Miracle-dz/UniFAR-FTUs huggingface dataset:
Image quality improvements of electronic portal imaging devices by multi-level gain calibration and temperature correction

Amorphous silicon (aSi:H) flat panel detectors are prevalent in radiotherapy for megavoltage imaging tasks. Any clinical and dosimetrical application requires a well-defined dose response of the system to achieve meaningful results. Due to radiation damages, panels deteriorate and the linearity of pixel response to dose as well as the stability with regard to changing operating temperatures get worse with time. Using a single level gain correction can lead to an error of about 23% when irradiating a flood field image with 100 MU min−1 on an old detector. A multi-level gain (MLG) correction is introduced, emending the nonlinearities and subpanel-related artifacts caused by insufficient radiation hardness of amplifiers in the read-out electronics. With rising temperature, offset values typically increase (up to 300 gray values) while the response at higher dose values per frame remain constant for a majority of pixels. To account for temperature-related image artifacts, two additional temperature correction methods have been developed. MLG in combination with temperature corrections can re-establish the aSi:H image quality to the performance required by reliable medical verification tools. Furthermore, the life span and recalibration intervals of these costly devices can be prolonged decisively.
Affinity maturation of antibodies assisted by in silico modeling

Rational engineering methods can be applied with reasonable success to optimize physicochemical characteristics of proteins, in particular, antibodies. Here, we describe a combined CDR3 walking randomization and rational design-based approach to enhance the affinity of the human anti-gastrin TA4 scFv. The application of this methodology to TA4 scFv, displaying only a weak overall affinity for gastrin17 (KD = 6 μM), resulted in a set of nine affinity-matured scFv variants with near-nanomolar affinity (KD = 13.2 nM for scFv TA4.112). First, CDR-H3 and CDR-L3 randomization resulted in three scFvs with an overall affinity improvement of 15- to 35-fold over the parental. Then, the modeling of two scFv constructs selected from the previous step (TA4.11 and TA4.13) was followed by a combination of manual and molecular dynamics-based docking of gastrin17 into the respective binding sites, analysis of apparent packing defects, and selection of residues for mutagenesis through phage display. Nine scFv mutants were obtained from the second maturation step. A final 454-fold improvement in affinity compared with TA4 was obtained. These scFvs showed an enhanced potency to inhibit gastrin-induced proliferation in Colo 320 WT and BxPc3 tumoral cells. In conclusion, we propose a structure-based rational method to accelerate the development of affinity-matured antibody constructs with enhanced potential for therapeutic use.
Kaempferol: A new immunosuppressant of calcineurin

Calcineurin (CN), the Ca2+/calmodulin (CaM)‐dependant protein phosphatase, is the target for immunosuppressive drugs cyclosporine A (CsA) and FK506. These immunosuppressants can inhibit CN activity after binding with respective immunophilins. Based on the model of screening by using p‐nitrophenyl phosphate as a substrate for preliminary screening and 32P‐labeled 19‐residue phosphopeptide as a specific substrate for final determination, we found Kaempferol, a natural flavonol, could inhibit CN activity in purified enzyme and Jurkat T‐cells. Unlike CsA and FK506, CN inhibition by kaempferol is independent of matchmaker protein and the inhibitory manner is noncompetitive. Through investigation of inhibitions for CNA and a series of its truncated mutants, we suggested that Kaempferol could directly act on the catalytic domain. Data also indicated that the CN inhibition by kaempferol could be enhanced when the enzyme was activated in the presence of CaM and CNB. CNB is necessary for mediating inhibition of enzyme by kaempferol. The result of RT‐PCR also indicated that kaempferol had an inhibitory activity against IL‐2 gene expression in activated Jurkat cells. All data suggested that kaempferol could be a new immunosuppressant of CN. © 2008 IUBMB IUBMB Life, 60(8): 549–554, 2008
Diffuse reflectance near infrared spectroscopy can distinguish normal from enzymatically digested cartilage

