Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein structure comparison using the Markov transition model of evolution

A number of automatic protein structure comparison methods have been proposed; however, their similarity score functions are often decided by the researchers' intuition and trial‐and‐error, and not by theoretical background. We propose a novel theory to evaluate protein structure similarity, which is based on the Markov transition model of evolution. Our similarity score between structures i and j is defined as log P(j → i)/P(i), where P(j → i) is the probability that structure j changes to structure i during the evolutionary process, and P(i) is the probability that structure i appears by chance. This is a reasonable definition of structure similarity, especially for finding evolutionarily related (homologous) similarity. The probability P(j → i) is estimated by the Markov transition model, which is similar to the Dayhoff's substitution model between amino acids. To estimate the parameters of the model, homologous protein structure pairs are collected using sequence similarity, and the numbers of structure transitions within the pairs are counted. Next these numbers are transformed to a transition probability matrix of the Markov transition. Transition probabilities for longer time are obtained by multiplying the probability matrix by itself several times. In this study, we generated three types of structure similarity scores: an environment score, a residue–residue distance score, and a secondary structure elements (SSE) score. Using these scores, we developed the structure comparison program, Matras (MArkovian TRAnsition of protein Structure). It employs a hierarchical alignment algorithm, in which a rough alignment is first obtained by SSEs, and then is improved with more detailed functions. We attempted an all‐versus‐all comparison of the SCOP database, and evaluated its ability to recognize a superfamily relationship, which was manually assigned to be homologous in the SCOP database. A comparison with the FSSP database shows that our program can recognize more homologous similarity than FSSP. We also discuss the reliability of our method, by studying the disagreement between structural classifications by Matras and SCOP. Proteins 2000;41:108–122. © 2000 Wiley‐Liss, Inc.
Angiotensin II in adrenergic-induced alterations in glomerular hemodynamics.

UNLABELLED Micropuncture analysis of glomerular ultrafiltration (SNGFR) was conducted in Munich-Wistar rats to assess the functional responses to moderate-frequency (3-Hz) renal nerve stimulation. Angiotensin II inhibition (ANG II-inhib) was produced by the intravenous administration of [Sar1, Ala8] angiotensin II or MK 421 to investigate whether it modulates the effects of renal nerve stimulation. Micropuncture measurements were obtained before and during renal nerve stimulation. Renal nerve stimulation decreased SNGFR approximately 25% (from 49.9 +/- 2.3 to 38.0 +/- 1.4 nl X min-1 X g kidney wt-1), the result of decreased glomerular capillary hydrostatic pressure gradient and nephron plasma flow. These decreases were due to increased afferent (approximately 43%) and efferent (approximately 30%) arteriolar resistances, since the glomerular ultrafiltration coefficient remained unaffected. The effects of renal nerve stimulation during ANG II-inhib were less in magnitude than in renal nerve stimulation alone: SNGFR decreased from 48.0 +/- 1.5 to 44.8 +/- 2.0 nl X min-1 X g kidney wt-1 after renal nerve stimulation. The net renal production of norepinephrine was augmented by renal nerve stimulation but it was not influenced by ANG II-inhib. IN CONCLUSION renal nerve stimulation can regulate glomerular ultrafiltration by altering vascular resistances, and angiotensin II appears to be a critical factor for the full functional expression of renal nerve stimulation at the glomerulus.
Increase Efficiency of Photovoltaic Pumping System Based BLDC Motor Using Fuzzy Logic MPPT Control

The aim of this paper is presentation of an approach for modeling , control and optimization of a photovoltaic pumping system which contains a PV generator , DC-DC boost converter, MPPT controller, DC-AC inverter and a BLDC motor. We use an intelligent control method for searching the maximum power point (MPP). This method uses a fuzzy logic controller applied to a drive a DC–DC converter to an optimal operating point using PV panel’s measured variables. The PWM signals are generated by the interaction of the motor speed closed-loop system and the current hysteresis. The motor reference current is compared with the motor speed feedback signal. The considered model has been implemented in Matlab /simulink environment. The results show the effectiveness of the proposed method under variation irradiation ,in order to increase the performance of the water pumping system. Key-Words: Pumping system, photovoltaic, MPPT, BLDC, Fuzzy logic, Optimization
Transformation and Upgrading of China's Industrial Structure:Process,Issues and Trends

China's industry has entered into a new developing stage when the structure transformation and upgrading has become a must.Despite the obvious achievements made on the country's industrial restructuring during the Eleventh Five-Year Plan period,there are still some outstanding issues that limit and affect the transformation and upgrading of China's industrial structure.This paper makes a comprehend analysis of factors such as the developing conditions and policy environment for the last five years,and promotes some judgments referring to the developing trend of China's industrial structure for the coming Twelfth Five-Year Plan period.Relevant policies and measures are suggested in terms of system reform,industry policies and developing environment as to lead and promote the transformation and upgrading of the industrial structure.
Shape of the relapse curve and long-term abstinence among untreated smokers.

