Miracle-dz/UniFAR-FTUs huggingface dataset:
Patient-reported outcome after rheumatoid arthritis-related surgery in the lower extremities

Background and purpose Although decreasing with the development of effective pharmacological regimes, joint surgery has improved the function and quality of life of patients with rheumatoid arthritis (RA). Few studies have assessed patient-reported outcomes after RA surgery to the lower extremities. Here we report patient-relevant outcome after RA-related surgery based on the first data from the Swedish National Register of Rheuma Surgery (RAKIR). Patients and methods 258 RA patients (212 women) who had joint surgery performed at the Department of Orthopaedics, Spenshult Hospital between September 2007 and June 2009 were included. Mean age at surgery was 64 (20–86) years. The patients completed the SF-36 and HAQ questionnaires preoperatively and 6 months postoperatively, and 165 patients completed them after 12 months. Results Improvement was seen as early as at 6 months. At 12 months, 165 patients (141 women)—including hip (n = 15), knee (n = 27), foot (n = 102), and ankle (n = 21) patients—reported statistically significant improvements from preoperatively to 12 months postoperatively in HAQ (mean change: –0.11) and SF-36 subscales physical function (11), role physical (12), bodily pain (13), social functioning (6.4), and role emotional (9.4). Hip and knee patients reported the greatest improvements. Interpretation Orthopedic RA-related surgery of the lower extremities has a strong effect on pain and physical function. Improvement is evident as early as 6 months postoperatively and remains after 12 months.
Vitamin D deficiency is highly prevalent in COPD and correlates with variants in the vitamin D-binding gene

Introduction Vitamin D deficiency has been associated with many chronic illnesses, but little is known about its relationship with chronic obstructive pulmonary disease (COPD). Objectives Serum 25-hydroxyvitamin D (25-OHD) levels were measured in 414 (ex)-smokers older than 50 years and the link between vitamin D status and presence of COPD was assessed. The rs7041 and rs4588 variants in the vitamin D-binding gene (GC) were genotyped and their effects on 25-OHD levels were tested. Results In patients with COPD, 25-OHD levels correlated significantly with forced expiratory volume in 1 s (FEV1) (r=0.28, p<0.0001). Compared with 31% of the smokers with normal lung function, as many as 60% and 77% of patients with GOLD (Global Initiative for Obstructive Lung Disease) stage 3 and 4 exhibited deficient 25-OHD levels <20 ng/ml (p<0.0001). Additionally, 25-OHD levels were reduced by 25% in homozygous carriers of the rs7041 at-risk T allele (p<0.0001). This correlation was found to be independent of COPD severity, smoking history, age, gender, body mass index, corticosteroid intake, seasonal variation and rs4588 (p<0.0001). Notably, 76% and 100% of patients with GOLD stage 3 and 4 homozygous for the rs7041 T allele exhibited 25-OHD levels <20 ng/ml. Logistic regression corrected for age, gender and smoking history further revealed that homozygous carriers of the rs7041 T allele exhibited an increased risk for COPD (OR 2.11; 95% CI 1.20 to 3.71; p=0.009). Conclusion Vitamin D deficiency occurs frequently in COPD and correlates with severity of COPD. The data warrant vitamin D supplementation in patients with severe COPD, especially in those carrying at-risk rs7041 variants.
A new hybrid stemming algorithm for Persian

Stemming has been an influential part in Information retrieval and search engines. There have been tremendous endeavours in making stemmer that are both efficient and accurate. Stemmers can have three method in stemming, Dictionary based stemmer, statistical-based stemmers, and rule-based stemmers. This paper aims at building a hybrid stemmer that uses both Dictionary based method and rule-based method for stemming. This ultimately helps the efficacy and accurateness of the stemmer.
Risk factors for motor vehicle crashes in older women.

