Miracle-dz/UniFAR-FTUs huggingface dataset:
Measurement and analysis of nonexponential signal decay curves in brain diffusion and muscle relaxation magnetic resonance studies in humans

Detailed measurement and analysis of two important processes in magnetic resonance imaging (MRI) are described. The processes of interest are the apparent diffusion coefficient (ADC) behavior of water protons in the brain and the transverse relaxation (T2) behavior of water protons in muscle. The method described for the brain water diffusion study allows for more detailed sampling of the brain signal decay with b‐factor than is usually performed. Prolonged scan times are avoided using a line scan format with the tradeoff being reduced volume coverage. The method described for the muscle studies also provides greater sampling of the T2 decay curves than is generally performed. The main advantage of the line scan format in this case, however, lies in the ability to perform “single‐shot” sampling of the decay curve which may prove useful for studying temporal changes of muscle during exercise. In either case, the high sampling of the relevant decay curves allows us to explore the limits of the usual assumption of monoexponential decay with two complimentary computational methods. These are discrete and continuum exponential signal modeling, respectively. For both processes studied, the assumption of monoexponential decay is found lacking. The results indicate the potential for greater tissue characterization and highlight the need for biophysical modeling of multicomponent decay behavior in vivo. © 1999 John Wiley & Sons, Inc. Int J Imaging Syst Technol 10, 294–303, 1999
ADAM metallopeptidase with thrombospondin type 1 motif 2 inactivation reduces the extent and stability of carbon tetrachloride–induced hepatic fibrosis in mice

ADAMTS2 belongs to the “ADAM metallopeptidase with thrombospondin type 1 motif” (ADAMTS) family. Its primary function is to process collagen type I, II, III, and V precursors into mature molecules by excising the aminopropeptide. This process allows the correct assembly of collagen molecules into fibrils and fibers, which confers to connective tissues their architectural structure and mechanical resistance. To evaluate the impact of ADAMTS2 on the pathological accumulation of extracellular matrix proteins, mainly type I and III collagens, we evaluated carbon tetrachloride–induced liver fibrosis in ADAMTS2‐deficient (TS2−/−) and wild‐type (WT) mice. A single carbon tetrachloride injection caused a similar acute liver injury in deficient and WT mice. A chronic treatment induced collagen deposition in fibrous septa that were made of thinner and irregular fibers in TS2−/− mice. The rate of collagen deposition was slower in TS2−/− mice, and at an equivalent degree of fibrosis, the resorption of fibrous septa was slightly faster. Most of the genes involved in the development and reversion of the fibrosis were similarly regulated in TS2−/− and WT mice. Conclusion: These data indicate that the extent of fibrosis is reduced in TS2−/− mice in comparison with their WT littermates. Inhibiting the maturation of fibrillar collagens may be a beneficial therapeutic approach to interfering with the development of fibrotic lesions. (HEPATOLOGY 2007.)
Gaussian process based online dynamic modeling of neuromuscular blockade

A non-parameter modeling methodology for the online dynamically modeling of nonlinear neuromuscular blockade (NMB) is presented in this paper. A big challenge of modeling NMB is the responses from muscular are quite different from people to people and the individual dynamic may change during the procedure of operation. Gaussian process (GP) is a kind of probabilistic and non-parametric modeling method in on need of any information about the plant structure. It just builds the data relationship between the input and output by statistical approaches. In order to tackle the difference in patients, an online dynamic GP modeling technique is used which can avoid the traditional static models' defects, i.e., it is only suitable for an individual patient and the controller designed based on the traditional model is not robust. Furthermore, a moving window technique is adopted in order to improve the local accuracy of Gaussian process model and reduce the calculation burden. The training data set size is fixed and the old ones are dropped as soon as the new data are available.
Toward affective brain-computer interfaces : exploring the neurophysiology of affect during human media interaction

