innate, protective role in C difficile colitis. We studied the impact of C difficile toxins on the regulation of HIF-1 and evaluated the role of HIF-1alpha in C difficile-mediated injury/inflammation. METHODS We assessed HIF-1alpha mRNA and protein levels and DNA binding in human mucosal biopsy samples and Caco-2 cells following exposure to C difficile toxins. We used the mouse ileal loop model of C difficile toxin-induced intestinal injury. Mice with targeted deletion of HIF-1alpha in the intestinal epithelium were used to assess the effects of HIF-1alpha signaling in response to C difficile toxin. RESULTS Mucosal biopsy specimens and Caco-2 cells exposed to C difficile toxin had a significant increase in HIF-1alpha transcription and protein levels. Toxin-induced DNA binding was also observed in Caco-2 cells. Toxin-induced HIF-1alpha accumulation was attenuated by nitric oxide synthase inhibitors. In vivo deletion of intestinal epithelial HIF-1alpha resulted in more severe, toxin-induced intestinal injury and inflammation. In contrast, stabilization of HIF-1alpha with dimethyloxallyl glycine attenuated toxin-induced injury and inflammation. This was associated with induction of HIF-1-regulated protective factors (such as vascular endothelial growth factor-alpha, CD73, and intestinal trefoil factor) and down-regulation of proinflammatory molecules such as tumor necrosis factor and Cxcl1. CONCLUSIONS HIF-1alpha protects the intestinal mucosa from C difficile toxins. The innate protective actions of HIF-1alpha in response to C difficile toxins be developed as therapeutics for C difficile-associated disease.
Optimal Energy Transfer in Light-Harvesting Systems

Photosynthesis is one of the most essential biological processes in which specialized pigment-protein complexes absorb solar photons, and with a remarkably high efficiency, guide the photo-induced excitation energy toward the reaction center to subsequently trigger its conversion to chemical energy. In this work, we review the principles of optimal energy transfer in various natural and artificial light harvesting systems. We begin by presenting the guiding principles for optimizing the energy transfer efficiency in systems connected to dissipative environments, with particular attention paid to the potential role of quantum coherence in light harvesting systems. We will comment briefly on photo-protective mechanisms in natural systems that ensure optimal functionality under varying ambient conditions. For completeness, we will also present an overview of the charge separation and electron transfer pathways in reaction centers. Finally, recent theoretical and experimental progress on excitation energy transfer, charge separation, and charge transport in artificial light harvesting systems is delineated, with organic solar cells taken as prime examples.
View-Dependent Adaptive Cloth Simulation

This thesis describes a method for view-dependent cloth simulation using dynamically adaptive mesh refinement and coarsening. Given a prescribed camera motion, the method adjusts the criteria controlling refinement to account for visibility and apparent size in the camera’s view. Objectionable dynamic artifacts are avoided by anticipative refinement and smoothed coarsening. This approach preserves the appearance of detailed cloth throughout the animation while avoiding the wasted effort of simulating details that would not be discernible to the viewer. The computational savings realized by this method increases as the scene complexity grows, producing a 2× speed-up for a single character and more than 4× for a small group.
The City of Los Angeles.

PROJECT DESCRIPTION: A proposed mixed-use development consisting of 860 residential units and 40,000 square-feet (sq. ft.) of commercial retail space. The project consists of two sites on either side of Cesar Chavez Ave., east of Figueroa St. The sites are zoned C2-2D and R5-2D. Total area of the two sites is 7.7 acres (332,000 sq. ft.). A total of no less than 1084 parking spaces would be provided. The two sites would be connected by a pedestrian bridge. Additionally, another pedestrian bridge would be built to connect the proposed project to an existing complex on the southwest corner of Cesar Chavez Ave. and Figueroa St. The site on the south side of Cesar Chavez Ave. would have 600 residential units, 27,000 sq. ft. of commercial retail space and no less than 754 parking spaces. The site on the north side of Cesar Chavez Ave. would have 260 residential units, 13,000 sq. ft. of commercial retail space and 330 parking spaces. The entitlements being requested are: Site Plan review, Street Vacation, CRA Chinatown Redevelopment Plan Consistency review, pedestrian bridges approval and encroachment permits, Haul Route permits, Grading permits, Shoring permits, Building permits and certificates of occupancy.
In-Network Aggregation in Wireless Sensor Networks

Sensor networks consist of small computing devices capable of producing digital representations of real-world phenomena. Due to size and battery power limitations, these devices typically have limited storage capacity, limited energy resources, and limited network bandwidth. Data produced by nodes in the network propagates through the network via wireless links. When compared to local processing of data, wireless transmission is extremely expensive. Researchers at the University of California, Santa Barbara estimate that sending a single bit over radio is at least three orders of magnitude more expensive than executing a single instruction [10]. The limited amount of energy, bandwidth, and storage capacity available to sensor nodes calls for specialized optimizations of queries injected into the network.
Effect of intravenous fructose on the P-31 MR spectrum of the liver: dose response in healthy volunteers.

Dynamic phosphorus-31 magnetic resonance (MR) spectroscopy of the liver after intravenous administration of fructose has been suggested as a test of liver function. To establish dose-response curves of the phosphorus metabolites in the normal human liver, each of four healthy volunteers was given two to four different fructose doses on separate days: 62.5, 125, 250, 375, or 500 mg per kilogram of body weight. P-31 MR spectra of the liver were acquired with a 2-T whole-body magnetic, both before and after fructose administration, at 2.5-minute intervals over at least 30 minutes. The fructose load caused a significant, linearly dose-dependent accumulation of phosphomonoesters (r = .72, P less than .01) and a decrease in inorganic phosphate (r = .78, P less than .005) and adenosine triphosphate (r = .73, P less than .01). On the basis of these experiments, dynamic P-31 MR spectroscopy seems promising in the assessment of liver function.