Miracle-dz/UniFAR-FTUs huggingface dataset:
Work in progress: A machine learning approach for assessment and prediction of teamwork effectiveness in software engineering education

One of the challenges in effective software engineering (SE) education is the lack of objective assessment methods of how well student teams learn the critically needed teamwork practices, defined as the ability: (i) to learn and effectively apply SE processes in a teamwork setting, and (ii) to work as a team to develop satisfactory software (SW) products. In addition, there are no effective methods for predicting learning effectiveness in order to enable early intervention in the classroom. Most of the current approaches to assess achievement of SE teamwork skills rely solely on qualitative and subjective data taken as surveys at the end of the class and analyzed only with very rudimentary data analysis. In this paper we present a novel approach to address the assessment and prediction of student learning of teamwork effectiveness in software engineering education based on: a) extracting only objective and quantitative student team activity data during their team class project; b) pairing these data with related independent observations and grading of student team effectiveness in SE process and SE product components in order to create “training database” and c) applying a machine learning (ML) approach, namely random forest classification (RF), to the above training database in order to create ML models, ranked factors and rules that can both explain (e.g. assess) as well as provide prediction of the student teamwork effectiveness. These student team activity data are being collected in joint and already established (since 2006) SE classes at San Francisco State University (SFSU), Florida Atlantic University (FAU) and Fulda University, Germany (Fulda), from approximately 80 students each year, working in about 15 teams, both local and global (with students from multiple schools).
Four-dimensional Rotations in Coherent Optical Communications

To model electromagnetic wave propagation for coherent communications without polarization dependent losses, the unitary 2 ×2 Jones transfer matrix formalism is typically used. In this study, we propose an alternative formalism to describe such transformations based on rotations in four-dimensional (4d) Euclidean space. This formalism is usually more attractive from a communication theoretical perspective, since decisions and symbol errors can be related to geometric concepts such as Euclidean distances between points and decision boundaries. Since 4d rotations is a richer description than the conventional Jones calculus, having six rather than four degrees of freedom (DOF), we propose an extension of the Jones calculus to handle all six DOF. In addition, we show that the two extra DOF in the 4d description represents transformations that are nonphysical for propagating photons, since they does not obey the fundamental quantum mechanical boson commutation relations. Finally, we exemplify on how the nonphysical rotations can change the polarization-phase degeneracy of well-known constellations such as single-polarization QPSK, polarization-multiplexed (PM-)QPSK and polarization-switched (PS-) QPSK. For example, we show how PM-QPSK, which is well known to consist of four polarization states each having four-fold phase degeneracy, can be represented as eight states of polarizations, each with binary phase degeneracy.
OhrR, a transcription repressor that senses and responds to changes in organic peroxide levels in Xanthomonas campestris pv. phaseoli

We report the physiological role of OhrR as an organic peroxide sensor and transcription repressor in Xanthomonas campestris pv. phaseoli. In vivo exposure of X. campestris pv. phaseoli to either tert‐butyl or cumene hydroperoxides efficiently neutralized OhrR repression of expression from the OhrR‐regulated P1 promoter. H2O2 was a weak and non‐physiological inducer of the system while other oxidants and metabolites of organic peroxide metabolism did not induce the expression from the P1. Northern blotting results indicated a correlation between concentrations of tert‐butyl hydroperoxide used in the treatment and the induction of ohr (an OhrR‐regulated gene) expression. In addition, the levels of ohr mRNA in cultures induced by various concentrations of tert‐butyl hydroperoxide were reduced in cells with high levels of an organic peroxide metabolising enzyme (AhpC‐AhpF) but not in cells with high catalase levels suggesting that organic peroxide interacts with OhrR. DNA band shift experiments using purified OhrR and the P1 promoter fragment showed that organic peroxide treatment prevented binding of the protein to the P1 promoter by oxidation of OhrR, as the inhibition of binding to the P1 promoter was reversed by addition of a reducing agent, DTT. The highly conserved cysteine residue C22 of OhrR is required for organic peroxide inducible gene expression. A mutant protein, OhrRC22S can repress the P1 promoter activity but is insensitive to organic peroxide treatment. Thus, OhrR is the first transcription repressor characterized that appeared to evolve to physiologically sense organic peroxides.
Adenovirus infection in paediatric allogeneic stem cell transplantation recipients is a major independent factor for significantly increasing the risk of treatment related mortality