Affective Brain-Computer Interfaces (aBCI), the sensing of emotions from brain activity, seems a fantasy from the realm of science fiction. But unlike faster-than-light travel or teleportation, aBCI seems almost within reach due to novel sensor technologies, the advancement of neuroscience, and the refinement of machine learning techniques. However, as for so many novel technologies before, the challenges for aBCI become more obvious as we get closer to the seemingly tangible goal. One of the primary challenges on the road toward aBCI is the identification of neurophysiological signals that can reliably differentiate affective states in the complex, multimodal environments in which aBCIs are supposed to work. Specifically, we are concerned with the nature of affect during the interaction with media, such as computer games, music videos, pictures, and sounds. In this thesis we present three studies, in which we employ a variety of methods to shed light on the neurophysiology of affect in the context of human media interaction as measured by electroencephalography (EEG): we evaluate active affective human-computer interaction (HCI) using a neurophysiological indicator identified from the literature, we explore correlates of affect induced by natural, multimodal media stimuli, and we study the separability of complex affective responses into context-specific and general components.
Receipt of chemotherapy among medicare patients with cancer by type of supplemental insurance.

PURPOSE Medicare beneficiaries with cancer bear a greater portion of their health care costs, because cancer treatment costs have increased. Beneficiaries have supplemental insurance to reduce out-of-pocket costs; those without supplemental insurance may face barriers to care. This study examines the association between type of supplemental insurance coverage and receipt of chemotherapy among Medicare patients with cancer who, per National Comprehensive Cancer Network treatment guidelines, should generally receive chemotherapy. PATIENTS AND METHODS This retrospective, observational study included 1,200 Medicare patients diagnosed with incident cancer of the breast (stage IIB to III), colon (stage III), rectum (stage II to III), lung (stage II to IV), or ovary (stage II to IV) from 2000 to 2005. Using the National Cancer Institute Patterns of Care Studies and linked SEER-Medicare data, we determined each Medicare patient's supplemental insurance status (private insurance, dual eligible [ie, Medicare with Medicaid], or no supplemental insurance), consultation with an oncologist, and receipt of chemotherapy. Using adjusted logistic regression, we evaluated the association of type of supplemental insurance with oncologist consultation and receipt of chemotherapy. RESULTS Dual-eligible patients were significantly less likely to receive chemotherapy than were Medicare patients with private insurance. Patients with Medicare only who saw an oncologist had comparable rates of chemotherapy compared with Medicare patients with private insurance. CONCLUSION Dual-eligible Medicare beneficiaries received recommended cancer chemotherapy less frequently than other Medicare beneficiaries. With the increasing number of Medicaid patients under the Affordable Care Act, there will be a need for patient navigators and sufficient physician reimbursement so that low-income patients with cancer will have access to oncologists and needed treatment.
A New Controlling Parameter in Design of Above Knee Prosthesis

— In this paper after reviewing some previous studies, in order to optimize the above knee prosthesis, beside the inertial properties a new controlling parameter is informed. This controlling parameter makes the prosthesis able to act as a multi behavior system when the amputee is opposing to different environments. This active prosthesis with the new controlling parameter can simplify the control of prosthesis and reduce the rate of energy consumption in comparison to recently presented similar prosthesis “Agonist-antagonist active knee prosthesis”. In this paper three models are generated, a passive, an active, and an optimized active prosthesis. Second order Taylor series is the numerical method in solution of the models equations and the optimization procedure is genetic algorithm. Modeling the prosthesis which comprises this new controlling parameter (SEP) during the swing phase represents acceptable results in comparison to natural behavior of shank. Reported results in this paper represent 3.3 degrees as the maximum deviation of models shank angle from the natural pattern. The natural gait pattern belongs to walking at the speed of 81 m/min.
Performance and stability analysis of buffered slotted ALOHA protocols using tagged user approach

