Miracle-dz/UniFAR-FTUs huggingface dataset:
Classification of Protein Sequences

1 The need for accurate, automated protein classification methods continues to increase as advances in biotechnology uncovers new proteins at a fast rate. G-protein coupled receptors (GPCRs) are a particularly difficult superfamily of proteins to classify due to the extreme diversity among its members; yet, they are an important subject in pharmacological research being the target of approximately 60% of current drugs (Muller, 2000). A comparison of BLAST, k-NN, HMM and SVM with alignment-based features by Karchin et al. (2002) has suggested that classifiers at the complexity of SVM are needed to attain high accuracy in GPCR subfamily classification. Here, analogous to document classification, we applied Decision Tree and Naïve Bayes classifiers with chi-square feature selection on n-gram counts to the GPCR family and subfamily classification task. Using the dataset and evaluation protocol from the previous study, we found the Naïve Bayes classifier surpassing the reported accuracy of SVM by 4.8% and 6.1% in level I and II subfamily classification with an accuracy of 93.2% and 92.4% respectively. The Decision Tree, while inferior to SVM, still outperforms HMM in both level I and II subfamily classification. Moreover, the n-grams selected by chi-square feature selection show evidence of biological importance. Thus, the document classification approach has resulted in a simpler, more accurate and interpretable classifier.
Policy-based access control for weakly consistent replication

Combining access control with weakly consistent replication presents a challenge if the resulting system is to support eventual consistency. If authorization policy can be temporarily inconsistent, any given operation may be permitted at one node and yet denied at another. This is especially troublesome when the operation in question involves a change in policy. Without a careful design, permanently divergent state can result. We describe and evaluate the design and implementation of an access control system for weakly consistent replication where peers are not uniformly trusted. Our system allows for the specification of fine-grained access control policy over a collection of replicated items. Policies are expressed using a logical assertion framework and access control decisions are logical proofs. Policy can grow to encompass new nodes through fine-grain delegation of authority. Eventual consistency of the replicated data is preserved despite the fact that access control policy can be temporarily inconsistent.
Cerebral Blood Flow in Preterm Infants during the First Week of Life

ABSTRACT. Forty‐two preterm infants of 28–33 weeks of gestation were studied once during the first week of life by 133‐Xenon clearance after intravenous injection to estimate global cerebral blood flow. Count rates detected over the chest were corrected for chest wall contribution and used as arterial input function. A neonatal blood‐brain partition coefficient of Xenon was used for the calculation of a mean flow estimator (CBF‐∞). The techique was internally validated by use of differently obtained arterial input functions. In 11 infants wihout respiratory distress, CBF‐∞ was 19.8 ml/100 g/min ±5.3 SD. In 24 infants treated with mechanical ventilation CBF‐∞ was 11.8 ml/100 g/min ±3.2 SD. In 7 infants treated with continous positive airway pressure CBF‐∞ was 21.3 ml/100 g/min ±12.0 SD. When the reduction of CBF‐∞ associated with mechanical ventilation was taken into account, the 9 infants with subependymal/intraventricular haemorrhage had increased CBF‐∞. The effects of gestational age, birthweight, mode of delivery, postnatal age, mean arterial blood pressure, PaCO2, blood haemoglobin and phenobarbitone medication were also analysed and found inconsistent. In conclusion, CBF was lower than expected and in infants requring mechanical ventilation the values were lower still.
Explaining inconsistent code

A code fragment is inconsistent if it is not part of any normally terminating execution. Examples of such inconsistencies include code that is unreachable, code that always fails due to a run-time error, and code that makes conflicting assumptions about the program state. In this paper, we consider the problem of automatically explaining inconsistent code. This problem is difficult because traditional fault localization techniques do not apply. Our solution relies on a novel algorithm that takes an infeasible code fragment as input and generates a so-called error invariant automaton. The error invariant automaton is an abstraction of the input code fragment that only mentions program statements and facts that are relevant for understanding the cause of the inconsistency. We conducted a preliminary usability study which demonstrated that error invariant automata can help programmers better understand inconsistencies in code taken from real-world programs. In particular, access to an error invariant automata tripled the speed at which programmers could diagnose the cause of a code inconsistency.
Development of Monoclonal Antibodies against HIV-1 p24 Protein and Its Application in Colloidal Gold Immunochromatographic Assay for HIV-1 Detection