BACKGROUND Motor vehicle crash and fatality rates are higher per mile driven for elderly drivers, with an exponential increase above age 75. Identifying elderly drivers who are at risk for automobile crashes may help direct interventions to reduce their high rate of injuries and deaths. METHODS Subjects were 1416 women aged 65 to 84 enrolled in the Portland, Ore. site of the Study of Osteoporotic Fractures. Motor vehicle crash information for the years 1986-1995 for each participant was obtained from the Oregon State Department of Transportation. Items from questionnaires, interviews, and physical examinations were tested prospectively for associations with the occurrence of motor vehicle crashes. RESULTS About one third of participants (415 of 1416) had a motor vehicle crash during a mean follow-up time of 5.7 years. After adjustment for age and weekly driving mileage, risk factors significantly associated with motor vehicle crashes were a fall in the previous year [hazard ratio (HR) 1.53, 95% confidence interval (CI) 1.26-1.86], a greater orthostatic systolic blood pressure drop (HR 1.11 per 12.5 mm Hg, 95% CI 1.01-1.22), and increased foot reaction time (HR 1.10 per 0.06 second, 95% CI 1.00-1.22). Other neuromuscular tests, functional status, medical diagnoses, vision tests, and cognitive tests did not predict motor vehicle crashes in this study population. CONCLUSIONS This prospective study with extended follow-up of a large cohort of elderly women has identified crash risk factors that can be measured in the clinical setting. Further study is needed to determine if interventions aimed at these risk factors can decrease the risk of motor vehicle crashes.
Whiskers Area as Extracerebral Reference Tissue for Quantification of Rat Brain Metabolism Using 18F-FDG PET: Application to Focal Cerebral Ischemia

Diseases and dysfunction of the central nervous system are often associated with regional changes in cerebral glucose metabolism, which can be measured in vivo by PET using 18F-FDG as the tracer. For quantification, the arterial tracer input function must be determined. For rodents in particular, direct measurement of blood radioactivity concentration is scarcely feasible for follow-up of individual animals because of the invasiveness of blood sampling. We show that the whiskers area of the rat's muzzle serves as an extracerebral reference region. The derived model also takes into account local variations of the lumped constant, which is crucial in pathologic tissue. Methods: In 11 rats, the reference tissue kinetic parameters were determined from PET data and measured whole blood radioactivity concentration. Parametric images of cerebral kinetic rate constants were calculated using the directly measured input function, the reference tissue time–activity curve with individually fitted reference kinetic parameters, and the reference time–activity curve with fixed reference kinetic parameters calculated from the fitted parameters averaged over all animals. The need for kinetic modeling in disease models is demonstrated in 5 rats subjected to acute focal cerebral ischemia. 18F-FDG metabolism and transport rate constants and local cerebral glucose metabolic rates were calculated. Results: Cerebral kinetic constants derived from the 3 methods corresponded closely. The maximum difference in whole-brain kinetic parameters observed between the directly measured input function and the reference tissue time–activity curve with individually fitted reference kinetic parameters was less than 5%. Taking fixed reference parameters (the reference time–activity curve with fixed reference kinetic parameters calculated from the fitted parameters averaged over all animals) still provided whole-brain kinetic parameters with an accuracy of approximately 90%. In the rats subjected to focal cerebral ischemia, 18F-FDG kinetic parameters in healthy tissue were not significantly different from whole-brain kinetic parameters in naive rats. The ischemic region was characterized by preserved glucose metabolism, although 18F-FDG uptake was elevated significantly—that is, the lumped constant in the ischemic region was different from that of healthy brain tissue. Conclusion: The method presented here allows for the quantitative noninvasive determination of cerebral glucose consumption in rats, takes into account local variations of the lumped constant, and is suitable for follow-up measurements of individuals.
Learning Dialogue Strategies from Older and Younger Simulated Users

Older adults are a challenging user group because their behaviour can be highly variable. To the best of our knowledge, this is the first study where dialogue strategies are learned and evaluated with both simulated younger users and simulated older users. The simulated users were derived from a corpus of interactions with a strict system-initiative spoken dialogue system (SDS). Learning from simulated younger users leads to a policy which is close to one of the dialogue strategies of the underlying SDS, while the simulated older users allow us to learn more flexible dialogue strategies that accommodate mixed initiative. We conclude that simulated users are a useful technique for modelling the behaviour of new user groups.
Two primate-specific small non-protein-coding RNAs in transgenic mice: neuronal expression, subcellular localization and binding partners