A non-destructive, diffuse reflectance near infrared spectroscopy (DR-NIRS) approach is considered as a potential tool for determining the component-level structural properties of articular cartilage. To this end, DR-NIRS was applied in vitro to detect structural changes, using principal component analysis as the statistical basis for characterization. The results show that this technique, particularly with first-derivative pretreatment, can distinguish normal, intact cartilage from enzymatically digested cartilage. Further, this paper establishes that the use of DR-NIRS enables the probing of the full depth of the uncalcified cartilage matrix, potentially allowing the assessment of degenerative changes in joint tissue, independent of the site of initiation of the osteoarthritic process.
Ieee Transactions on Software Engineering Carisma: Context-aware Reflective Middleware System for Mobile Applications

— Mobile devices, such as mobile phones and personal digital assistants, have gained widespread popularity. These devices will increasingly be networked, thus enabling the construction of distributed applications that have to adapt to changes in context, such as variations in network bandwidth, battery power, connectivity, reachability of services and hosts, and so on. In this paper we describe CARISMA, a mobile computing middleware which exploits the principle of reflection to enhance the construction of adaptive and context-aware mobile applications. The mid-dleware provides software engineers with primitives to describe how context changes should be handled using policies. These policies may conflict. We classify the different types of conflicts that may arise in mobile computing and argue that conflicts cannot be resolved statically at the time applications are designed, but, rather, need to be resolved at execution time. We demonstrate a method by which policy conflicts can be handled; this method uses a micro-economic approach that relies on a particular type of sealed-bid auction. We describe how this method is implemented in the CARISMA middleware architecture, and sketch a distributed context-aware application for mobile devices to illustrate how the method works in practise. We show, by way of a systematic performance evaluation, that conflict resolution does not imply undue overheads, before comparing our research to related work and concluding the paper.
Long time persistence of residual 53BP1/γ-H2AX foci in human lymphocytes in relationship to apoptosis, chromatin condensation and biological dosimetry

Purpose: Novel assay for radiosensitivity is based on measurements of residual DNA repair foci produced by several proteins including phosphorylated H2AX (γ-H2AX), recombinase Rad51 (Rad51) and tumour suppressor p53 binding protein 1 (53BP1), which co-localise with radiation-induced DNA double-strand breaks (DSB). Here, we studied dose-response for residual 53BP1, Rad51, and γ-H2AX foci in relationship to apoptosis and chromatin condensation in human G0-lymphocytes. Materials and methods: Residual foci, apoptosis and condensation of chromatin were studied following irradiation with γ-rays at doses of 0.5–10 Gy. Results: No clear dose response for residual Rad51 was seen. Residual 53BP1/γ-H2AX foci remained in human lymphocytes up to four weeks after irradiation. No foci formed during radiation-induced apoptosis. We provide evidence that irreversible apoptotic condensation of chromatin is responsible for arrest of residual foci and preventing de novo focus formation. Similar linear dose dependences up to 2 Gy were observed for the 53BP1/γ-H2AX foci at all studied time points. At higher doses, saturation and decline were caused by preferential elimination of apoptotic lymphocytes with residual foci. While primary 53BP1 and γ-H2AX foci almost completely co-localised, co-localisation of residual foci did not exceed 17%, indicating that 53BP1 and γ-H2AX proteins may remain for different times at the locations of DSB repair. Conclusions: Prolonged persistence of residual 53BP1/γ-H2AX foci may be used for biological dosimetry within the dose range up to 2 Gy. While foci are not formed during radiation-induced apoptosis in human lymphocytes, elimination of apoptotic cells with residual foci may affect the dose response.
The Effect of Ambient Occlusion Shading on Perception of Sign Language Animations