Human immunodeficiency virus type 1 (HIV-1) p24 protein is the most abundant viral protein of HIV-1. This protein is secreted in blood serum at high levels during the early stages of HIV-1 infection, making it a biomarker for early diagnosis. In this study, a colloidal gold immunochromatographic assay (GICA) was established for detecting p24 protein using mouse monoclonal antibodies (mAbs). The HIV-1 p24 protein was expressed in E. coli strain BL21 and the purified protein was used to immunize mice. Stable hybridoma cell lines secreting anti-p24 monoclonal antibodies were obtained after ELISA screening and subcloning by limiting dilution. 34 different capture and labeling mAb pairs were selected by a novel antibody-capture indirect sandwich ELISA and then applied in GICA to detect p24 protein. The GICA method has a limit of detection (LOD) of 25 pg/mL and could detect p24 protein in all 10 positive samples obtained from the National Reference of HIV-1 p24 antigen. Out of 153 negative samples tested, 3 false positives results were obtained. The overall specificity of this test was 98.03%. The good sensitivity and specificity of this method make it a suitable alternative to provide a more convenient and efficient tool for early diagnosis of HIV infection.
Performance of Printed Polymer-Based RFID Antenna on Curvilinear Surface

The performance of flexible printed RFID tags affixed onto cylindrical containers is dependent on the inductive behavior of the bent antenna on the tag. Conductive polymeric coil antennas were screen printed onto flexible substrates, and the coil resistances, the inductances, and the S-parameters of the antenna coils were measured and analyzed. The RFID dies were mounted onto the antenna coils and the read ranges were characterized as a function of curvature. The results show that the coil inductance decreased slowly with increasing curvature, and the maximum read range of the tags was markedly reduced with the curvature. The decrease in the coil inductance and the maximum read range were hypothesized to vary with the projected bent coil area instead of the geometric coil area. Experimental results confirmed that the maximum read range of an RFID tag affixed on a curvilinear surface can be predicted by the classical inductive coupling model with the bent projected coil area. On the basis of the experimental and analytical results, a reading reliability factor of two is proposed as a design parameter for flexible RFID tags.
Intra-patient semi-automated segmentation of the cervix–uterus in CT-images for adaptive radiotherapy of cervical cancer

For online adaptive radiotherapy of cervical cancer, fast and accurate image segmentation is required to facilitate daily treatment adaptation. Our aim was twofold: (1) to test and compare three intra-patient automated segmentation methods for the cervix–uterus structure in CT-images and (2) to improve the segmentation accuracy by including prior knowledge on the daily bladder volume or on the daily coordinates of implanted fiducial markers. The tested methods were: shape deformation (SD) and atlas-based segmentation (ABAS) using two non-rigid registration methods: demons and a hierarchical algorithm. Tests on 102 CT-scans of 13 patients demonstrated that the segmentation accuracy significantly increased by including the bladder volume predicted with a simple 1D model based on a manually defined bladder top. Moreover, manually identified implanted fiducial markers significantly improved the accuracy of the SD method. For patients with large cervix–uterus volume regression, the use of CT-data acquired toward the end of the treatment was required to improve segmentation accuracy. Including prior knowledge, the segmentation results of SD (Dice similarity coefficient 85 ± 6%, error margin 2.2 ± 2.3 mm, average time around 1 min) and of ABAS using hierarchical non-rigid registration (Dice 82 ± 10%, error margin 3.1 ± 2.3 mm, average time around 30 s) support their use for image guided online adaptive radiotherapy of cervical cancer.
Fracture resistance of teeth restored with different post systems using new-generation adhesives.