In a rare occasion a single chromosomal locus was targeted twice by independent Alu-related retroposon insertions, and in both cases supported neuronal expression of the respective inserted genes encoding small non-protein coding RNAs (npcRNAs): BC200 RNA in anthropoid primates and G22 RNA in the Lorisoidea branch of prosimians. To avoid primate experimentation, we generated transgenic mice to study neuronal expression and protein binding partners for BC200 and G22 npcRNAs. The BC200 gene, with sufficient upstream flanking sequences, is expressed in transgenic mouse brain areas comparable to those in human brain, and G22 gene, with upstream flanks, has a similar expression pattern. However, when all upstream regions of the G22 gene were removed, expression was completely abolished, despite the presence of intact internal RNA polymerase III promoter elements. Transgenic BC200 RNA is transported into neuronal dendrites as it is in human brain. G22 RNA, almost twice as large as BC200 RNA, has a similar subcellular localization. Both transgenically expressed npcRNAs formed RNP complexes with poly(A) binding protein and the heterodimer SRP9/14, as does BC200 RNA in human. These observations strongly support the possibility that the independently exapted npcRNAs have similar functions, perhaps in translational regulation of dendritic protein biosynthesis in neurons of the respective primates.
Particle and Photon Detection: Counting and Energy Measurement

Fundamental limits for photon counting and photon energy measurement are reviewed for CCD and CMOS imagers. The challenges to extend photon counting into the visible/nIR wavelengths and achieve energy measurement in the UV with specific read noise requirements are discussed. Pixel flicker and random telegraph noise sources are highlighted along with various methods used in reducing their contribution on the sensor’s read noise floor. Practical requirements for quantum efficiency, charge collection efficiency, and charge transfer efficiency that interfere with photon counting performance are discussed. Lastly we will review current efforts in reducing flicker noise head-on, in hopes to drive read noise substantially below 1 carrier rms.
Regional Ischemic 'Preconditioning' Protects Remote Virgin Myocardium From Subsequent Sustained Coronary Occlusion

BackgroundOne or more brief episodes of coronary artery occlusion protect or “precondition” the myocardium perfused by that artery from a subsequent episode of sustained ischemia. We sought to determine whether ischemic preconditioning protects only those myocytes subjected to brief coronary occlusion or whether brief occlusions in one vascular bed also limit infarct size andfor attenuate contractile dysfunction in remote virgin myocardium subjected to subsequent sustained coronary occlusion. Methods and ResultsIn the preliminary limb of the study, six anesthetized dogs underwent four episodes of 5-minute circumflex branch occlusion plus 5-minute reperfusion, followed by 1 hour of sustained left anterior descending coronary artery occlusion and 4.5 hours of reflow. Subendocardial blood flow during left anterior descending coronary artery occlusion (measured by injection of radiolabeled microspheres) was 0.07±0.03 mL. min-1. g tissue-1, similar to the value of 0.07±0.02 mL. min-1. g-1 observed in a group of eight concurrent control dogs. However, infarct size (assessed by triphenyltetrazolium staining) in the circumflex preconditioned group averaged 4±1% of the myocardium at risk, significantly less (p<0.05) than the value of 13+4% observed in the concurrent controls. An additional 18 dogs were then randomized to undergo either four episodes of circumflex branch occlusion (n=8) or no intervention (n=10) before 1 hour of left anterior descending coronary artery occlusion and 4.5 hours of reflow. Subendocardial blood flow averaged 0.08±0.02 versus 0.08±0.03 mL. min-1. g-1 in the control versus circumflex preconditioned groups, yet infarct size was significantly smaller in circumflex preconditioned dogs than in the controls (6±2% versus 16±5% of the risk region; p<0.05). At 4.5 hours following reperfusion, segment shortening in the left anterior descending coronary artery bed (assessed by sonomicrometry) averaged -21+19%o of baseline in control animals versus 13±12% of baseline in the preconditioned group (p=NS). Circumflex preconditioning did not, however, have an independent beneficial effect on contractile function: Regression analysis revealed that the trend toward improved function in circumflex preconditioned dogs reflected the smaller infarct sizes in this group. ConclusionsBrief episodes of ischemia in one vascular bed protect remote, virgin myocardium from subsequent sustained coronary artery occlusion in this canine model. These data imply that preconditioning may be mediated by factor(s) activated, produced, or transported throughout the heart during brief ischemia/reperfusion.
Scalability-performance tradeoffs in MPLS and IP routing

