Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting kinetic constants of protein–protein interactions based on structural properties

Elucidating kinetic processes of protein–protein interactions (PPI) helps to understand how basic building blocks affect overall behavior of living systems. In this study, we used structure‐based properties to build predictive models for kinetic constants of PPI. A highly diverse PPI dataset, protein–protein kinetic interaction data and structures (PPKIDS), was built. PPKIDS contains 62 PPI with complex structures and kinetic constants measured experimentally. The influence of structural properties on kinetics of PPI was studied using 35 structure‐based features, describing different aspects of complex structures. Linear models for the prediction of kinetic constants were built by fitting with selected subsets of structure‐based features. The models gave correlation coefficients of 0.801, 0.732, and 0.770 for koff, kon, and Kd, respectively, in leave‐one‐out cross validations. The predictive models reported here use only protein complex structures as input and can be generally applied in PPI studies as well as systems biology modeling. Our study confirmed that different properties play different roles in the kinetic process of PPI. For example, kon was affected by overall structural features of complexes, such as the composition of secondary structures, the change of translational and rotational entropy, and the electrostatic interaction; while koff was determined by interfacial properties, such as number of contacted atom pairs per 100 Å2. This information provides useful hints for PPI design. Proteins 2010;79:720–734. © 2010 Wiley‐Liss, Inc.
An international outbreak of Salmonella enteritidis associated with lasagne; lessons on the need for cross-national co-operation in investigating food-borne outbreaks

We investigated an outbreak of Salmonella enteritidis involving at least 19 British tourists returning from one hotel in another European country. A retrospective cohort study of 47 hotel guests identified lasagne as the most likely vehicle of transmission (RR 11·5; 95% CI 3·0–44·1; P<0·0001). However, difficulties in information exchange and lack of formal mechanisms to agree on the aims of the cross-national investigation hampered efficient management of the outbreak. The factors leading to contamination of the food vehicle were not identified and therefore specific action to prevent reoccurrence could not be taken. There is need to develop protocols for cross-national investigations of outbreaks in Europe which should include specifying objectives, roles and responsibilities of investigators and control agencies, with formal reporting of the outcome of the investigation.
CD40-CD40 Ligand-Independent Activation of CD8+ T Cells Can Trigger Allograft Rejection1

In experimental transplantation, blockade of CD40-CD40 ligand (CD40L) interactions has proved effective at permitting long-term graft survival and has recently been approved for clinical evaluation. We show that CD4+ T cell-mediated rejection is prevented by anti-CD40L mAb therapy but that CD8+ T cells remain fully functional. Furthermore, blocking CD40L interactions has no effect on CD8+ T cell activation, proliferation, differentiation, homing to the target allograft, or cytokine production. We conclude that CD40L is not an important costimulatory molecule for CD8+ T cell activation and that following transplantation donor APC can activate recipient CD8+ T cells directly without first being primed by CD4+ T cells.
The abdominal constriction response and its suppression by analgesic drugs in the mouse.

