LLukas22/scidocs huggingface dataset:
A comparison of algorithms for the pairwise alignment of biological networks

MOTIVATION
As biological inquiry produces ever more network data, such as protein-protein interaction networks, gene regulatory networks and metabolic networks, many algorithms have been proposed for the purpose of pairwise network alignment-finding a mapping from the nodes of one network to the nodes of another in such a way that the mapped nodes can be considered to correspond with respect to both their place in the network topology and their biological attributes. This technique is helpful in identifying previously undiscovered homologies between proteins of different species and revealing functionally similar subnetworks. In the past few years, a wealth of different aligners has been published, but few of them have been compared with one another, and no comprehensive review of these algorithms has yet appeared.


RESULTS
We present the problem of biological network alignment, provide a guide to existing alignment algorithms and comprehensively benchmark existing algorithms on both synthetic and real-world biological data, finding dramatic differences between existing algorithms in the quality of the alignments they produce. Additionally, we find that many of these tools are inconvenient to use in practice, and there remains a need for easy-to-use cross-platform tools for performing network alignment.
Myiasis as a Rare Complication of Male Circumcision: A Case Report and Review of Literature

Introduction. Circumcision is a common procedure carried out around the world. Due to religious reasons, it is routinely done in Bangladesh, by both traditional as well as medically trained circumcisers. Complications include excessive bleeding, loss of foreskin, infection, and injury to the glans penis. Myiasis complicating male circumcision appears to be very rare. Case Presentation. In 2010, a 10-year-old boy presented to the OPD of Dhaka Medical College Hospital with severe pain in his penile region following circumcision 7-days after. The procedure was carried out by a traditional circumciser using unsterilized instruments and dressing material. After examination, unhealthy granulation tissue was seen and maggots started coming out from the site of infestation, indicating presence of more maggots underneath the skin. An emergency operation was carried out to remove the maggots and reconstruction was carried out at the plastic surgery department. Conclusion. There is scarcity of literature regarding complications following circumcision in developing countries. Most dangerous complications are a result of procedure carried out by traditional circumcisers who are inadequately trained. Incidence of such complications can be prevented by establishing a link between the formal and informal sections of healthcare to improve the safety of the procedure.
LLF Schedulability Analysis on Multiprocessor Platforms

LLF (Least Laxity First) scheduling, which assigns a higher priority to a task with smaller laxity, has been known as an optimal preemptive scheduling algorithm on a single processor platform. However, its characteristics upon multiprocessor platforms have been little studied until now. Orthogonally, it has remained open how to efficiently schedule general task systems, including constrained deadline task systems, upon multiprocessors. Recent studies have introduced zero laxity (ZL) policy, which assigns a higher priority to a task with zero laxity, as a promising scheduling approach for such systems (e.g., EDZL). Towards understanding the importance of laxity in multiprocessor scheduling, this paper investigates the characteristics of ZL policy and presents the first ZL schedulability test for any work-conserving scheduling algorithm that employs this policy. It then investigates the characteristics of LLF scheduling, which also employs the ZL policy, and derives the first LLF-specific schedulability test on multiprocessors. It is shown that the proposed LLF test dominates the ZL test as well as the state-of-art EDZL test.
The Unstructured Clinical Interview.

i n mental health, family, and community counseling settings, master's-level counselors engage in unstructured clinical interviewing to develop diagnoses based on the Diagnostic and Statistical Manual of Mental Disorders (4th ed., text rev.; DSM-IV-TR. American Psychiatric Association, 2000). Although counselors receive education about diagnosis and the DSMclassification system, the majority of them are not specifically trained in clinical interviewing. This article provides information about using the unstructured clinical interview to make a DSM-IV-TR diagnosis for adult clients with Axis I and Axis 11 disorders.
Feasibility of Using a Smartwatch to Intensively Monitor Patients With Chronic Obstructive Pulmonary Disease: Prospective Cohort Study

BACKGROUND
Acute exacerbations of chronic obstructive pulmonary disease (COPD) are associated with accelerated decline in lung function, diminished quality of life, and higher mortality. Proactively monitoring patients for early signs of an exacerbation and treating them early could prevent these outcomes. The emergence of affordable wearable technology allows for nearly continuous monitoring of heart rate and physical activity as well as recording of audio which can detect features such as coughing. These signals may be able to be used with predictive analytics to detect early exacerbations. Prior to full development, however, it is important to determine the feasibility of using wearable devices such as smartwatches to intensively monitor patients with COPD.


OBJECTIVE
We conducted a feasibility study to determine if patients with COPD would wear and maintain a smartwatch consistently and whether they would reliably collect and transmit sensor data.