Adenovirus infection is a significant complication in paediatric AlloSCT recipients with a mortality rate for disseminated adenovirus that may exceed 80%. We sought to determine the incidence, risk factors, and associated outcomes of adenovirus infection in 123 consecutive paediatric AlloSCT recipients. Adenovirus was diagnosed by antigen detection or viral culture, and was defined by isolation of virus with presence of correlating clinical symptoms. The probability of developing adenovirus infection was 12·3% (CI95 6·0–18·6). There were no statistically significant differences in probability of adenovirus infection in univariate analysis of risk factors including donor source, use of ATG/Alemtuzumab, ≥Grade II GVHD, among others (age, diagnosis, conditioning regimen). Probability of overall survival for patients that experienced adenovirus infection was 15·4% vs. 50% for those without adenovirus (P = 0·0286). In multivariate analysis, the most important risk factor for an increased risk of death was adenovirus infection [HR 3·15 (CI95 1·6–6·18) P = 0·0009]. In this series of paediatric AlloSCT recipients, the development of adenovirus infection was the leading multivariate predictor of treatment‐related mortality. Enhanced surveillance with adenovirus PCR and identification of the risk factors associated with poor outcomes from adenovirus infection may identify patients that may benefit from pre‐emptive therapeutic interventions including adenovirus‐specific cellular immunotherapies.
Novel Testbed implementation for resource allocation in cognitive radio for green communication

In this paper, the Testbed implementation of cognitive radio for green communication using Universal Software Radio peripheral (USRP) is investigated. The main objective of this Testbed is to create a realistic and accurate platform to implement and validate innovative and novel schemes for spectrum sensing and resource allocations for cognitive radio networks to achieve Green communication. For spectrum sensing energy detection method is used. Resource allocation to maximize energy efficiency is carried out using single user and multiuser system where subcarrier and power allocation is done sequentially to reduce complexity of the system. Testbed consists of two host computers connected to two USRP (2922) devices operating in the range 400MHz to 4.4GHz. Experimental results confirm that for single user system maximum energy efficiency achieved is 267 bits/Joule, In a multiuser system, maximum energy efficiency achieved is 145 bits/Joule.
The Spectrum of Brittle Diabetes

A group of 42 severely brittle insulin dependent diabetic patients were studied, and compared with a similar number of ‘stable’ diabetic patients. Brittle diabetics were predominantly female (86% v 45%, P<0.01), were of younger age (mean±SD 27.9±12.8 years v 40.1±13.6 years, P<0.001), and of shorter duration of diabetes (13.7±9.4 years v 19.6±11.2 years, P<0.01). Control as measured by glycosylated haemoglobin (HbA1) was poorer (13.7±3.1% v 10.1±1.5%, P <0.001), and daily insulin dose higher (98±81 u v 47±14 u, P <0.001). There was no difference in diabetic complication rates, but psychosocial disturbances (74% v 17%) and factitious instability (40% v 2%) were highly significantly more common amongst brittle patients. Examination of patterns of admission revealed most brittle diabetics to have hyperglycaemic problems (70%), mainly due to recurrent ketoacidosis (52%). Recurrent hypoglycaemia accounted for 12% of the group, and only 5/42 patients (12%) had mixed forms of instability. Brittle diabetes is thus characterized by young age and female sex, and usually manifests itself as recurrent ketoacidosis or other forms of hyperglycaemic instability. Psychosocial problems and factitious metabolic decompensation are common.
Development of a Weather Forecasting Code: A Case Study