OBJECTIVE To describe the relapse curve and rate of long-term prolonged abstinence among smokers who try to quit without treatment. METHOD Systematic literature review. DATA SOURCES Cochrane Reviews, Dissertation Abstracts, Excerpt Medica, Medline, Psych Abstracts and US Center for Disease Control databases plus bibliographies of articles and requests of scientists. STUDY SELECTION Prospective studies of self-quitters or studies that included a no-treatment control group. DATA EXTRACTION Two reviewers independently extracted data in a non-blind manner. DATA SYNTHESIS The number of studies was too small and the data too heterogeneous for meta-analysis or other statistical techniques. RESULTS There is a paucity of studies reporting relapse curves of self-quitters. The existing eight relapse curves from two studies of self-quitters and five no-treatment control groups indicate most relapse occurs in the first 8 days. These relapse curves were heterogeneous even when the final outcome was made similar. In terms of prolonged abstinence rates, a prior summary of 10 self-quitting studies, two other studies of self-quitters and three no-treatment control groups indicate 3-5% of self-quitters achieve prolonged abstinence for 6-12 month after a given quit attempt. CONCLUSIONS More reports of relapse curves of self-quitters are needed. Smoking cessation interventions should focus on the first week of abstinence. Interventions that produce abstinence rates of 5-10% may be effective. Cessation studies should report relapse curves.
Uplink traffic scheduling with QoS support in broadband wireless access networks

With the ever-growing demand for multimedia applications over broadband wireless access networks, an efficient traffic scheduler is deemed crucial for the provision of quality-of-service (QoS). A large number of traffic scheduler schemes have been proposed, and those equipped with channel-aware capability appear to be most promising. These schedulers are capable of exploiting the dynamic channel condition and traffic characteristics in order to improve the channel utilization and guarantee QoS. Nevertheless, there is still lack of clarity amongst the existing channel-aware schemes on which is the most suitable to support multiple traffic classes with diverse QoS requirements. Furthermore, the majority of existing traffic scheduling works focus on the downlink direction, hence this motivates us to study for the uplink case. In this paper, we compare the performance of the most promising scheme, namely, the modified largest weighted delay first (M-LWDF) scheduling algorithm against other representative traffic scheduling algorithms, i.e., weighted round robin (WRR), max-sum-capacity (MSC) and proportional fair (PF). We also discuss the effectiveness of each algorithm in meeting the desired QoS requirements.
Sensitivity of American Option Prices with Respect to the Variations of Local Volatility

In mathematical finance there are two well known and traditional technique s to deal American options: Solving parabolic partial differential equations and using the probabilistic approach. In this paper, we use purely probabilistic approach. We consider standard one-dimensional diffusion model with local volatility that is a func tion of time and current stock price and where the risk-free interest rate is constant. We estimate the continuity of American option prices w ith respect to the corresponding local volatilities.
Diversification,Government Subsidy and Agricultural Firms' Performance:An Empirical Research on Chinese Agricultural Listed Companies

Based on a sample of Chinese A-share listed agricultural companies,we investigate the effects on performance of corporate diversification,government subsidy and their interaction.We also explore whether these effects are moderated by firm size.Results of regression analysis show that corporate diversification has a negative effect on the agricultural firms' performance and government subsidy is positively correlated with the performance.They also interact significantly to affect the performance.However,the main effects and interaction effect are smaller in the bigger agricultural firms.Our research suggests that Chinese agricultural firms should prudentially choose diversification strategy and the policy maker should give priority to small-and-medium sized firms and seriously monitor the use of government subsidies.
Effects of several inhibitors on pure cultures of ruminal methanogens *

Aims: To examine the effects of five inhibitors of methanogenesis, 2‐bromoethanesulphonate (BES), 3‐bromopropanesulphonate (BPS), lumazine, propynoic acid and ethyl 2‐butynoate, on CH4 production of the ruminal methanogens Methanobrevibacter ruminantium, Methanosarcina mazei and Methanomicrobium mobile.
Application of Agent Technology in the Agile Supply Chain Management

The basic concepts and requirements of the agile supply chain are discussed.And combined with the advantages of the Agent technology, the structure of agile supply chain based on the CORBA distributed system platform is represented.According to the function and the action, Agent is classified into enterprise Agent and harmony Agent.And still the function of each Agent is defined while the implementation tool of Agent: JADE is introduced.
The Use of Mobile Health to Deliver Self-Management Support to Young People With Type 1 Diabetes: A Cross-Sectional Survey