METHODS
Patients with COPD were recruited from 3 hospitals and were provided with a smartwatch that recorded audio, heart rate, and accelerations. They were asked to wear and charge it daily for 90 days. They were also asked to complete a daily symptom diary. At the end of the study period, participants were asked what would motivate them to regularly use a wearable for monitoring of their COPD.


RESULTS
Of 28 patients enrolled, 16 participants completed the full 90 days. The average age of participants was 68.5 years, and 36% (10/28) were women. Survey, heart rate, and activity data were available for an average of 64.5, 65.1, and 60.2 days respectively. Technical issues caused heart rate and activity data to be unavailable for approximately 13 and 17 days, respectively. Feedback provided by participants indicated that they wanted to actively engage with the smartwatch and receive feedback about their activity, heart rate, and how to better manage their COPD.


CONCLUSIONS
Some patients with COPD will wear and maintain smartwatches that passively monitor audio, heart rate, and physical activity, and wearables were able to reliably capture near-continuous patient data. Further work is necessary to increase acceptability and improve the patient experience.
The effect of Fampridine-SR on cognitive fatigue in a randomized double-blind crossover trial in patients with MS.

BACKGROUND
Cognitive fatigue (CF) is a common complaint in persons with MS (PwMS). Fampridine-SR improves ambulation, fatigue and endurance, due to enhancing action potential formation by blocking potassium channels in demyelinated axons. Thus, through this same mechanism, it is hypothesized that Fampridine-SR could improve CF.


OBJECTIVE
To determine if Fampridine-SR objectively improves CF in PwMS.


METHODS
Sixty PwMS of any type with CF, defined as 3 or less correct responses when comparing the last third to the first third on the Paced Auditory Serial Addition Test (PASAT), were recruited from a tertiary care MS clinic in London (ON) Canada. Subjects also had to be between 18 and 64 years of age, inclusive, not had a relapse in the last 60 days or corticosteroids in the last 30 days, EDSS 0.0-7.0, and no other diagnosis that could cause cognitive impairment. A randomized double blind crossover design was used: subjects were randomized to either placebo or Fampridine-SR for 4 weeks, then after at least a one week washout, received the opposite treatment. Subjects were assessed before and after each treatment block. The primary outcome was the PASAT CF score after treatment with Fampridine-SR compared to placebo. T-tests and chi-square were used to compare demographics between the two groups (placebo-Fampridine-SR vs. Fampridine SR-placebo). Treatment effects were assessed using factorial ANOVA, with treatment (Fampridine-SR vs. placebo) and time (before and after treatment) as within-subject variables.


RESULTS
Of the 60 subjects randomized, 48 completed the study; three were removed due to an adverse event while in the treatment arm (one due to relapse while on placebo, one due to urinary retention and one due to dizziness and headache while on Fampridine-SR). The subjects had a mean age of 46.5±10.0 years, education of 13.6±1.9 years, and were diagnosed with MS 10.6±9.6 years ago. The majority were female (46, 76.7%), had relapsing remitting MS (41, 68.3%) with median EDSS of 3.5 (range 1.0-7.0). There were no significant demographic differences between the two groups. The treatment x time interaction within the factorial ANOVA on PASAT CF scores was statistically significant, F(1, 45)=8.28, p=0.006, suggesting there is a difference between the treatments (placebo vs. Fampridine-SR), over the course of the study. An evaluation of the mean scores suggests, however, that subjects saw a greater improvement when they were given the placebo, than when they were given the active medication. Similarly, individuals showed a greater increase in their information processing speed (as measured by the PASAT) over the course of treatment when they were given the placebo, as compared with the active medication F(1,45)=4.17, p=0.047.


CONCLUSION
Although this small pilot study does not suggest that Fampridine-SR results in a statistically significant improvement of CF in MS patients, as compared to placebo, individuals demonstrated an improvement in both information processing speed and CF, suggesting further studies are warranted.
A Note on Two Classical Shock Filters and Their Asymptotics

We establish in 2D, the PDE associated with a classical debluring filter, the Kramer operator and compare it with another classical shock filter.
ect of atropine on gastro-oesophageal reflux and transient lower oesophageal sphincter relaxations in patients with gastro-oesophageal reflux disease