MPLS (Multi-Protocol Label Switching) has recently emerged to facilitate the engineering of network traffic. This can be achieved by directing packet flows over paths that satisfy multiple requirements. MPLS has been regarded as an enhancement to traditional IP routing, which has the following problems: (1) all packets with the same IP destination address have to follow the same path through the network; and (2) paths have often been computed based on static and single link metrics. These problems may cause traffic concentration, and thus degradation in quality of service. In this paper, we investigate by simulations a range of routing solutions and examine the tradeoff between scalability and performance. At one extreme, IP packet routing using dynamic link metrics provides a stateless solution but may lead to routing oscillations. At the other extreme, we consider a recently proposed Profile-based Routing (PBR), which uses knowledge of potential ingress-egress pairs as well as the traffic profile among them. Minimum Interference Routing (MIRA) is another recently proposed MPLS-based scheme, which only exploits knowledge of potential ingress-egress pairs but not their traffic profile. MIRA and the more conventional widest-shortest path (WSP) routing represent alternative MPLS-based approaches on the spectrum of routing solutions. We compare these solutions in terms of utility, bandwidth acceptance ratio as well as their scalability (routing state and computational overhead) and load balancing capability. While the simplest of the per-flow algorithms we consider, the performance of WSP is close to dynamic per-packet routing, without the potential instabilities of dynamic routing.
Induction of hepatitis C virus-specific cytotoxic T lymphocytes in mice by an intrahepatic inoculation with an expression plasmid.

We assessed the possibility of intrahepatic inoculation with a plasmid encoding hepatitis C virus (HCV) proteins to elicit HCV-specific cytotoxic T lymphocytes (CTL) in mice as a conventional animal model of HCV infection. BALB/c mice were intrahepatically or intramuscularly inoculated with an expression plasmid DNA encoding HCV structural proteins under the control of the elongation factor 1-alpha promoter. Expressions of HCV-core protein and envelope proteins (E1 and E2) in hepatocytes were detected immunohistochemically 6 days after inoculation. CTL responses were examined using target cells either pulsed with a specific peptide or infected with a recombinant vaccinia virus expressing HCV structural protein. Both intrahepatically and intramuscularly DNA-inoculated mice developed CD8(+), MHC class I-restricted CTL responses that recognized the peptide pulsed as well as HCV proteins expressing target cells. These studies demonstrated the usefulness of a murine model of HCV infection induced by direct intrahepatic DNA inoculation for understanding the immunopathogenic mechanisms in HCV infection.
Comparison of PCR, culture, and histopathology for diagnosis of tuberculous pericarditis