After intraperitoneal injection of a noxious agent, the rat and the mouse show a response consisting of a wave of constriction and elongation passing caudally along the abdominal wall, sometimes accompanied by twisting of the trunk and followed by extension of the hind limbs (Vander Wende & Margolin, 1956; Siegmund, Cadmus & Lu, 1957). This response has been variously called " writhing" (Vander Wende & Margolin, 1956), " stretching" (Koster, Anderson & de Beer, 1959), " cramping " (Murray & Miller, 1960} and " squirming " (Whittle, 1964a). Because of the emotional implications of these terms, it was later called the " abdominal constriction response " (Collier, Hammond, Horwood-Barrett & Schneider, 1964). We describe here an examination of the ability of a number of substances, including some occurring in tissues and causing pain in man (Keele & Armstrong, 1964), to elicit abdominal constriction responses in mice. Vander Wende & Margolin (1956) and Siegmund et al. (1957) showed that codeine, morphine and pethidine, given subcutaneously, and procaine, given intraperitoneally, suppressed the abdominal constriction response. They concluded that the response was nociceptive and they used it as a basis for testing analgesic drugs. The antinociceptive tests developed from this work have the advantage that they are sensitive to antipyretic drugs (Siegmund et al., 1957; Hendershot & Forsaith, 1959; Koster et at., 1959; Keith, 1960) and to narcotic antagonists (Taber, Greenhouse & Irwin, 1964; Blumberg, Wolf & Dayton, 1965; Pearl & Harris, 1966). These tests have, however, three disadvantages: (1) exposure of animals to peritoneal stimulation intense enough to induce repeated abdominal constrictions for longer than necessary is ethically undesirable and needlessly time consuming; (2) increased permeability of blood vessels accompanies peritoneal irritation (Northover, 1963, 1964) and the development of abdominal constrictions (Whittle, 1963, 1964a and b), and so an antinociceptive effect cannot easily be distinguished from an anti-inflammatory; and (3) the test produces many false positives (Hendershot & Forsaith, 1959; Emele & Shanaman, 1963; Brittain, Lehrer & Spencer, 1963; Okun, Liddon & Lasagna, 1963). We describe new forms of abdominal constriction test in the mouse, in which some of these disadvantages are lessened. Preliminary accounts of this work have been published (Collier et al., 1964; Collier, James & Schneider, 1966).
Effective pain relief from intra‐articular saline with or without morphine 2 mg in patients with moderate‐to‐severe pain after knee arthroscopy: a randomized, double‐blind controlled clinical study

Background: Intra‐articular (IA) morphine has given good and prolonged pain relief in some studies when given at the end of arthroscopic procedures in the knee joint. However, similar studies have not been able to document any local analgesic effect of morphine. A large number of the negative studies have not demonstrated any assay sensitivity. We have documented that around 40% of patients have only very mild or no pain after arthroscopic procedures in the knee joint. This obviously is a confounding factor, reducing assay sensitivity when all patients are included in IA morphine studies.
Fusion of human and machine intelligence for telerobotic systems

A new intelligent fusion scheme for human operator command and autonomous planner/controller in telerobotic system has been developed based on the event-based planning and control theory. It provides a unified model to integrate a human operator control command with action planning and control of autonomous operation. As a result, the telerobotic system can perform tasks which cannot be done by either human operator or autonomous planner/controller alone. This scheme lays down a foundation for planning and control of a general robotic system involving human operators, and provides a natural and efficient way to fuse the human intelligence with the machine intelligence. The scheme is implemented and tested on a PUMA 560 robotic system. The experimental results of obstacle avoidance, and hybrid force/position control with a commanded force are presented.
Investigating the mechanism of hysteresis effect in graphene electrical field device fabricated on SiO₂ substrates using Raman spectroscopy.

The hysteresis effect is a common problem in graphene field-effect transistors (FETs). Usually, the external doping to graphene is considered to be responsible for the hysteresis behavior, but is not yet clearly understood. By monitoring the doping of graphene and the hysteresis in graphene FETs under different atmospheres using in situ Raman spectroscopy, it is confirmed that the electrochemical doping of O(2) /H(2) O redox couple to graphene is responsible for the hysteresis effect. In addition, Raman spectra of graphene on SiO(2) substrate show stronger doping than that suspended, which indicates that SiO(2) substrate plays an important role in the doping of graphene. Herein it is proposed that the doping species (H(2) O and O(2) ) are bounded at the interface of graphene/SiO(2) substrate by hydrogen-bonds with the silanol groups on SiO(2) substrate. The dynamic equilibrium process of the charge-transfer between H(2) O/O(2) redox couple and graphene under electrical field modulation is carefully analyzed using Marcus-Gerischer theory. This work provides a clear view to the mechanism of the hysteresis effect, and is of benefit to a reliable design to suppress the hysteresis in graphene FETs.
Crocin reduces Aspergillus fumigatus‐induced airway inflammation and NF‐κB signal activation