Computational science is increasingly supporting advances in scientific and engineering knowledge. The unique constraints of these types of projects result in a development process that differs from the process more traditional information technology projects use. This article reports the results of the sixth case study conducted under the support of the Darpa High Productivity Computing Systems Program. The case study aimed to investigate the technical challenges of code development in this environment, understand the use of development tools, and document the findings as concrete lessons learned for other developers' benefit. The project studied here is a major component of a weather forecasting system of systems. It includes complex behavior and interaction of several individual physical systems (such as the atmosphere and the ocean). This article describes the development of the code and presents important lessons learned.
Age-dependent resistance to murine retrovirus-induced spongiform neurodegeneration results from central nervous system-specific restriction of virus replication

The murine retrovirus CasBrE causes a noninflammatory spongiform degeneration of the central nervous system (CNS). Mice inoculated as neonates develop viremia and are susceptible to disease. However, mice inoculated at 10 days of age do not develop viremia and are totally resistant to the neurologic disease. We recently described a highly neurovirulent chimeric virus, FrCasE (J. L. Portis, S. Czub, C. F. Garon, and F. J. McAtee, J. Virol. 64:1648-1656, 1990), which contains the env gene of CasBrE. Mice inoculated at 10 days of age with this virus developed a viremia comparable to that in neonatally inoculated mice but, surprisingly, were still completely resistant to the neurodegenerative disease. A comparison of the tissue distribution of virus replication for mice inoculated at 1 or 10 days of age was determined by Southern blot analysis for the quantification of viral DNA and by infectious-center assay for the quantification of virus-producing cells. The levels of virus replication in the spleens were comparable in the two groups. In contrast, virus replication in the CNS of the resistant 10-day-old mice was markedly restricted (100- to 1,000-fold). Intracerebral inoculation did not overcome this restriction. A similar pattern of CNS-specific restriction of virus replication and resistance to disease was observed in athymic NIH Swiss nude mice inoculated at 10 days of age, suggesting that T-cell immunity was not involved. From our results, we conclude that the age-dependent resistance to disease is a consequence of the restriction of virus replication within the CNS due to the developmental state of the organ.
Photo image classification using pre-trained deep network for density-based spatiotemporal analysis system

Recently, during natural disasters like earthquakes, typhoons, flood, and heavy snowfall, messages and photos describing the situations faces by people are actively posted on social media sites. Therefore, the development of an analysis system using the data on social media sites to enhance situation awareness in the real world is an important research topic. In our previous work, we developed a density-based spatiotemporal analysis system to enhance situation awareness during emergency situations. The system could identify areas related to an observed emergency topic using tweet classifier, spatiotemporal clustering, and photo image classifier using the Bag-of-Features (BoF) model. In this paper, we propose a novel density-based spatiotemporal analysis system with a photo image classifier that used a pretrained deep network. The pre-trained deep network is integrated into the conventional photo image classifier instead of the BoF model. The proposed system can enhance situation awareness compared to our previous system by accurately classifying the photo images related to an observed emergency topic. To evaluate the proposed system, we used actual photo images attached to tweets related to “heavy rain” in Japan. The experimental results showed that the proposed system can classify photo images related to “heavy rain” more sensitively than our previous system.
The feasibility of substituting left atrial wall strain for flow velocity of left atrial appendage

Abstract Objective: Non-valvular atrial fibrillation (NVAF) is frequently complicated by thromboembolism. Left atrial appendage (LAA) flow is a predictor of LAA thrombosis. LAA flow is measured by transesophageal echocardiography (TEE), which is a semi-invasive diagnostic tool. Recently, speckle-tracking methods have been adapted for the evaluation of local cardiac function. We hypothesised that if we could determine LAA wall motion utilising a speckle tracking technique, we could non-invasively analyse LAA flow. Methods: Sixty-three NVAF patients including 38 with chronic atrial fibrillation (CAF), 14 with paroxysmal AF (PAF) and 11 with atrial flutter (AFL) were enrolled in this study. Normal sinus rhythm (NSR) patients with non-thromboembolic cerebral infarction were also included. Immediately after obtaining a 2D movie of the LAA through the aortic oblique short axis view by transthoracic echocardiography, LAA flow velocity was measured by TEE. Mean strains between the posterior and anterior walls were measured using a speckle-tracking technique. Results: Ten patients exhibited a thrombus and 11 had spontaneous echo contrast (SEC) in the auricle. Mean strain value was similar between CAF and PAF, although LAA flow velocity for CAF was significantly reduced compared with PAF (median value 13.7 cm/s versus 36.1 cm/s, p = <.00001). Mean strain of CAF with thrombus/SEC was significantly reduced compared with NSR patients (median value 1.52% versus 3.17%, p = .00181). Furthermore, mean strain was correlated with LAA flow velocity (R = 0.399, R2 = 0.1595, p = .000615). Conclusions: LAA wall strain identified via speckle-tracking methods may presage LAA peak flow velocity. This technique may contribute to stratification of thrombosis risks in the LAA.
Comparison between Fetal Spinal-Cord- and Forebrain-Derived Neural Stem/Progenitor Cells as a Source of Transplantation for Spinal Cord Injury