This paper presents a new approximation approach to analyze slotted ALOHA (S-ALOHA) systems with finite user population having either finite or infinite user buffer capacity. By assuming a symmetric channel, the performance analysis of the overall system is determined by the performance of an arbitrarily selected user, called the tagged user. The service time distribution for the tagged user buffer is found using a state flow graph. This distribution is then applied to the queueing analysis of the tagged user using available classical queueing theory results. The proposed approach can be applied to analysis of systems with a very large user population and user buffer capacity. The distributions and mean values of the important performance indices such as waiting time, queue size, and interdeparture time are obtained. The stability of the system with infinite buffer capacity is also studied. The region of transmission probability p in which the system is always stable and has best performance is obtained. Though the system with finite buffer capacity is considered to be always stable, a comprehensive analysis of the equilibrium points in the system is presented. The analysis presented will allow a proper choice of transmission probability so that the system always operates at the desired equilibrium point.
Mexican Cervical Cancer Screening Study II: 6-Month and 2-Year Follow-up of HR-HPV Women Treated With Cryotherapy in a Low-Resource Setting

Objective To determine the efficacy and tolerance of cryotherapy in a visual inspection with acetic acid (VIA) triage protocol after primary human papillomavirus (HPV) screening in a low-resource setting. Materials and Methods This continuous series conducted over 2 years enrolled nonpregnant, high-risk HPV (HR-HPV)–positive women between the ages of 30 and 50 years, who resided in the state of Michoacán, Mexico, and had a history of no Pap smear screening or knowledge of Pap smear results within the last 3 years. These women were initially enrolled in the Mexican Cervical Cancer Screening Study II (MECCS II) trial and were treated with cryotherapy after VIA triage. They subsequently followed up at 6 months and 2 years for repeat VIA, colposcopy, and biopsy. Results A total of 291 women were treated with cryotherapy, of whom 226 (78%) followed up at 6 months. Of these 226 women, 153 (68%) were HR-HPV–negative; there were no findings of cervical intraepithelial neoplasia grade 2 (CIN2) or worse. The remaining 73 women (32%) were HR-HPV–positive; of these women, 2 had CIN2 and 3 had CIN3. Only 137 women followed up at 2 years. Of these 137 women, 116 were HR-HPV–negative and 21 were HR-HPV–positive. Of the 21 women positive for HR-HPV, 9 had negative biopsy results, 11 had CIN1, and 1 had no biopsy. The clearance rate of HR-HPV was 83% (95% confidence interval: 0.78–0.87). There were no biopsy findings of CIN2 or worse at 2 years. Before cryotherapy, of the 226 women, 15 (6.6%) were positive for endocervical curettage (ECC) and 5 (2.2%) were referred for surgical management. Of these 15 ECC-positive women, 10 (67%) followed up at 6 months and it was shown that no patient was ECC positive at that time point. Moreover, of the 15 ECC-positive women, 11 (73%) followed up at 2 years and it was shown that no patient was ECC positive at that time point. In our study, VIA had a false-positive rate of 5%. Conclusions Cryotherapy was an effective, acceptable, and well-tolerated means of treating cervical dysplasia in a low-resource setting.
Virulence Genotype and Phylogenetic Origin in Relation to Antibiotic Resistance Profile among Escherichia coli Urine Sample Isolates from Israeli Women with Acute Uncomplicated Cystitis

ABSTRACT To clarify the virulence and phylogenetic implications of antimicrobial agent resistance in Escherichia coli, 100 E. coli isolates from urine samples of Israeli women with acute uncomplicated cystitis were analyzed by molecular phylotyping and virulence genotyping for comparison with resistance phenotypes. The differences between the isolates that were resistant and susceptible to trimethoprim-sulfamethoxazole and ampicillin were minimal. In contrast, ciprofloxacin resistance was associated with greatly reduced inferred virulence and categorical shifts away from the highly virulent phylogenetic group B2, which explained much of the virulence effect. The results of amplification fingerprinting suggested that most ciprofloxacin-resistant isolates represented unique clonal groups and were not derived from clonal groups with more highly virulent susceptible isolates. These findings suggest that virulence and antimicrobial resistance are not mutually exclusive in E. coli clinical isolates. Instead, the relationship between virulence and antimicrobial resistance varies according to the particular resistance phenotype; for ciprofloxacin resistance, the relationship is strongly influenced by phylogenetic background. The basis for the concentration of ciprofloxacin resistance in non-B2 phylogenetic groups remains unknown.
Possible new mechanism of cortisol action in female reproductive organs: physiological implications of the free hormone hypothesis.