The goal of the study reported in the paper was to determine whether Ambient Occlusion Shading (AOS) has a perception of American Sign Language (ASL) finger spelling animations. Seventy-one (71) subjects participated in the study; all subjects were fluent in ASL. The participants were asked to watch forty (40) sign language animation clips representing twenty (20) finger spelled words. Twenty (20) clips did not show ambient occlusion, whereas the other twenty (20) were rendered using ambient occlusion shading. After viewing each animation, subjects were asked to type the word being finger-spelled and rate its legibility. Findings show that the presence of AOS had a perception of the signed words. Subjects were able to recognize the animated words rendered with AOS with higher level of accuracy, and the legibility ratings of the animations showing AOS were consistently higher across subjects.
Mucormycosis in Children: Review and Recommendations for Management

Mucormycosis represents the third most common invasive fungal infection in children, and recent studies have suggested a rising incidence. Its case fatality rate is high, especially for neonates. Clinical presentation is influenced by underlying risk factors; associations with immunosuppression, neutropenia, diabetes, and prematurity have been described. It has been implicated in several hospital outbreaks. Diagnosis requires a high index of suspicion and evaluation with histopathology, culture, and, increasingly, molecular identification. Surgical debridement and antifungal therapies are the cornerstone for combatting invasive mucormycosis. However, the severity and relative rarity of this disease make comparative clinical trials for evaluating antifungal therapies in children difficult to conduct. Hence, therapeutic decisions are derived mainly from retrospective case series, in vitro data, and animal models. In this review, we summarize the literature on the epidemiology and diagnosis of this invasive fungal infection and provide suggestions on the management of mucormycosis in children.
Brief Memory and Executive Test: evaluation of a new screening test for cognitive impairment due to small vessel disease.

BACKGROUND cerebral small vessel disease (SVD) is the most common cause of vascular cognitive impairment (VCI). Despite this, there is a paucity of rapid simple screening tools to identify cognitive impairment in SVD and differentiate it from other common dementia types. OBJECTIVE to validate a new screening test for cognitive impairment in SVD, the Brief Memory and Executive Test (BMET) battery, and examine its ability to detect SVD and differentiate it from Alzheimer's disease (AD). SUBJECTS 45 patients with SVD, 27 patients with AD and 80 normal controls. METHODS the BMET includes brief tests of executive functioning and processing speed, with comparative tests of memory and orientation. Group discrimination was calculated using discriminant function analysis. RESULTS the BMET took an average of 10 min to administer. It showed high sensitivity (91%) and specificity (85%) in differentiating SVD patients with cognitive impairment from AD patients. As a comparison the mini-mental state examination had lower sensitivity (63%) and specificity (62%). CONCLUSIONS the BMET is a simple and quick to administer clinical tool for the detection of VCI in SVD and its differentiation from AD impairment. Further multicentre studies are required to evaluate and compare it with other existing screening tests.
Tailoring of Nutritional Support for Older Adults in the Community

Abstract A study in Ontario, Canada of 137 elderly home delivered meal recipients, 90 women and 47 men, confirmed the expected nutritional risk factors of living situation, functionality, morbidity and medication use. They were more pronounced among women than men. Seven-day food records showed energy intakes below the average for healthy Canadians of a similar age and gender. The probability of nutritional risk was highest for calcium, magnesium, zinc and folate with some gender differences, except for folate. While home delivered meals, if fully utilized, can provide considerable nutrition support, energy/nutrient inadequacies may persist among recipients unable to complement the meal appropriately. These older adults may require diet counseling and additional support including targeted nutritional supplementation.
GROWTH AND PHYSIOLOGICAL RESPONSES OF TOMATO (LYCOPERSICON ESCULENTUM MILL.) TO SIMULATED ACID RAIN

This investigation was undertaken to ascertain the effect of simulated acid rain (SAR) on growth, yield and physiological parameters of tomato. SAR exposure (pH 3.0 and 4.0) caused white-to-tan spots on the abaxial and adaxial surface of tomato leaves. SAR exposure at pH 3.0 and 4.0 significantly suppressed pigment synthesis, shoot and root dry weights and yield of tomato. The effects were more pronounced at lower pH 3.0. Reducing and nonreducing sugars were significantly diminished to varying degree by SAR solutions of pH 3.0 and 4.0 and the effect being more accentuated at pH 3.0. Nonreducing sugars declined to a greater extent than did the reducing sugars and this effect was more pronounced in SAR-treatment of pH 3.0. SAR-exposure of pH 3.0 and 4.0 resulted in accumulation of soluble phenols as an induced mechanism against SAR stress. The results are discussed in the light of physiological responses of plants to abiotic stresses.
Relationship of Delayed Enhancement by Magnetic Resonance to Myocardial Perfusion by Positron Emission Tomography in Hypertrophic Cardiomyopathy