AIM The aim of this study was to investigate the fracture strength of three post systems cemented with a dual cure composite resin luting cement by using different adhesive systems. METHODS AND MATERIALS In this study 63 extracted anterior teeth with single roots were endodontically prepared and filled. Teeth were randomly assigned to one of three post systems placed into the prepared canals: Group I - titanium posts (n=21) (Filpost); Group II - glass fiber posts (n=21) (Mirafit White); and Group III zirconia posts (n=21) (CosmoPost). Each group was again randomly divided into three subgroups according to the bonding materials used [Single Bond (n=7), Clearfil SE Bond (n=7), and Prompt L Pop (n=7)]. A dual cured resin cement (Rely X ARC) was used for bonding the posts into the root canals. Standard cores were made by a composite resin (Clearfil Photocore) using core build-ups. The samples were tested in the compression test machine for 1 mm/min and fracture resistance of the teeth were recorded. The data was analyzed by using two-way analysis of variance (ANOVA) and Duncan's New Multiple Range Tests. A significance level of p<. 05 was used for all comparisons. RESULTS There was a significant difference in fracture resistance between the post systems (p<0.05) and the interaction of adhesive resins and post systems (p<0.05). Mirafit White was more resistant to fracture than other groups; Filpost showed the least resistance to fracture. CosmoPost post system bonded with Single Bond recorded the lowest fracture resistance (p<0.05). CONCLUSION Endodontically treated anterior teeth restored with glass fiber posts exhibited higher failure loads than teeth restored with zirconia and titanium posts. Self-etching adhesives are better alternatives to etch-and-rinse adhesive systems for luting post systems. CLINICAL SIGNIFICANCE Under the condition of this study, glass fiber posts are preferable to restore endodontically treated anterior teeth.
Ethical Behavior and Information Systems Codes: The Effects of Code Communication, Awareness, Understanding, and Enforcement

The ethical behavior of information systems personnel remains a key IS management problem in need of attention. Codes of ethics have become important mechanisms for influencing ethical behavior, yet their efficacy has not been proven. The communication and enforcement of codes within an organization are thought to be necessary for ensuring a code’s success in influencing employee behavior. This study examined the effect of code communication on ethical behavior through its effects on code awareness and understanding. Using data collected from 186 IS professionals, results revealed that code understanding by IS professionals was a significant determinant of their ethical behavior. Understanding was significantly influenced by communication and awareness. Enforcement was also found have a significant influence on behavior. Results have important implications for organizations using or intending to use codes of ethics to influence the behavior of IS personnel.
Arterial imaging outcomes and cardiovascular risk factors in recently menopausal women: a randomized trial.

BACKGROUND Whether menopausal hormone therapy (MHT) protects against cardiovascular disease (CVD) remains unclear. OBJECTIVE To assess atherosclerosis progression and CVD risk factors after MHT initiated in early menopause. DESIGN Randomized, controlled trial. (ClinicalTrials.gov: NCT00154180). SETTING Nine U.S. academic centers. PARTICIPANTS Healthy menopausal women aged 42 to 58 years between 6 and 36 months from last menses without prior CVD events who had a coronary artery calcium (CAC) score less than 50 Agatston units and had not received estrogen or lipid-lowering therapy for at least 90 days. INTERVENTION Oral conjugated equine estrogens (o-CEE), 0.45 mg/d, or transdermal 17β-estradiol (t-E2), 50 mcg/d, each with 200 mg of oral progesterone for 12 days per month, or placebo for 48 months. MEASUREMENTS Primary end point was annual change in carotid artery intima-media thickness (CIMT). Secondary end points included changes in markers of CVD risk. RESULTS Of 727 randomly assigned women, 89.3% had at least 1 follow-up CIMT and 79.8% had CIMT at 48 months. Mean CIMT increases of 0.007 mm/y were similar across groups. The percentages of participants in whom CAC score increased did not differ significantly across groups. No changes in blood pressure were observed with o-CEE or t-E2. Low- and high-density lipoprotein cholesterol levels improved and levels of C-reactive protein and sex hormone-binding globulin but not interleukin-6 increased with o-CEE. Insulin resistance decreased with t-E2. Serious adverse events did not differ by treatment. LIMITATION Power to compare clinical events was insufficient. CONCLUSION Four years of early MHT did not affect progression of atherosclerosis despite improving some markers of CVD risk. PRIMARY FUNDING SOURCE Aurora Foundation.
Qualitative and Quantitative Issues of Lymph Nodes as Prognostic Factor in Colon Cancer

