Miracle-dz/UniFAR-FTUs huggingface dataset:
Weight Gain and Risk of Impaired Fasting Glucose After Smoking Cessation

Background Observation of early changes in fasting plasma glucose level induced by post-smoking cessation weight gain is useful in predicting the risks of diabetes mellitus (DM) and impaired fasting glucose (IFG). We investigated the effect of post-smoking cessation weight gain on early changes in the risk of a high fasting plasma glucose (IFG) level (≥100 mg/dL). Methods In 946 subjects who underwent repeated health examinations after smoking cessation, changes in body mass index (BMI) and the odds ratio (OR) for IFG risk (adjusted for sex, age, BMI, fasting plasma glucose at year 1, and alcohol consumption) were calculated every year for 3 years after smoking cessation. Results After smoking cessation, the rate of BMI increase significantly increased in quitters: 2.36% at year 2 (never smokers: 0.22%, current smokers: 0.39%) and 0.46% at year 3 (never smokers: 0.14%, current smokers: 0.32%). However, it decreased by 0.15% at year 4 (never smokers: 0.12%, current smokers: 0.26%). The ORs for quitters did not significantly increase at any time during the follow-up period. However, among quitters who had smoked at least 20 cigarettes per day, it was significantly higher (OR 1.51, 95% confidence interval 1.1–2.01 at year 1 and 1.71, 1.23–2.38 at year 2). Conclusions The time course of the risk of IFG after smoking cessation was similar to that for the rate of BMI increase. In contrast to the findings of previous reports, the increase in IFG risk after smoking cessation was brief and disappeared in the absence of a significant increase in BMI.
Diagnostic Value of Clinical Parameters in the Prediction of Aspirin-Exacerbated Respiratory Disease in Asthma

Purpose Aspirin-exacerbated respiratory disease (AERD) has attracted a great deal of attention because of its association with increased asthma severity. However, oral aspirin challenge (OAC) to diagnose AERD is a time-consuming procedure, and some patients experience serious complications. Thus, we evaluated diagnostic values of non-invasive clinical parameters to predict AERD in asthmatic patients. Methods A total of 836 Korean subjects were recruited from an asthma cohort. They underwent OAC, and clinical parameters including the history of aspirin hypersensitivity, nasal polyposis, and chronic sinusitis of aspirin-tolerant asthma (ATA) and AERD asthmatic patients were compared. Results Significant differences (P<0.01) were found in eight parameters: age at diagnosis, body mass index, FEV1%, PC20, history of urticaria, nasal polyps, chronic sinusitis, and history of aspirin hypersensitivity. After logistic regression analysis based on the eight clinical parameters, nasal polyps, history of aspirin intolerance, sinusitis, and log [PC20 methacholine] remained significantly associated with AERD (P<0.05). The sensitivity and specificity of the history of aspirin hypersensitivity to predict AERD were 64.7% and 92.0%, respectively, and the positive and negative predictive values were 56.9% and 94.1%, respectively. Overall, the accuracy of the test was 88.2%. The accuracy of the tests for nasal polyps and chronic sinusitis were 67.3% and 60.4%, respectively. Conclusions Among clinical parameters associated with AERD, the history of aspirin hypersensitivity has the best positive and negative predictive values for the oral aspirin challenge test. Because the false-positive and -negative rates were still high, additional non-invasive methods are needed to reduce the rate of false outcomes.
Evaluation of the porous-coated anatomic hip at 12 years.

A total of 55 consecutive cementless total hip arthroplasties were done for osteoarthritis by 1 surgeon, who was not a designer of the implant, using 1 surgical technique and Porous-Coated Anatomic (Howmedica, Rutherford, NJ) hip implants. Of hips, 53 were prospectively evaluated, and 39 were followed for an average of 12.3 years (range, 10-16 years). Eight patients (8 hips) died, and 6 of 53 hips (11.3%) required revision for aseptic loosening at an average of 6.5 years. Five of 53 (9.4%) acetabular components were revised at an average of 7.9 years. Four of 53 (7.6%) femoral components were revised at an average of 5.1 years. Survivorship of these total hip arthroplasties was 98 +/- 3.9 at 5 years, 88.9 +/- 9.2 at 10 years, and 86.7 +/- 9.9 at 13 years with revision as the endpoint.
Deletion at chromosome arm 9p in relation to BRAF/NRAS mutations and prognostic significance for primary melanoma