Background—Atropine reduces the rate of reflux episodes in normal subjects by inhibition of transient lower oesophageal sphincter (LOS) relaxations. The aim of this study was to investigate the eVect of atropine on the rate and mechanisms of reflux in patients with reflux disease. Methods—Oesophageal motility and pH were recorded for one hour after a meal in 15 patients with reflux disease. On separate days, atropine (15 μg/kg bolus intravenously, 4 μg/kg/h infusion) or saline were given and maintained for the recording period. Results—Atropine significantly reduced basal LOS pressure from 7.1 (2.2) to 2.9 (1.3) mmHg (mean (SEM)).Atropine also reduced the rate of reflux episodes from 5.0 (2.0–8.75) to 1.0 (0–6.25) per hour (median (interquartile range)) largely because of a decrease in the rate of transient LOS relaxations from 2.0 (0–4.75) to 0 (0–0) per hour and abolition of reflux during swallow induced LOS relaxation. There was no change in the rate of reflux episodes because of absent basal LOS pressure. Conclusions—Atropine inhibits reflux in patients with reflux disease largely by inhibition of transient LOS relaxations and swallow induced LOS relaxation. These findings suggest that pharmacological control of reflux through control of transient LOS relaxations is possible in patients with reflux disease.
Prototype of pedestrian-to-vehicle communication system for the prevention of pedestrian accidents using both 3G wireless and WLAN communication

For the realization of a safe road traffic environment a wireless communication system which makes an information network between pedestrians and vehicles has been needed. A prototype of pedestrian-to-vehicle communication system was developed by using a cellular phone and a car navigation system equipped with GPS and wireless communication function. By interoperation of 3G wireless network and wireless LAN, it was possible to communicate in a wide area and with little delay time in a local area. The system can exchange the necessary information between pedestrians and vehicles, inform of the location of the ones that have an accident risk, and give an alarm by employing the developed algorithm for estimating the collision risk between each pedestrian and vehicle. The effectiveness of the system was shown by simulation of traffic situations.
Efficacy of Cognitive Behavioral Therapy for Insomnia in Adolescents: A Randomized Controlled Trial with Internet Therapy, Group Therapy and A Waiting List Condition.

STUDY OBJECTIVES
To investigate the efficacy of cognitive behavioral therapy for insomnia (CBTI) in adolescents.


DESIGN
A randomized controlled trial of CBTI in group therapy (GT), guided internet therapy (IT), and a waiting list (WL), with assessments at baseline, directly after treatment (post-test), and at 2 months follow-up.


SETTING
Diagnostic interviews were held at the laboratory of the Research Institute of Child Development and Education at the University of Amsterdam. Treatment for GT occurred at the mental health care center UvAMinds in Amsterdam, the Netherlands.


PARTICIPANTS
One hundred sixteen adolescents (mean age = 15.6 y, SD = 1.6 y, 25% males) meeting DSM-IV criteria for insomnia, were randomized to IT, GT, or WL.


INTERVENTIONS
CBTI of 6 weekly sessions, consisted of psychoeducation, sleep hygiene, restriction of time in bed, stimulus control, cognitive therapy, and relaxation techniques. GT was conducted in groups of 6 to 8 adolescents, guided by 2 trained sleep therapists. IT was applied through an online guided self-help website with programmed instructions and written feedback from a trained sleep therapist.


MEASUREMENTS AND RESULTS
Sleep was measured with actigraphy and sleep logs for 7 consecutive days. Symptoms of insomnia and chronic sleep reduction were measured with questionnaires. Results showed that adolescents in both IT and GT, compared to WL, improved significantly on sleep efficiency, sleep onset latency, wake after sleep onset, and total sleep time at post-test, and improvements were maintained at follow-up. Most of these improvements were found in both objective and subjective measures. Furthermore, insomnia complaints and symptoms of chronic sleep reduction also decreased significantly in both treatment conditions compared to WL. Effect sizes for improvements ranged from medium to large. A greater proportion of participants from the treatment conditions showed high end-state functioning and clinically significant improvement after treatment and at follow-up compared to WL.


CONCLUSIONS
This study is the first randomized controlled trial that provides evidence that cognitive behavioral therapy for insomnia is effective for the treatment of adolescents with insomnia, with medium to large effect sizes. There were small differences between internet and group therapy, but both treatments reached comparable endpoints.


CLINICAL TRIAL REGISTRATION
This study was part of the clinical trial: Effectiveness of cognitive behavioral therapy for sleeplessness in adolescents; URL: http://www.isrctn.com/ISRCTN33922163; registration: ISRCTN33922163.
Cumulative risk and child development.

Childhood multiple risk factor exposure exceeds the adverse developmental impacts of singular exposures. Multiple risk factor exposure may also explain why sociodemographic variables (e.g., poverty) can have adverse consequences. Most research on multiple risk factor exposure has relied upon cumulative risk (CR) as the measure of multiple risk. CR is constructed by dichotomizing each risk factor exposure (0 = no risk; 1 = risk) and then summing the dichotomous scores. Despite its widespread use in developmental psychology and elsewhere, CR has several shortcomings: Risk is designated arbitrarily; data on risk intensity are lost; and the index is additive, precluding the possibility of statistical interactions between risk factors. On the other hand, theoretically more compelling multiple risk metrics prove untenable because of low statistical power, extreme higher order interaction terms, low robustness, and collinearity among risk factors. CR multiple risk metrics are parsimonious, are statistically sensitive even with small samples, and make no assumptions about the relative strengths of multiple risk factors or their collinearity. CR also fits well with underlying theoretical models (e.g., Bronfenbrenner's, 1979, bioecological model; McEwen's, 1998, allostasis model of chronic stress; and Ellis, Figueredo, Brumbach, & Schlomer's, 2009, developmental evolutionary theory) concerning why multiple risk factor exposure is more harmful than singular risk exposure. We review the child CR literature, comparing CR to alternative multiple risk measurement models. We also discuss strengths and weaknesses of developmental CR research, offering analytic and theoretical suggestions to strengthen this growing area of scholarship. Finally, we highlight intervention and policy implications of CR and child development research and theory.
Six-month angiographic outcome after successful repeat percutaneous intervention for in-stent restenosis.