For patients undergoing curative resections for colon cancer, the nodal status represents the strongest prognostic factor, yet at the same time the most disputed issue as well. Consequently, the qualitative and quantitative aspects of lymph node evaluation are thus being scrutinized beyond the blunt distinction between ‘node positive' (pN+) and ‘node negative' (pN0) disease. Controversy ranges from a minimal or ‘least-unit' strategy as exemplified by the ‘sentinel node' to a maximally invasive or ‘all inclusive' approach by extensive surgery. Ranging between these two extremes of node sampling strategies are factors of quantitative and qualitative value, which may be subject to modification. Qualitative issues may include aspects of lymph node harvest reflected by surgeon, pathologist and even hospital performance, which all may be subject to modification. However, patient's age, gender and genotype may be non-modifiable, yet influence node sample. Quantitative issues may reflect the balance between absolute numbers and models investigating the relationships of positive to negative nodes (lymph node ratio; log odds of positive lymph nodes). This review provides an updated overview of the current controversies and a state-of-the-art perspective on the qualitative and quantitative aspects of using lymph nodes as a prognostic marker in colon cancer.
‘Who's the Man and Who's the Woman?’ Same-sex Couples in Queensland ‘Doing’ Gender and Domestic Labour

This article reports an exploratory study that investigated domestic labour in same-sex households, to the best of my knowledge the first in Australia to do so. In-depth semi-structured interviews with 12 couples in Southeast Queensland reveal that these lesbians and gay men do not take on heteronormative gender roles when doing domestic labour, and that their practices reflect a variety of styles of sharing, with no pattern emerging as clearly dominant. Theoretical frameworks conceptualising gender as performative, and queer theory's figuring of identity as a constellation of multiple and unstable positions, suggest how the performance of gender may vary in different domains of social and cultural space, and in relation to other actors in those spaces. I have conceptualised this process by means of an analogy with the modulation of sound such that each person adjusts the balance between treble (conventionally feminine behaviours, attitudes and attributes) and bass (conventionally masculine behaviours and attributes). Rather than being ‘the man’ or ‘the woman’, or even displaying a single form of gay masculinity or lesbian femininity, lesbians and gay men can be seen to perform varying degrees of masculinity and femininity in the private space of the home, and in relation to their intimate partners, by the way they engage with domestic labour. Finally, I reflect on how the socio-geographical specificities of being situated in Southeast Queensland may have impacted on this research.
Estimating local Beckmann roughness for complex BSDFs

Many light transport related techniques require an analysis of the blur width of light scattering at a path vertex, for instance a Beckmann roughness. Such use cases are for instance analysis of expected variance (and potential biased countermeasures in production rendering), radiance caching or directionally dependent virtual point light sources, or determination of step sizes in the path space Metropolis light transport framework: recent advanced mutation strategies for Metropolis Light Transport [Veach 1997], such as Manifold Exploration [Jakob 2013] and Half Vector Space Light Transport [Kaplanyan et al. 2014] employ local curvature of the BSDFs (such as an average Beckmann roughness) at all interactions along the path in order to determine an optimal mutation step size. A single average Beckmann roughness, however, can be a bad fit for complex measured materials (such as [Matusik et al. 2003]) and, moreover, such curvature is completely undefined for layered materials as it depends on the active scattering layer. We propose a robust estimation of local curvature for BSDFs of any complexity by using local Beckmann approximations, taking into account additional factors such as both incident and outgoing direction.
Splenectomy for Relapsing Thrombotic Thrombocytopenic Purpura