The so-called free hormone hypothesis predicts that the biological activity of a given steroid correlates with the free protein-unbound concentration rather than with the total concentration (i.e. free plus protein-bound). Cortisol is a glucocorticoid with many diverse functions and the free hormone hypothesis seems to apply well to the observed effects of cortisol. The ovaries express glucocorticoid receptors and are affected by cortisol, but lack the necessary enzymes for cortisol synthesis. Ovarian follicles modulate the biological activity of cortisol by (1) follicular production of especially progesterone and 17 alpha-hydroxy-progesterone which, within the follicle, reach levels that displace cortisol from its binding proteins, in particular, cortisol-binding protein, making it available for biological action and (2) a developmental regulated expression of two types of 11 beta-hydroxysteroid dehydrogenase (i.e. 11 beta-HSD type 1 and type 2), which oppose the action of one another, the 11 beta-HSD type 2 predominantly inactivating cortisol to cortisone, while 11 beta-HSD type 1 reverses this reaction. As a result, a high concentration of cortisol available for biological action is present in the preovulatory follicle just prior to ovulation and it has been suggested that cortisol may function to reduce the inflammatory-like reactions occurring in connection with ovulation. This paper suggests (1) that the function of the oviduct is also affected by the high levels of free cortisol released in preovulatory follicular fluid at ovulation and (2) that formation and function of the corpus luteum benefits from a high local concentration of free cortisol, whereas the surrounding developing follicles may experience negative effects. If this hypothesis proves correct it may describe a new physiological mechanism by which cortisol interacts with the female reproductive organs, showing that the biologically active concentration of a steroid locally can be regulated to serve specific functions.
Characterization of Novel Peroxisome Proliferator-activated Receptor γ Coactivator-1α (PGC-1α) Isoform in Human Liver*

Peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) is a transcriptional coactivator that contributes to the regulation of numerous transcriptional programs including the hepatic response to fasting. Mechanisms at transcriptional and post-transcriptional levels allow PGC-1α to support distinct biological pathways. Here we describe a novel human liver-specific PGC-1α transcript that results from alternative promoter usage and is induced by FOXO1 as well as glucocorticoids and cAMP-response element-binding protein signaling but is not present in other mammals. Hepatic tissue levels of novel and wild-type transcripts were similar but were only moderately associated (p < 0.003). Novel mRNA levels were associated with a polymorphism located in its promoter region, whereas wild-type transcript levels were not. Furthermore, hepatic PCK1 mRNA levels exhibited stronger associations with the novel than with the wild-type transcript levels. Except for a deletion of 127 amino acids at the N terminus, the protein, termed L-PGC-1α, is identical to PGC-1α. L-PGC-1α was localized in the nucleus and showed coactivation properties that overlap with those of PGC-1α. Collectively, our data support a role of L-PGC-1α in gluconeogenesis, but functional differences predicted from the altered structure suggest that L-PGC-1α may have arisen to adapt PGC-1α to more complex metabolic pathways in humans.
Methods for measuring glycogen cycling.

Simultaneous synthesis and breakdown of glycogen is called glycogen cycling. The extent of hyperglycemia and decreased glycogen stores in diabetes mellitus may relate in part to the extent cycling occurs. Four methods have been introduced to estimate its extent in liver in humans. 1) In the fasted state, the rate of net hepatic glycogenolysis, i.e., glycogen breakdown minus synthesis, is estimated using NMR, and the rate of glycogenolysis is estimated from deuterium labeling of blood glucose on (2)H(2)O ingestion. 2) The rate of glycogen synthesis is estimated from the rate of labeling of carbon 1 of glycogen on [1-(13)C]glucose infusion, monitored by NMR, and the rate of breakdown from the rate of disappearance of that labeling on unlabeled glucose infusion. 3) The rate of synthesis from glucose-1-P, formed by glycogenolysis, is measured by the decrease in the (3)H/(14)C ratio in acetaminophen glucuronide on acetaminophen and [2-(3)H,6-(14)C]galactose administration. 4) The rate of synthesis is estimated from the dilution of label from labeled galactose in its conversion to the acetaminophen glucuronide, and the rate of glycogenolysis is estimated from the amount of label in blood glucose. In the first method, the fate of glucose-6-P is assumed to be only to glycogen and glucose. In the second, only glucose-6-P molecules formed by breakdown that are not cycled back to glycogen are measured. In the third, (3)H is assumed to be removed completely during cycling, and only the molecules cycled back to glycogen are measured. In the fourth, galactose conversion to glucose is assumed to be via glycogen. Quantitations in all four methods depend on assuming the order in which the molecules deposited in glycogen are released.
Complete Genome Sequence of Mycobacterium xenopi Type Strain RIVM700367