We report an investigation of gene dosage at 9p21.3 and mutations in BRAF and NRAS, as predictors of relapse and histological markers of poor melanoma prognosis. Formalin‐fixed primary melanomas from 74 relapsed and 42 nonrelapsed patients were sequenced for common BRAF and NRAS mutations (N = 71 results) and gene dosage at 9p21.3 including the genes CDKN2A (which encodes CDKN2A and P14ARF), CDKN2B (CDKN2B), and MTAP was measured using multiplexed ligation‐dependant probe amplification (MLPA), (N = 75 results). BRAF/NRAS mutations were detected in 77% of relapsers and 58% of nonrelapsers (Fisher's exact P = 0.17), and did not predict ulceration or mitotic rate. There was no relationship between BRAF/NRAS mutations and gene dosage at 9p21.3. Reduced gene dosage at MTAP showed a borderline association with BRAF mutation (P = 0.04) and reduced gene dosage at the interferon gene cluster was borderline associated with wild type NRAS (P = 0.05). Reduced gene dosage in the CDKN2A regions coding for CDKN2A was associated with an increased risk of relapse (P = 0.03). Reduced gene dosage across 9p21.3 was associated with increased tumor thickness, mitotic rate, and ulceration (P = 0.02, 0.02, and 0.002, respectively), specifically in coding regions impacting on CDKN2B and P14ARF and CDKN2A. Loss at MTAP (P = 0.05) and the interferon gene cluster (P = 0.03) on 9p21 was also associated with tumor ulceration. There was no association between reduced gene dosage at 9p21.3 and subtype or site of tumor. This study presents supportive evidence that CDKN2B, P14ARF, and CDKN2A may all play a tumor suppressor role in melanoma progression. © 2010 Wiley‐Liss, Inc.
Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks

Genome-wide linkage and association studies have demonstrated promise in identifying genetic factors that influence health and disease. An important challenge is to narrow down the set of candidate genes that are implicated by these analyses. Protein-protein interaction (PPI) networks are useful in extracting the functional relationships between known disease and candidate genes, based on the principle that products of genes implicated in similar diseases are likely to exhibit significant connectivity/proximity. Information flow? based methods are shown to be very effective in prioritizing candidate disease genes. In this article, we utilize the topology of PPI networks to infer functional information in the context of disease association. Our approach is based on the assumption that PPI networks are organized into recurrent schemes that underlie the mechanisms of cooperation among different proteins. We hypothesize that proteins associated with similar diseases would exhibit similar topological characteristics in PPI networks. Utilizing the location of a protein in the network with respect to other proteins (i.e., the "topological profile" of the proteins), we develop a novel measure to assess the topological similarity of proteins in a PPI network. We then use this measure to prioritize candidate disease genes based on the topological similarity of their products and the products of known disease genes. We test the resulting algorithm, Vavien, via systematic experimental studies using an integrated human PPI network and the Online Mendelian Inheritance in Man (OMIM) database. Vavien outperforms other network-based prioritization algorithms as shown in the results and is available at www.diseasegenes. org.
Research on Worm Attack Prevention using Content-Based Distributed Packet Filtering, its Implementation and Benchmarking

1 Summary The first half of the project period in 2005 has focused on completing the IXP1200 network processor worm filter design, implementation, and benchmarking, and completing performance evaluation of distributed worm filtering in both inter-domain and intra-domain Internet measurement topologies. The second half focuses on scalable protection against zero-day attacks, a critical threat facing the Internet today. The final report describes the main elements of these three parts. Network solutions for protecting against worm attacks that complement partial end system patch deployment is a pressing problem. We present a scalable worm filter architecture for deployment at ingress/egress transit points on the Internet, including firewalls and gateways. Content-based packet filtering at gigabit line rates, in general, is a challenging problem due to the signature explosion problem that curtails performance in the absence of hardcoded ASIC implementation. We show that for worm malware, in particular, buffer overflow worms which comprise a large segment of recent outbreaks, scalable—accurate, cut-through, and extensible—filtering performance is feasible. This is achieved by three architectural features: (f1) workload sensitivity that affects prioritized handling of non-worm traffic, (f2) worm specificity that exploits the structured nature of worm malware, and (f3) multi-level signature caching that enables programmability and exten-sibility at cut-through performance. We demonstrate the efficacy of the design by implementing it on an IXP1200 network processor platform with gigabit interfaces. We benchmark the worm filter network appliance on a suite of current/past worms and their polymorphic variants, showing gigabit line speed filtering prowess with minimal footprint on end-to-end network performance. Current solutions for worm protection focus on the individual's responsibility and vigilance, where each user or organization is expected to keep abreast of patch developments and diligently affect timely software updates before harm is visited. For both technical and non-technical reasons, end system solutions suffer from the Achilles' heel of partial deployment which curtails their effectiveness at preventing large-scale outbreaks. We describe an infrastructure solution for worm attack prevention that uses distributed worm filtering to affect system-wide protection. We show that for the inter-domain Internet as well as intra-domain ISP networks, content-based worm filtering at strategically selected sites representing a mere 1.5% deployment suffices to yield effective containment. We show that containment performance undergoes a phase transition at a critical filter density whose value depends on the filter placement algorithm, with the engineering consequence that deployment below the critical filter density is ineffective and deployment above superfluous. Distributed …
Standardized Ultrasound Report for Thyroid Nodules: The Endocrinologist's Viewpoint