Background Young people living with type 1 diabetes face not only the challenges typical of adolescence, but also the challenges of daily management of their health and evolving understanding of the impact of their diagnosis on their future. Adolescence is a critical time for diabetes self-management, with a typical decline in glycemic control increasing risk for microvascular diabetes complications. To improve glycemic control, there is a need for evidence-based self-management support interventions that address the issues pertinent to this population, utilizing platforms that engage them. Increasingly, mobile health (mHealth) interventions are being developed and evaluated for this purpose with some evidence supporting improved glycemic control. A necessary step to enhance effectiveness of such approaches is to understand young people’s preferences for this mode of delivery. Objective A cross-sectional survey was conducted to investigate the current and perceived roles of mHealth in supporting young people to manage their diabetes. Methods Young adults (16-24 years) with type 1 diabetes in Auckland, New Zealand, were invited to take part in a survey via letter from their diabetes specialist. Results A total of 115 young adults completed the survey (mean age 19.5 years; male 52/115, 45%; European 89/115, 77%), with all reporting they owned a mobile phone and 96% (110/115) of those were smartphones. However, smartphone apps for diabetes management had been used by only 33% (38/115) of respondents. The most commonly reported reason for not using apps was a lack of awareness that they existed. Although the majority felt they managed their diabetes well, 63% (72/115) reported wanting to learn more about diabetes and how to manage it. A total of 64% (74/115) respondents reported that they would be interested in receiving diabetes self-management support via text message (short message service, SMS). Conclusions Current engagement with mHealth in this population appears low, although the findings from this study provide support for the use of mHealth in this group because of the ubiquity and convenience of mobile devices. mHealth has potential to provide information and support to this population, utilizing mediums commonplace for this group and with greater reach than traditional methods.
A Longitudinal Study Comparing Bereavement Phenomena in Recently Bereaved Spouses, Adult Children and Parents

Objective: The study investigated previous research findings and clinical impressions which indicated that the intensity of grief for parents who had lost a child was likely to be higher than that for widows/widowers, who in turn were likely to have more intense reactions than adult children losing a parent. Method: In order to compare the intensities of the bereavement reactions among representative community samples of bereaved spouses (n = 44), adult children (n = 40) and parents (n = 36), and to follow the course of such phenomena, a detailed Bereavement Questionnaire was administered at four time points over a 13–month period following the loss. Results: Measures based on items central to the construct of bereavement showed significant time and group differences in accordance with the proposed hypothesis. More global items associated with the construct of resolution showed a significant time effect, but without significant group differences. Conclusions: Evidence from this study supports the hypothesis that in non-clinical, community-based populations the frequency with which core bereavement phenomena are experienced is in the order: bereaved parents bereaved spouses bereaved adult children.
Mural attenuation in normal small bowel and active inflammatory Crohn's disease on CT enterography: location, absolute attenuation, relative attenuation, and the effect of wall thickness.

OBJECTIVE The purpose of our study was to measure relative and absolute wall attenuations and wall thickness in normal small bowel on contrast-enhanced CT enterography and to study the efficacy of relative attenuation, absolute attenuation, and wall thickness in distinguishing normal from active inflammatory Crohn's disease of the terminal ileum. MATERIALS AND METHODS Using a case-control study design, we reviewed 630 CT enterography examinations, of which 191 were normal and 36 had active inflammatory Crohn's disease in the terminal ileum. In healthy individuals, wall thickness and attenuation in distended and collapsed loops were measured in the duodenum and four abdominal quadrants. Wall thickness and attenuation were also measured in the terminal ileum. All measurements of intraarterial attenuation were taken at the same slice level. In the examinations of patients with Crohn's disease, only terminal ileum wall thickness and attenuation as well as arterial attenuation at the same slice level were measured. Normal segments were compared with a linear model. Terminal ileum data were fit to a multivariate logistic regression model. RESULTS Relative attenuation and absolute attenuation in the normal distended and collapsed duodenum and left upper quadrant were significantly greater than in all other segments (p < 0.001 and < 0.048 for relative attenuation and p < 0.001 and < 0.032 for absolute attenuation, respectively). Relative attenuation and wall thickness models and absolute attenuation and wall thickness models discriminated normal from active terminal ileum Crohn's disease significantly better than the same measurements without wall thickness (p = 0.017 and 0.001, respectively). When the bowel wall is > 3 mm, a relative attenuation cutoff of 0.5 is 89% sensitive and 81% specific. CONCLUSION In normal small bowel, when wall measurement is taken into account, the duodenum and jejunum have a greater relative attenuation and absolute attenuation than other segments. Relative attenuation and absolute attenuation with wall thickness models discriminate normal from active terminal ileum Crohn's disease better than the same measurements without wall thickness.
Counterexamples for Directed and Node Capacitated Cut-Trees