ABSTRACT Mycobacterium xenopi is a slow-growing, thermophilic, water-related Mycobacterium species. Like other nontuberculous mycobacteria, M. xenopi more commonly infects humans with altered immune function, such as chronic obstructive pulmonary disease patients. It is considered clinically relevant in a significant proportion of the patients from whom it is isolated. We report here the whole genome sequence of M. xenopi type strain RIVM700367.
Mycoplasma pneumoniae isolated from patients with respiratory infection in Kanagawa Prefecture in 1976-2006: emergence of macrolide-resistant strains.

*Corresponding author: Mailing address: Kanagawa Prefectural Institute of Public Health, Shimomachiya 1-3-1, Chigasaki, Kanagawa 253-0087, Japan. Tel: +81-467-83-4400, Fax: +81467-83-4457, E-mail: okazaki.i73r@pref.kanagawa. jp We have been closely following the trend of Mycoplasma pneumoniae infections in Kanagawa Prefecture since 1976. We report here its isolation rates and the frequency of macrolideresistant strains during the period. Pharyngeal swabs obtained from patients with respiratory infections were used for isolation of M. pneumoniae. The liquid media used were PPLO broth (Difco Laboratories, Detroit, Mich., USA) and BBL Mycoplasma broth base (Becton, Dickinson and Co., Baltimore, Md., USA), both supplemented with 20% horse serum (Invitrogen Corp., Carlsbad, Calif., USA) inactivated by heating at 56°C for 30 min, 10% house-made yeast extract, 1% glucose, 1,000 U/ml penicillin G and 0.025% thallium acetate. The agar medium (prepared in 60 mm Petri dishes) was 1.5% agar (Bacto agar; Becton, Dickinson) prepared in the above liquid medium. The diphasic medium was prepared in screw-cap tubes (12 mm in diameter and 100 mm in height); the upper layer consisted of 2 ml of the liquid medium and the bottom layer 1 ml of the agar medium, both supplemented with 0.002% phenol red and 0.001% methylene blue. Color change of the medium indicated a positive culture of M. pneumoniae. All the cultures were performed aerobically at 37°C. Typical colonies appearing on the agar plates were selected and inoculated into the liquid medium containing 0.002% phenol red for expansion. M. pneumoniae was identified by serological (1) or polymerase chain reaction (2) studies. Among 2,414 swab specimens obtained from acute respiratory infection cases in 1976-2006, 585 (24.2%) were positive for M. pneumoniae. Frequency peaks for isolation of M. pneumoniae appeared regularly at 4-year intervals until the first half of the 1990’s, but from then the pattern started to degrade (Fig. 1). This trend parallels that of reported M. pneumoniae cases across Japan (3). We tested 381 M. pneumoniae isolated in 1985-2006 for sensitivities (MIC; μg/ml) to erythromycin (EM), josamycin (JM), minocycline and tetracycline. The sensitivity test was done by a broth microdilution method previously described (4). The results are shown in Table 1. While none of the isolates before 1999 were resistant to these antibiotics, strains resistant to EM and JM were found among isolates in 2003. Resistant strains were isolated every year from 2003 to 2006. In total, among the 85 isolates in the period 2000-2006, 15 (17.6%) were resistant to EM and JM. The nucleotide sequencing of the V domain of 23S rRNA in the resistant strains revealed replacement of adenine by guanine at a nucleotide position 2063 or 2064, i.e., A2063G or A2064G (5). These