Background: Ultrasonography (US) plays a crucial role in the diagnostic management of thyroid nodules, but its widespread use in clinical practice might generate heterogeneity in ultrasound reports. Objectives: The aims of the study were to propose (a) a standardized lexicon for description of thyroid nodules in order to reduce US reports of interobserver variability and (b) a US classification system of suspicion for thyroid nodules in order to promote a uniform management of thyroid nodules. Methods: Relevant published articles were identified by searching MEDLINE at PubMed combining the following search terms: ultrasonography, thyroid, nodule, malignancy, carcinoma, and classification system. Results were supplemented with our data and experience. Results: A standardized US report should always document position, extracapsular relationships, number, and the following characteristics of each thyroid lesion: shape, internal content, echogenicity, echotexture, presence of calcifications, margins, vascularity, and size. Combining the previous US features, each thyroid nodule can be tentatively classified as: malignant, suspicious for malignancy, borderline, probably benign, and benign. Conclusions: We propose a standardized US report and a tentative US classification system that may become helpful for endocrinologists dealing with thyroid nodules in their clinical practice. The proposed classification does not allow to bypass the required cytological confirmation, but may become useful in identifying the lesions with a lower risk of neoplasm.
articleAdjuvant glycerol is not beneficial in experimental pneumococcal meningitis

Background: Bacterial meningitis in children causes high rates of mortality and morbidity. In a recent clinical trial, oral glycerol significantly reduced severe neurological sequelae in paediatric meningitis caused by Haemophilus influenzae type b, and a tendency towards a benefit of adjunctive glycerol was seen in pneumococcal meningitis. Methods: Here we examined the effects of glycerol in pneumococcal meningitis of infant rats and adult mice. All animals received ceftriaxone, and glycerol or placebo. Brain damage, hearing loss, and inflammatory parameters were
Modeling and simulation of biological systems from image data

This essay provides an introduction to the terminology, concepts, methods, and challenges of image‐based modeling in biology. Image‐based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like “what is the functional role of shape” or “how are biological shapes generated and regulated” can be addressed in the framework of image‐based systems biology. The combination of image quantification, model building, and computer simulation is illustrated here using the example of diffusion in the endoplasmic reticulum.
A chorus-section detecting method for musical audio signals

This paper describes a method for obtaining a list of chorus (refrain) sections in compact-disc recordings of popular music. The detection of chorus sections is essential for the computational modeling of music understanding and is useful in various applications, such as automatic chorus-preview functions in music browsers or retrieval systems. Most previous methods detected as a chorus a repeated section of a given length and had difficulty in identifying both ends of a chorus section and in dealing with modulations (key changes). By analyzing relationships between various repeated sections, our method called RefraiD can detect all the chorus sections in a song and estimate both ends of each section. It can also detect modulated chorus sections by introducing a similarity that enables modulated repetition to be judged correctly. Experimental results with a popular-music database show that this method detects the correct chorus sections in 80 of 100 songs.
The Identification and Discrimination of Synthetic Vowels

A series of thirteen two-formant vowels was synthesized and used as the basis of labelling and discrimination tests with a group of English-speaking listeners. The sounds varied only in F1/F2 plot and the resulting vowel qualities were such that listeners found no difficulty in assigning each sound to one of three phonemic categories, those of the vowels in bid, bed and bad. The results of the tests were compared with those previously obtained in experiments involving the consonant phonemes /b, d, g/. It appears from the data that the phoneme boundaries in the case of the three vowel phonemes are less sharply defined than in the case of the stop consonants. The labelling functions for the vowels show a gradual slope and the discrimination functions do not show any marked increase in sensitivity to change in the region of the phoneme boundaries. It is clear also that the listeners were able to discriminate differences very much smaller than would need to be distinguished simply in order to place vowels in the appropriate category. The results show further that the effect of sequence or acoustic context in the perception of vowels is very considerable. In all the aspects examined in these experiments, the perception of synthetic vowels is found to be different from that of synthetic stop consonants. These differences lend some support to the hypothesis that the degree of articulatory discontinuity between sounds may be correlated with the sharpness of the phonemic boundaries that separate them.
Statistical properties of inelastic Lorentz gas