Recently, we have shown that the transplantation of spinal-cord-derived neural stem/progenitor cells (NSPCs) can contribute to the repair of injured spinal cords in adult rats, which may correspond to a behavioral recovery. To apply these results to clinical practice, a system for supplying human NSPCs on a large scale must be established. However, human spinal-cord-derived NSPCs are known to have a low proliferation rate, compared with forebrain-derived NSPCs. This low proliferative potency limits the feasibility of large-scale spinal cord-derived NSPC use. Thus, forebrain-derived NSPCs should be examined as an alternative to spinal-cord-derived NSPCs for the treatment of spinal cord injuries. In this study, we compared spinal-cord- and forebrain-derived NSPCs transplanted into injured spinal cords with respect to their fates in vivo as well as the animals’ functional recovery. Both spinal-cord- and forebrain-derived NSPCs promoted functional recovery in rats with spinal cord injuries. While both spinal-cord- and forebrain-derived NSPCs survived, migrated and differentiated into neurons, astrocytes and oligodendrocytes in response to the microenvironment within the injured spinal cord after transplantation, forebrain-derived NSPCs differentiated into more neurons and fewer oligodendrocytes, compared to spinal-cord-derived NSPCs. Neurons that had differentiated from the transplanted forebrain-derived NSPCs were shown to be positive for neurotransmitters like GABA, glutamate and glycine, although authentic glycinergic neurons are not normally present within the forebrain. Thus, at least a subpopulation of the transplanted forebrain-derived NSPCs differentiated into spinal-cord-type neurons. In conclusion, forebrain-derived NSPCs could be used as an alternative to spinal-cord-derived NSPCs as a potential therapeutic agent for spinal cord injuries.
First Use of a Brief 60-second Mindfulness Exercise in an Orthopedic Surgical Practice; Results from a Pilot Study.

Background Mindfulness based interventions may be useful for patients with musculoskeletal conditions in orthopedic surgical practices as adjuncts to medical procedures or alternatives to pain medications. However, typical mindfulness programs are lengthy and impractical in busy surgical practices. We tested the feasibility, acceptability and preliminary effect of a brief, 60-second mindfulness video in reducing pain and negative emotions in patients presenting to an orthopedics surgical practice. Methods This was an open pilot study. Twenty participants completed the Numerical Rating Scale to assess pain intensity, the State Anxiety subscale of the State Trait Anxiety Scale to assess state anxiety, and emotional thermometers to assess distress, anxiety, anger and depression immediately prior to and following the mindfulness video exercise. At the end of the exercise patients also answered three questions assessing satisfaction with the mindfulness video. Results Feasibility of the mindfulness video was high (100%). Usefulness, satisfaction and usability were also high. Participants showed improvements in state anxiety, pain intensity, distress, anxiety, depression and anger after watching the video. These changes were both statistically significant and clinically meaningful, when such information was available. Conclusion People with musculoskeletal pain seeking orthopedic care seem receptive and interested in brief mindfulness exercises that enhance comfort and calm.
HIV infection and glycemic response to newly initiated diabetic medical therapy