Chronic obstructive pulmonary disease (COPD) is a chronic airway inflammation and its exacerbation is often accompanied by Aspergillus fumigatus (A. fumigatus) infection. Increasing evidences demonstrated the potent antioxidant and ‐inflammatory effects of crocin. However, the role of crocin in A. fumigatus‐induced inflammation is still unknown. We aimed to evaluate the role of crocin in inflammation response induced by A. fumigatus in human bronchial epithelial cells and the possible mechanisms. BEAS‐2B and NHBE cells were pretreated with crocin for 24 h, and then A. fumigatus conidia were added for 24 h. A. fumigatus treatment exhibited a significant higher TNF‐α, IL‐8, IL‐6, and IL‐1β level (P < 0.05), whereas crocin pretreatment significantly inhibited A. fumigatus induced the pro‐inflammatory cytokines (P < 0.05). NF‐κB inhibitor PDTC inhibited pro‐inflammatory cytokines release triggered by A. fumigatus (P < 0.05). Furthermore, crocin suppressed A. fumigatus induced NF‐κB p65 nuclear translocation, the phosphorylation of IKKα and IκBα, the degradation of IκBα and NF‐κB reporter activity. Crocin pretreatment also resulted in an inhibition of A.fumigatus‐induced ROS production (P < 0.05). Taken together, these results indicate that crocin may prevent A. fumigatus‐induced inflammation through suppressing NF‐κB signal pathway.
Blood lipids of cows at different stages of lactation.

Abstract The levels and uptake by the mammary gland of blood lipid components, acetate, ketone bodies, and glucose during early or late lactation were compared to the values during the dry period. During the dry period, levels of plasma phospholipids, cholesterol esters, and free cholesterol dropped to 38.0, 51.7, and 63.9%, respectively, whereas plasma triglycerides rose to 146% of the late-lactation levels. The only positive arteriovenous difference observed consistently during the dry period was for plasma acetate. During early lactation, levels of total plasma triglycerides were lower, whereas those of phospholipids and cholesterol esters were similar to levels of the same components during the dry period. The arteriovenous differences for blood glucose and ketone bodies during early lactation were higher than during any other period. No consistent arteriovenous differences for plasma phospholipids, cholesterol esters, free cholesterol, or free fatty acids were observed during any period, except for the large and consistently positive arteriovenous differences for free fatty acids in two out of three cows during early lactation.
Effect of Gurmar and shilajit on body weight of young rats.

General debility and loss of body weight is commonly associated with diabetes meIlitus. This seems to be related to the deficiency of insulin, responsible for the inhibition of oxidative phosphorylation (10) and decreased synthesis of proteins (17) which in turn reduces the elaboration of anterior pituitary trophic hormones (9). Moreover the growth stimulating and nitrogen retaining effects of somatotropin are also inhibited in diabetes (14), (11), (16). This inhibition is likely to become more marked during ketosis because of increased secretion of adrenocortical steroids (19), (16) which are known to antagonise growth promoting effect of somatotropin (18). A few of the Ayurvedic antidiabetic remedies, Tribang shila containing shilajit and Gurmar (Gymnema sylvestre) have been reported to prevent reduction in body weight, induced by the diabetogenic doses of the anterior pituitary hormones (5). It would therefore be of interest to investigate the effect of these drugs on body weight of young rats in view of the tonic property of the former (2), (3), (15) and insulin promoting and adrenocortical inhibitory effects of the latter drug (12), \6), (7).
Lernen mit Medien Wiederkehrendes und Aktuelles in der E-Learning-Debatte

Mit neuen Medien von der Schrift bis zum Computer ging stets die Frage nach deren Nutzen für die Pädagogik und speziell die Mediendidaktik einher. Vor allem im Kontext der Erwachsenenbildung aber auch in der Schulbildung kreisen diese Debatten bis heute um den zentralen Begriff E-Learning. Im Folgenden soll zunächst die Karriere dieses Begriffs nachgezeichnet sowie die pädagogischen Argumentationsmuster der Debatten kritisch reflektiert werden. Dabei stößt man auch auf „wiederkehrende Erwartungen“ (Schrape 2012) und Begründungen, was vermuten lässt, dass die Disziplin sich früherer Erkenntnisse nicht konsequent vergewissert. Wie auch in der Medienwirkungsdebatte gibt es in der Debatte um das Lernen mit Medien viel alten Wein in neuen Schläuchen.
Biochemical Characterization of a Novel Haloalkane Dehalogenase from a Cold-Adapted Bacterium

ABSTRACT A haloalkane dehalogenase, DpcA, from Psychrobacter cryohalolentis K5, representing a novel psychrophilic member of the haloalkane dehalogenase family, was identified and biochemically characterized. DpcA exhibited a unique temperature profile with exceptionally high activities at low temperatures. The psychrophilic properties of DpcA make this enzyme promising for various environmental applications.
Potentiation of mast cell mediator release by adenosine.