TO THE EDITOR: My colleagues and I were the first to point out that as more patients survived their initial episode of thrombotic thrombocytopenic purpura, relapses were not rare but rather might afflict more than one third of patients [1]. Our experience impels me to question on two counts the value of splenectomy purported by Crowther and colleagues [2]. First, we have seen several patients with a pattern of relapses over a few years who spontaneously cease experiencing relapses. Thus, any intervention (or nonintervention) in such patients, who were preselected for frequent relapses, would seem to result in a lower rate of subsequent relapses. Pertinent examples are a middle-aged woman and a 60-year-old man who each had four episodes of thrombotic thrombocytopenic purpura over 6 years. Neither patient had any further episodes over several years. If splenectomy had been done for the first patient, it would seem to have been highly effective in preventing relapses. The second patient actually underwent splenectomy during the first episode! Second, I must reemphasize the generally more benign course and outcome of relapsed thrombotic thrombocytopenic purpura [1]. We have treated more than 15 patients with relapse through more than 30 relapse episodes. In contrast to the 20% mortality rate we observed with first-episode thrombotic thrombocytopenic purpura, in 20 years we have witnessed no deaths or any long-lasting residue resulting from relapse. In fact, episodes of relapse almost always respond to treatment more quickly than do first episodes. One explanation is that patients having relapse are attuned to symptoms of recurrence and thus seek medical attention earlier. Further, by virtue of surviving their first episode, these patients have demonstrated responsiveness to therapy. Data supporting the efficacy of splenectomy in preventing relapses are unconvincing. The procedure entails its own morbidity and risks, and I cannot recommend it for relapses of thrombotic thrombocytopenic purpura.
Real-Time Classification of Patients with Balance Disorders vs. Normal Subjects Using a Low-Cost Small Wireless Wearable Gait Sensor

Gait analysis using wearable wireless sensors can be an economical, convenient and effective way to provide diagnostic and clinical information for various health-related issues. In this work, our custom designed low-cost wireless gait analysis sensor that contains a basic inertial measurement unit (IMU) was used to collect the gait data for four patients diagnosed with balance disorders and additionally three normal subjects, each performing the Dynamic Gait Index (DGI) tests while wearing the custom wireless gait analysis sensor (WGAS). The small WGAS includes a tri-axial accelerometer integrated circuit (IC), two gyroscopes ICs and a Texas Instruments (TI) MSP430 microcontroller and is worn by each subject at the T4 position during the DGI tests. The raw gait data are wirelessly transmitted from the WGAS to a near-by PC for real-time gait data collection and analysis. In order to perform successful classification of patients vs. normal subjects, we used several different classification algorithms, such as the back propagation artificial neural network (BP-ANN), support vector machine (SVM), k-nearest neighbors (KNN) and binary decision trees (BDT), based on features extracted from the raw gait data of the gyroscopes and accelerometers. When the range was used as the input feature, the overall classification accuracy obtained is 100% with BP-ANN, 98% with SVM, 96% with KNN and 94% using BDT. Similar high classification accuracy results were also achieved when the standard deviation or other values were used as input features to these classifiers. These results show that gait data collected from our very low-cost wearable wireless gait sensor can effectively differentiate patients with balance disorders from normal subjects in real time using various classifiers, the success of which may eventually lead to accurate and objective diagnosis of abnormal human gaits and their underlying etiologies in the future, as more patient data are being collected.
The Economic and Social Context of Southern San Rock Art [and Comments and Reply]

This paper suggests a new theoretical framework for understanding southern San rock art. The traditional explanations have been either innatist or functionalist. To escape the tautology of the former and the restrictions of the latter it is suggested that the articulation between the art and the social relations of production be sought. This articulation was expressed in the activities of medicine men, whose symbolic work acted upon the reproduction of the natural order by making rain and controlling animals and then upon the social relations necessary for efficient production and distribution by reducing tensions within the camp. By reports of supposed out-of-body travel the medicine men also reflected the networks of links between camps which facilitated the reproduction of the social formation over extended periods that might include times of extreme strain on local resources. At least some of the medicine men were also artists and painted symbols of trance performance as well as representations of their hallucinatory experiences. The art thus contributed to a pooling of religious experience and imparted a special reality to the cognitive system on which the practice of symbolic work was based.