Background— Presence of delayed enhancement (DE) on cardiac magnetic resonance (CMR) is associated with worse clinical outcomes in hypertrophic cardiomyopathy. We investigated the relationship between DE on CMR and myocardial ischemia in hypertrophic cardiomyopathy. Methods and Results— Hypertrophic cardiomyopathy patients (n=47) underwent CMR for assessment of DE and vasodilator stress ammonia positron emission tomography to quantify myocardial blood flow and coronary flow reserve. The summed difference score for regional myocardial perfusion was also assessed. Patients in the DE group (n=35) had greater left ventricular wall thickness (2.09±0.44 versus 1.78±0.34 cm; P=0.03). Stress myocardial blood flow (2.25±0.46 versus 1.78±0.43 mL/min per gram; P=0.01) and coronary flow reserve (2.78±0.32 versus 2.01±0.52; P<0.001) were significantly lower in DE-positive patients. Summed difference score (median, 5 versus 0; P<0.0001) was significantly higher in patients with DE. A coronary flow reserve <2.00 was seen in 18 patients (51%) with DE but in none of the DE-negative patients (P<0.0001). CMR and positron emission tomography showed visually concordant DE and regional myocardial perfusion abnormalities in 31 patients and absence of DE and perfusion defects in 9 patients. Four DE-positive patients demonstrated normal regional myocardial perfusion, and 3 DE-negative patients had (apical) regional myocardial perfusion abnormalities. Conclusions— We found a close relationship between DE by CMR and microvascular function in most of the patients studied. However, a small proportion of patients had DE in the absence of perfusion abnormalities, suggesting that microvascular dysfunction and ischemia are not the sole causes of DE in hypertrophic cardiomyopathy patients.
Correlation between intrahepatic hepatitis B virus cccDNA levels and other activity markers in patients with HBeAg-negative chronic hepatitis B infection

Objective The aim of this study was to demonstrate the relation between intrahepatic (IH) hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) levels and the other HBV replicative intermediates and hepatocyte expression of HBV antigens. Patients and methods Patients with hepatitis B surface antigen (HBsAg) positivity, hepatitis B early antigen negativity, serum HBV DNA levels 104 copies/ml or more, and constantly or intermittently increased alanine aminotransferase levels were included. Results Fifty-nine patients were included. There was a good correlation between the levels of IH HBV cccDNA and serum HBV DNA (P<0.001). Serum HBsAg levels were weakly correlated with IH HBV cccDNA levels and moderately correlated with serum HBV DNA (r=0.322, P=0.017; r=0.489, P=0.001, respectively). There were no significant correlation between serum HBsAg level and histologic activity index groups (P=0.691), but stage 0, 1, and greater than 2 fibrosis groups were positively correlated with serum HBsAg levels (P=0.019). IH cccDNA and serum HBV DNA were significantly different in hepatitis B core antigen staining groups (P=0.008 and <0.001, respectively) but there was no significant correlation between HBsAg staining groups and HBV replication markers. There was a weak correlation between serum HBsAg levels and IH HBsAg and hepatitis B core antigen levels (r=0.333, P=0.012; r=0.366, P=0.006, respectively). In multivariate analysis, alanine aminotransferase, age, fibrosis stage, and serum HBsAg quantitation were the most important factors predicting IH HBV cccDNA level. Conclusion Histopathologic damage, serum HBV DNA levels, and IH HBV replication markers have a more complex and dynamic process. However, both serum and IH HBV replication markers provide important knowledge about the activity of the disease.
Wireless network coding with physical-layer security