Nucleic acid amplification techniques for the diagnosis of tuberculosis (TB) are rapidly being developed. Scant work, however, has focused on pericardial TB. Using cryopreserved specimens from a prior study of pericarditis, we compared PCR to culture and histopathology for the diagnosis of tuberculous pericarditis in 36 specimens of pericardial fluid and 19 specimens of pericardial tissue from 20 patients. Fluid and tissue were cultured on Lowenstein-Jensen and Middlebrook solid media and in BACTEC radiometric broth. Tissue specimens were stained with hematoxylin-eosin, Ziehl-Neelsen, auramine O, and Kinyoun stains and were examined for granuloma formation and acid-fast bacilli. PCR was performed with both fluid and tissue with IS6110-based primers specific for the Mycobacterium tuberculosis complex by published methods. Sixteen of the 20 patients had tuberculous pericarditis and 4 patients had other diagnoses. TB was correctly diagnosed by culture in 15 (93%) patients, by PCR in 13 (81%) patients, and by histology in 13 of 15 (87%) patients. PCR gave one false-positive result for a patient with Staphylococcus aureus pericarditis. Considering the individual specimens as the unit of analysis, M. tuberculosis was identified by culture in 30 of 43 specimens (70%) from patients with tuberculous pericarditis and by PCR in 14 of 28 specimens (50%) from patients with tuberculous pericarditis (P > 0.15). The sensitivity of PCR was higher with tissue specimens (12 of 15; 80%) than with fluid specimens (2 of 13; 15%; P = 0.002). In conclusion, the overall accuracy of PCR approached the results of conventional methods, although PCR was much faster. Therefore, PCR merits further development in this regard. The sensitivity of PCR with pericardial fluid was poor, and false-positive results with PCR remain a concern.
Sample-Adaptive Multiple Kernel Learning

Existing multiple kernel learning (MKL) algorithms \textit{indiscriminately} apply a same set of kernel combination weights to all samples. However, the utility of base kernels could vary across samples and a base kernel useful for one sample could become noisy for another. In this case, rigidly applying a same set of kernel combination weights could adversely affect the learning performance. To improve this situation, we propose a sample-adaptive MKL algorithm, in which base kernels are allowed to be adaptively switched on/off with respect to each sample. We achieve this goal by assigning a latent binary variable to each base kernel when it is applied to a sample. The kernel combination weights and the latent variables are jointly optimized via margin maximization principle. As demonstrated on five benchmark data sets, the proposed algorithm consistently outperforms the comparable ones in the literature.
Patterns of Antidepressant Medication Use Among Pregnant Women in a United States Population

This article describes the pattern of reported antidepressant use around the time of pregnancy in a population‐based sample of women who delivered live‐born babies without birth defects. Data were used from the National Birth Defects Prevention Study, an ongoing case‐control study of risk factors for birth defects covering 10 US states. Mothers of live‐born infants without birth defects (controls) born between 1998 and 2005 were randomly selected from each site. Information on the mother's characteristics and exposure to antidepressants was collected via a standardized telephone interview. Among 6582 mothers included in the study, 298 (4.5%) reported use of an antidepressant in the period of 3 months before through the end of pregnancy. Use of selective serotonin‐reuptake inhibitors was reported most often (3.8%), followed by bupropion (0.7%). A statistically significant decline was observed, from 3.1% to 2.3% (P < .001), in reported use of antidepressants between the first and second month after conception. The frequency of reported antidepressant use at any time during pregnancy increased from 2.5% in 1998 to 8.1% in 2005 (P < .001) in 4 states. The findings show an increase in reported antidepressant use over a 9‐year period and a substantial decrease in use around the usual time of pregnancy recognition.
Phosphorylation of G Protein-Coupled Receptors: From the Barcode Hypothesis to the Flute Model

Seven transmembrane G protein-coupled receptors (GPCRs) are often phosphorylated at the C terminus and on intracellular loops in response to various extracellular stimuli. Phosphorylation of GPCRs by GPCR kinases and certain other kinases can promote the recruitment of arrestin molecules. The arrestins critically regulate GPCR functions not only by mediating receptor desensitization and internalization, but also by redirecting signaling to G protein-independent pathways via interactions with numerous downstream effector molecules. Accumulating evidence over the past decade has given rise to the phospho-barcode hypothesis, which states that ligand-specific phosphorylation patterns of a receptor direct its distinct functional outcomes. Our recent work using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance (19F-NMR) spectroscopy led to the flute model, which provides preliminary insight into the receptor phospho-coding mechanism, by which receptor phosphorylation patterns are recognized by an array of phosphate-binding pockets on arrestin and are translated into distinct conformations. These selective conformations are recognized by various effector molecules downstream of arrestin. The phospho-barcoding mechanism enables arrestin to recognize a wide range of phosphorylation patterns of GPCRs, contributing to their diverse functions.