We show that there is no cut-tree for various connectivity concepts, hence pointing out to errors in the papers of Schnorr [SIAM J. Comput. , 8 (1979), pp. 265-275] and Gusfield and Naor [Networks, 21 (1991), pp. 505-520]. Gomory and Hu [SIAM J. Appl. Math., 9 (1961), pp. 551-560] constructed a cut-tree for undirected graphs which compactly represents a minimum cut for each pair of vertices. This has a straightforward generalization to directed Eulerian graphs, cf. Gupta [SIAM J. Appl. Math., 15 (1967), pp. 168-171]. A generalization for arbitrary directed graphs was given by Schnorr. There is a well-known transformation of vetex connectivity to directed edge connectivity; directed edge cuts correspond to vertex cuts in some weak sense. The result of Schnorr was later applied by Gusfield and Naor [8] for such a cut-tree construction. In this paper counterexamples are described to show that for directed graphs there is no cut-tree and therefore the cut-tree results of Schnorr and Gusfield and Naor are incorrect. Our final example shows that, without weakening the notion of vertex connectivity, it is impossible to construct vertex cut-trees for undirected graphs in general.
Bactericidal activity of neutrophils with reduced oxidative burst from adults with bronchiectasis

Recent work has shown that the most common abnormality on screening of immune function in cohort of adult subjects with bronchiectasis was a low neutrophil oxidative burst. To assess the functional significance of a low oxidative burst in subjects with idiopathic bronchiectasis. Neutrophils with a low oxidative burst were obtained from six bronchiectasis patients and assessed for their ability to kill Staphylococcus aureus. The results were compared with those obtained using neutrophils from 12 healthy controls subjects and control neutrophils treated with dimethylthiourea (DMTU), an inhibitor of the oxidative burst. The results showed that the bronchiectasis subjects had significantly reduced killing of bacteria compared with controls (p<0.001). The addition of DMTU to neutrophils of control subjects significantly impaired both the oxidative burst and bactericidal activity. The addition of interferon‐γ enhanced oxidative burst in both groups. Abnormal neutrophil function in some subjects with bronchiectasis may account for their high rate of infection.
Path planning and control of a mobile base with nonholonomic constraints

Summary Motion Planning and control of mobile vehicles with nonholonomic constraints are in their infancy. A systematic approach for modeling and base; motion control of a mobile vehicle is presented. A nonlinear coordinate transformation that takes into account the complete dynamics with nonholonomic constraints is used in order to obtain a linear system in space coordinates. An input-output feedback linearization inner loop is subsequently designed to transform this system into a linear-point mass system in the coordinates corresponding to the control objectives. A rigorous yet simple approach to motion planning through optimization techniques is presented for these mobile vehicles. The resulting Cartesian trajectory generated from the motion planning algorithm is employed as the reference trajectory in the outer loop, which is designed based on a Lyapunov function candidate. The net result is a base motion controller that gives capabilities to these mobile vehicles not only for tracking a Cartesian trajectory but also to achieve a desired final orientation (docking angle).
Penicillin Resistance Not a Factor in Outcome from Invasive Streptococcus pneumoniae Community-Acquired Pneumonia in Adults When Appropriate Empiric Therapy Is Started

Background:Invasive Streptococcus pneumoniae pneumonia among adults due to penicillin-resistant or intermediate resistant strains was investigated to determine whether these patients responded poorly to common antibiotic regimens compared to pneumonia due to susceptible strains. Methods:During a 21-year period (1983–2003), clinical outcome was analyzed among 3 groups of adults, 19 with resistant, 33 with intermediate, and 133 with susceptible invasive S pneumoniae pneumonia admitted to hospitals in Huntington, West Virginia. Adults with resistant and intermediate infections were matched by age and month of admission to a group of 133 adults with penicillin-susceptible infections. All isolates of resistant and intermediate infections were capsular serotypes/serogroups 6, 9, 14, 19, and 23, and isolates of susceptible infections included 24 different serotypes/serogroups. Case fatality rates were calculated for deaths that occurred during the first 7, first 14, and first 21 days of hospitalization. Minimal inhibitory concentration (MIC) was determined by E-test and capsular serotype by Quellung procedures. Results:The resistant and susceptible groups did not differ in several measures of severity of illness, including admission vital signs, duration of fever, mean total leukocyte count, number of lobes involved, preexisting underlying diseases, and antibiotic treatment regimens. There were no significant differences in case fatality rates between the 3 groups of pneumonia by days in hospital, age, severity of illness, and empiric antibiotic treatment regimen with a cephalosporin and a macrolide, the most common antibiotic regimen. Conclusions:These findings provide evidence that combination antibiotic regimens effective in the treatment of invasive susceptible S pneumoniae pneumonia are equally effective in the treatment of invasive resistant (MIC = 2–4 &mgr;g/mL) and of intermediate (MIC = 0.1–1 &mgr;g/mL) S pneumoniae pneumonia.