The inelastic Lorentz gas in cooling states is studied. It is found that the inelastic Lorentz gas is localized and that the mean square displacement of the inelastic Lorentz gas obeys a power of a logarithmic function of time. It is also found that the scaled position distribution of the inelastic Lorentz gas has an exponential tail, while the distribution is close to the Gaussian near the peak. Using a random walk model, we derive an analytical expression of the mean square displacement as a function of time and the restitution coefficient, which well agrees with the data of our simulation. The exponential tail of the scaled position distribution function is also obtained by the method of steepest descent.
Resolution recovery for list-mode reconstruction in SPECT

We developed an iterative reconstruction method for SPECT which uses list-mode data instead of binned data. It uses a more accurate model of the collimator structure. The purpose of the study was to evaluate the resolution recovery and to compare its performance to other iterative resolution recovery methods in the case of high noise levels The source distribution is projected onto an intermediate layer. Doing this we obtain the complete emission radiance distribution as an angular sinogram. This step is independent of the acquisition system. To incorporate the resolution of the system we project the individual list-mode events over the collimator wells to the intermediate layer. This projection onto the angular sinogram will define the probability a photon from the source distribution will reach this specific location on the surface of the crystal, thus being accepted by the collimator hole. We compared the SPECT list-mode reconstruction to MLEM, OSEM and RBI. We used Gaussian shaped point sources with different FWHM at different noise levels. For these distributions we calculated the reconstructed images at different number of iterations. The modeling of the resolution in this algorithm leads to a better resolution recovery compared to other methods, which tend to overcorrect.
Post-mortem re-cloning of a transgenic red fluorescent protein dog

Recently, the world's first transgenic dogs were produced by somatic cell nuclear transfer. However, cellular senescence is a major limiting factor for producing more advanced transgenic dogs. To overcome this obstacle, we rejuvenated transgenic cells using a re-cloning technique. Fibroblasts from post-mortem red fluorescent protein (RFP) dog were reconstructed with in vivo matured oocytes and transferred into 10 surrogate dogs. One puppy was produced and confirmed as a re-cloned dog. Although the puppy was lost during birth, we successfully established a rejuvenated fibroblast cell line from this animal. The cell line was found to stably express RFP and is ready for additional genetic modification.
Thin film transistor & method of manufacturing the same

A method for fabricating a semiconductor thin film transistor is disclosed. The method for fabricating the semiconductor thin film transistor comprises the steps of: a) forming a gate wire(13) having a plurality of hemisphere grains on a surface of a semiconductor substrate(21); b) forming a gate insulating layer(22) and a semiconductor layer(212) on the gate wire(23) of the semiconductor substrate(21); and c) forming an impurity region(29) on both sides of the gate wire(23). Thereby, since the length of the gate is reduced, an off current due to a short channel offset is increased and an electrical property of the semiconductor device is significantly improved.
Validation of the salivary urea test as a method to diagnose chronic kidney disease.

BACKGROUND Serum urea correlates very well to salivary urea, which can be used as a low-cost, easily accessible and noninvasive diagnostic method for screening patients in early stages of kidney disease, especially in developing countries where resources are limited, giving the possibility of establishing secondary prevention programs later. METHODS One hundred and one people were enrolled: 11 with creatinine clearance (CrCl) less than 10 ml/min per 1.73 m(2); 10 with CrCl of 11-20 ml/min per 1.73 m(2); 12 with CrCl of 21-50 ml/min per 1.73 m(2); 26 with CrCl of 51-80 ml/min per 1.73 m(2) and 42 with CrCl of 81-170 ml/min per 1.73 m(2), to analyze salivary urea test accuracy through construction of a receiver operating characteristic curve. RESULTS Salivary urea cutoff point of 20 mg/dL and a CrCl of 80 ml/min per 1.73 m(2) showed sensitivity (S) of 0.98, specificity (SP) of 0.29, pretest probability (PPT) of 0.58, positive predictive value (PPV) of 0.66, negative predictive value (NPV) of 0.92, posttest positive probability (PTPP) of 0.66 and posttest negative probability (PTNP) of 0.09. A cutoff point of 40 mg/dL and a CrCl of 80 ml/min per 1.73 m(2) showed S=0.80, SP=0.71, PPT=0.58, PPV=0.80, NPV=0.71, PTPP=0.79 and PTNP=0.28. A cutoff point of 100 mg/dL and a CrCl of 80 ml/min per 1.73 m(2) showed S=0.22, SP=1, PPT=0.58, PPV=1, NPV=0.48, PTPP=1 and PTNP=0.52. Receiver operating characteristic curve analysis showed that the best cutoff point for salivary urea was 40 mg/dL. CONCLUSION The salivary urea test has a great capacity to discriminate patients with chronic kidney disease from healthy people, and it was shown that the best cutoff point is 40 mg/dL.