Since extracellular adenosine can alter adenylate cyclase activity and cell function in a variety of tissues, the effect of adenosine on mediator release was studied with isolated rat mast cells. Adenosine did not alter the rate of spontaneous release, but histamine release induced by anti-IgE, concanavalin A (Con A), 48/80, or the calcium ionophore A23187 was markedly enhanced by 1 nM to 0.1 mM adenosine. Mast cells preincubated in the presence of 10 µM adenosine and then challenged with 0.1 µg/ml of A23187 released 71.5% (± 7.4 SEM) of the cellular histamine compared to a 38.2% (± 3.0 SEM) release from control cells. Adenosine caused a 3.0-fold (± 0.2 SEM) increase in the rate of release occurring 30 to 60 sec after A23187 addition, but did not change the duration of mediator release. Adenosine did not appear to decrease the minimum concentration of ionophore required to stimulate release. The poorly metabolized adenosine analog 2-chloroadenosine (100 µM) potentiated release approximately 2-fold whereas dipyridamole, an inhibitor of mast cell uptake of adenosine, did not inhibit adenosine potentiation suggesting that adenosine actions on mast cells may be mediated by direct activation of cell-surface receptors. Adenosine modestly potentiated the fall in cyclic AMP levels occurring 30 to 60 sec after ionophore challenge, raising the possibility that potentiation may be mediated by alterations in cyclic AMP metabolism. Mast cells suspended in media containing 1 mM EGTA and no added calcium demonstrated adenosine potentiation of A23187-induced release indicating that the adenosine effect was not mediated by increased translocation of calcium into the cells. Adenosine potentiation was completely blocked by 100 µM theophylline, a known inhibitor of adenosine binding, with 50% inhibition of release occurring at 3 µM theophylline. These studies indicate that adenosine may be an important modulator of mast cell function in complex tissues and that part of the pharmacologic action of theophylline in human bronchial asthma may be through inhibition of adenosine binding, rather than direct effects on cyclic AMP metabolism.
A Framework for Evaluating the Quality of Multimedia Learning Resources

This article presents the structure and theoretical foundations of the Learning Object Review Instrument (LORI), an evaluation aid available through the E-Learning Research and Assessment Network at http://www.elera. net. A primary goal of LORI is to balance assessment validity with efficiency of the evaluation process. The instrument enables learning object users to create reviews consisting of ratings and comments on nine dimensions of quality: content quality, learning goal alignment, feedback and adaptation, motivation, presentation design, interaction usability, accessibility, reusability, and standards compliance. The article presents research and practices relevant to these dimensions and describes how each dimension can be interpreted to evaluate multimedia learning resources.
The long term effectiveness of combined therapy by behavior modification and very low calorie diet: 2 years follow-up.

Seventy refractory obese subjects were assigned to one of three treatments; (a) very low calorie diet (VLCD) alone; (b) behavior modification alone; and (c) combined therapy by VLCD and behavior modification. Fifteen obese patients were treated by VLCD for 1-2 months on the outpatient clinic; 16 obese patients were treated by a combined therapy and 39 subjects were treated by behavior modification alone. Formula diet used in this program was Optifast 70 (420 kcal/day). The behavior modification had been performed for 4 months with eight group meetings, using the revised textbook based on the Learn Program (University of Pennsylvania). Effects on weight reduction and its maintenance during 2 years follow-up were compared in each treatment group. There were no significant differences between average weight loss of patients treated by VLCD (7.5 +/- 2.1 kg/month) and that attained by the combined therapy (8.3 +/- 2.3 kg/month). At 2 years after the termination of the VLCD treatment, 67 percent of patients had regained more than half of their reduced weight, with an average weight regain of 4.3 +/- 3.5 kg. In contrast, 12 of 16 (75 percent) and 33 of 39 (85 percent) patients had maintained their reduced weight for 2 years after the combined therapy or the behavior modification program. Continuing weight loss of 1.0 +/- 0.7 kg by the combined therapy and 1.3 +/- 2.2 kg by the behavior modification were observed at 2 years of follow-up. Weight reducing effect of combined therapy by behavior modification and VLCD was almost identical with that obtained by VLCD alone in a short term observation of one month. (ABSTRACT TRUNCATED AT 250 WORDS)
A three-year evaluation of restorations placed with a smear-layer-mediated dentin bonding agent in non-carious cervical lesions.