Today, relaying at routers is secure because we encrypt the confidential messages. We allow routers to have full access to contents of received packets and rest assured that the confidential contents cannot be decrypted, with the underlying assumption that adversaries in the network including the routers are computationally bounded. Nonetheless, as technology develops, much higher computational capability may be achieved. The network is not secure any more when routers or eavesdroppers at routers have infinite computational power. Indeed, there are non-computational security based schemes against external eavesdroppers, which make the eavesdroppers fail in receiving correct data, but unfortunately they cannot be used for security at routers, because we need to achieve not only security but also error-free data forwarding at routers, which is much more challenging. This paper proposes secure wireless network coding to achieve physical-layer security at routers by taking advantages of interference and noise, which are usually considered harmful. We exploit the interference to design network coding protocols to achieve not only security, but also error-free data forwarding at a high rate. Noise, which leads to the randomness of wireless channels, also contributes to providing security in our scheme. With the help of both interference and noise, wireless network coding can be a crucial approach to achieve security at routers, which traditional store-and-forward routing cannot achieve.
Mining Road Traffic Accident Data to Improve Safety: Role of Road-Related Factors on Accident Severity in Ethiopia

Road traffic accidents (RTAs) are a major public health concern, resulting in an estimated 1.2 million deaths and 50 million injuries worldwide each year. In the developing world, RTAs are among the leading cause of death and injury; Ethiopia in particular experiences the highest rate of such accidents. Thus, methods to reduce accident severity are of great interest to traffic agencies and the public at large. In this work, we applied data mining technologies to link recorded road characteristics to accident severity in Ethiopia, and developed a set of rules that could be used by the Ethiopian Traffic Agency to improve safety.
Active vision for dexterous grasping of novel objects

How should a robot direct active vision so as to ensure reliable grasping? We answer this question for the case of dexterous grasping of unfamiliar objects. By dexterous grasping we simply mean grasping by any hand with more than two fingers, such that the robot has some choice about where to place each finger. Such grasps typically fail in one of two ways, either unmodeled objects in the scene cause collisions or object reconstruction is insufficient to ensure that the grasp points provide a stable force closure. These problems can be solved more easily if active sensing is guided by the anticipated actions. Our approach has three stages. First, we take a single view and generate candidate grasps from the resulting partial object reconstruction. Second, we drive the active vision approach to maximise surface reconstruction quality around the planned contact points. During this phase, the anticipated grasp is continually refined. Third, we direct gaze to improve the safety of the planned reach to grasp trajectory. We show, on a dexterous manipulator with a camera on the wrist, that our approach (80.4% success rate) outperforms a randomised algorithm (64.3% success rate).
Concordant Genetic Estimators of Migration Reveal Anthropogenically Enhanced Source-Sink Population Structure in the River Sculpin, Cottus gobio

River systems are vulnerable to natural and anthropogenic habitat fragmentation and will often harbor populations deviating markedly from simplified theoretical models. We investigated fine-scale population structure in the sedentary river fish Cottus gobio using microsatellites and compared migration estimates from three FST estimators, a coalescent maximum-likelihood method and Bayesian recent migration analyses. Source-sink structure was evident via asymmetry in migration and genetic diversity with smaller upstream locations emigration biased and larger downstream subpopulations immigration biased. Patterns of isolation by distance suggested that the system was largely, but not entirely, in migration-drift equilibrium, with headwater populations harboring a signal of past colonizations and in some cases also recent population bottlenecks. Up- vs. downstream asymmetry in population structure was partly attributable to the effects of flow direction, but was enhanced by weirs prohibiting compensatory upstream migration. Estimators of migration showed strong correspondence, at least in relative terms, especially if pairwise FST was used as an indirect index of relative gene flow rather than being translated to Nm. Since true parameter values are unknown in natural systems, comparisons among estimators are important, both to determine confidence in estimates of migration and to validate the performance of different methods.