Objectives:Type 2 diabetes (DM2) is increasingly common in HIV-infected individuals. Antiretroviral agents and chronic inflammation may adversely affect glycemic control. However, little is known about the effectiveness of diabetic medical therapy in HIV-infected patients. The objective of this study was to compare the effectiveness of initial diabetic medical therapy in patients with and without HIV infection. Design:A retrospective cohort study was conducted among adults with DM2 initiating diabetic medications within the Centers for AIDS Research Network of Integrated Clinical Systems cohort. Methods:Generalized estimating equations were used to compare changes in hemoglobin A1c (HbA1c) through the year after initiation of therapy, controlling for baseline HbA1c and demographic and clinical covariates. Results:Two hundred and eighty-six HIV-infected patients and 858 age and sex-matched HIV-uninfected patients initiated diabetic medications during the study period. Overall, patients had an adjusted absolute mean reduction in HbA1c of 1.04% [95% confidence interval (CI) −0.87 to −1.22] during the first year of therapy. HIV-infected patients achieved significantly smaller reductions in HbA1c, with an absolute mean difference of −0.17% (95% CI −0.28 to −0.06; P = 0.003). On subanalyses, HIV-infected patients on a protease inhibitor-based regimen had significantly smaller reductions in HbA1c compared to HIV-uninfected patients (adjusted absolute difference −0.21%, 95% CI −0.35 to −0.08; P = 0.002). Conclusion:Patients with HIV infection who initiate diabetic medical therapy achieve smaller reductions in HbA1c than patients without HIV infection in the course of routine clinical care. This less robust response may in part be related to use of antiretrovirals that exacerbate insulin resistance, specifically protease inhibitors.
Accuracy and the effect of possible subject‐based confounders of magnitude‐based MRI for estimating hepatic proton density fat fraction in adults, using MR spectroscopy as reference

To determine the accuracy and the effect of possible subject‐based confounders of magnitude‐based magnetic resonance imaging (MRI) for estimating hepatic proton density fat fraction (PDFF) for different numbers of echoes in adults with known or suspected nonalcoholic fatty liver disease, using MR spectroscopy (MRS) as a reference.
Perfect tracking control using a phase plane for a wheeled inverted pendulum under hardware constraints

A wheeled inverted pendulum cannot balance without control, and it is important to save motion in a control range. In some situations, however, to avoid a collision, the maximum acceleration and deceleration must be applied. A motion-planning method for a wheeled inverted pendulum (“body” hereafter)-which uses full performance from all attitudes under hardware constraints-was developed. The developed method involves two steps. First, a linear combination of zeroth to fourth differentials of parameters based on the motion equation of a wheeled inverted pendulum is obtained. Second, the arbitrary attitude of the wheeled inverted pendulum and hardware constraints are expressed on a phase plane containing angular rate of body motion and an angular inclination of the body. By executing these two steps, a motion plan can be expressed on the phase plane. A simulation based on a model confirmed that the movement plan formulated by this technique can be followed with no error.
Early versus Late Application of Subthalamic deep brain Stimulation to Parkinson’s disease patients with motor complications (ELASS): protocol of a multicentre, prospective and observational study

Introduction Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a well-established surgical treatment for Parkinson’s disease (PD). However, there is currently no consensus on the best timing for this surgery. The aim of our study is to compare the therapeutic efficacy of bilateral STN DBS in patients with PD with early and late motor complications. Methods and analysis 200 patients with PD will be enrolled in this multicentre, prospective, observational study, and will be followed up for 4 years. Patients with PD who meet the criteria for STN DBS surgery will be allocated to either the early stimulation group or the late stimulation group based on the duration of their motor complications. The primary outcome will be changes in quality of life from baseline to 4 years, measured using the 39-item Parkinson’s Disease Questionnaire Summary Index. The secondary outcomes include changes in motor function measured using Movement Disorder Society-revised Unified Parkinson’s Disease Rating Scale (MDS-UPDRS) Part III, self-reported experiences of daily living measured using MDS-UPDRS Part I B and Part II, good ’on' time recorded by the patients using a diary and safety profile of both groups. Ethics and dissemination The study received ethical approval from the Medical Ethical Committee of the First Affiliated Hospital, Sun Yat-sen University. The results of this study will be published in peer-reviewed journals and presented at international conferences. Trial registration number NCT01922388; Pre-results.