PURPOSE To evaluate the handling characteristics, clinical behavior, and effectiveness of Coltene ART Bond/Brilliant restorations in mixed Class V preparations in maxillary premolar and canine teeth of adult patients over a three-year period. MATERIALS AND METHODS Single-center, uncontrolled, clinical evaluation of 50 restorations in 26 patients extending over 36 months. RESULTS At three years, 34 restorations, or 68% of those originally placed, in 20 patients were available for review. One of the 34 restorations had been lost 15 months after placement. In terms of marginal integrity and staining, anatomic form, surface texture and staining, and postoperative sensitivity, over 90% of the restorations reviewed at three years were rated alpha. Following difficulties in obtaining excellent color match in relation to 14 (28%) of the restorations at the time of placement, only 44% of the restorations were rated alpha at three years. CONCLUSION It was concluded that with the possible exception of excellent color match, ART Bond/Brilliant restorations may be found to perform favorably in mixed Class V lesions in selected adult patients over a period of at least three years. The findings indicate that resin composite restorations placed with a smear-layer mediated dentin bonding agent may be found to have a favorable clinical outcome in non-carious cervical lesions.
The Design And Implementation Of A Web-Based Teaching Assistant System

When distance learning becomes more and more popular, prodding the students into high and constant motivation has been an interesting research issue these years. In this paper, we introduce a Web-based learning system which provides a dynamic interaction environment for the students to share their information with each other. The system aims to make the distance learning program a fascinating game allowing students to get their scores and ranking interactively.
A New Representation and Planner for Computer Batch Job Scheduling, Execution Monitoring, Problem Diagnosis and Correction

Modern enterprise computer environments use commercial schedulers to run and monitor computer batch jobs and processes. Currently the job schedules must be manually designed to include diagnosis and error correction behaviours for failed jobs or failures must be handled by support staff at execution time, requiring them to be on call while these jobs run. Automating these manual tasks using planning techniques requires a compact representation of contingent plans, handling and monitoring of actions which have a variable duration, actions which are triggered by external events and planning for knowledge goals. Currently these features are not provided by any existing single planner. We present a novel plan representation which drawing on existing scheduler representations provides all these features in an integrated manner. A planner implementation using this representation with a new action logic is described along with key worked examples from the domain.
Stroke patients after neurological inpatient rehabilitation: a prospective study to determine whether functional status or health-related quality of life predict living at home 2.5 years after discharge

We carried out a prospective study to determine whether stroke patients’ functional status or health-related quality of life would predict whether they lived at home 2.5 years after discharge from neurological inpatient rehabilitation. We carried out a single-center prospective cohort study. The outcome ‘home care’ versus ‘death’ or ‘institutionalization’ (nursing home admission) was evaluated 30 months after discharge. A total of 204 stroke survivors with remaining moderate to severe functional deficits at admission to neurological inpatient rehabilitation were included. Clinical data were obtained at admission to and/or discharge from inpatient rehabilitation. Functional status was determined using the Barthel Index; health-related quality of life was assessed using the SF-36 and EQ-5D. The outcome was assessed by telephone interview. Predictors of living at home were calculated using binary logistic regression analysis. In total, 30 months after discharge, 75% of the stroke survivors were still living at home. Multivariate analysis showed that patients continued to live at home significantly more frequently when they had fewer mortality-relevant comorbidities (P=0.001), a higher BMI (P=0.040), a higher increase in functional independence during inpatient rehabilitation (P=0.017), and above all, a better health-related quality of life, measured using the EQ-5D (P<0.001), at discharge. Stroke survivors’ health-related quality of life measured with the EQ-5D and the change in functional status during multimodal neurological rehabilitation appear to be the strongest clinically relevant long-term predictors of staying at home.