BACKGROUND
In-stent restenosis is an increasing clinical problem. Discordant results have been published regarding the risk of recurrent restenosis after repeat angioplasty for the treatment of in-stent restenosis.


METHODS AND RESULTS
One hundred three consecutive patients (107 vessels) underwent repeat percutaneous intervention for the treatment of in-stent restenosis and were entered in a prospective angiographic follow-up program. Repeat balloon angioplasty was performed at 93 lesions (87%) and additional stenting at 14 lesions (13%). The primary success rate was 98%. Six-month angiographic follow-up was performed in 85% of eligible patients. Restenosis was determined by quantitative angiography. Restenosis defined as a >50% diameter stenosis at follow-up was observed at 22% of lesions. The rate of target-lesion revascularization at 6 months was 17%. Repeat intervention for diffuse in-stent restenosis and severe stenosis before repeat intervention were associated with significantly higher rates of recurrent restenosis.


CONCLUSIONS
The overall restenosis rate after repeat intervention for in-stent restenosis is low. The subgroup of patients with diffuse and/or severe in-stent restenosis, however, is at higher risk of recurrent restenosis and may benefit from alternative therapeutic strategies.
Contrast-enhanced harmonic endoscopic ultrasound.

Second-generation intravenous blood-pool ultrasound contrast agents are increasingly used in endoscopic ultrasound (EUS) for characterization of microvascularization, differential diagnosis of benign and malignant focal lesions, and improving staging and guidance of therapeutic procedures. Although initially used as Doppler signal enhancers, second-generation microbubble contrast agents are now used with specific contrast harmonic imaging techniques, which benefit from the highly nonlinear behavior of the microbubbles. Contrast-specific modes based on multi-pulse technology are used to perform contrast-enhanced harmonic EUS based on a very low mechanical index (0.08 - 0.12). Quantification techniques based on dynamic contrast-enhanced ultrasound have been recommended for perfusion imaging and monitoring of anti-angiogenic treatment, mainly based on time-intensity curve analysis. Most of the clinical applications include the differential diagnosis of focal pancreatic masses, with adenocarcinoma having a distinct hypovascular (hypo-enhanced) appearance compared with neuroendocrine tumors, which are hypervascular (with strong arterial hyper-enhancement). However, pseudotumoral chronic pancreatitis and autoimmune pancreatitis also have an iso- or hypervascular appearance, making the differential diagnosis difficult. Even more promising is the use of dynamic contrast-enhanced harmonic EUS for the longitudinal monitoring of the effects of chemotherapy and/or anti-angiogenic therapy in advanced digestive cancers, which are difficult to examine by conventional cross-sectional imaging techniques.
The Anti-Clot Treatment Scale (ACTS) in clinical trials: cross-cultural validation in venous thromboembolism patients

BACKGROUND
The Anti-Clot Treatment Scale (ACTS) is a 15-item patient-reported instrument of satisfaction with anticoagulant treatment. It includes a 12-item ACTS Burdens scale and a 3-item ACTS Benefits scale. Its role in clinical trials and other settings should be supported by evidence that it is both clinically meaningful and scientifically sound. The aim of the study was to evaluate the measurement performance of the ACTS (Dutch, Italian, French, German and English language versions) in patients with venous thromboembolism based on traditional psychometric methods.


METHODS
ACTS Burdens and Benefits scale data from a large clinical trial (EINSTEIN DVT) involving 1336 people with venous thromboembolism were analysed at both the scale and item level. Five key psychometric properties were examined using traditional psychometric methods: acceptability, scaling assumptions, reliability (including internal consistency reliability, test-retest reproducibility); validity (including known groups and discriminant validity); and responsiveness. These methods of examination underpin the US Food and Drug Administration recommendations for patient-reported outcome instrument evaluation.


RESULTS
Overall, the 12-item ACTS Burdens scale and 3-item ACTS Benefits scale met the psychometric criteria evaluated at both item and scale levels, with the exception of some relatively minor issues in the Dutch language version, which were just below reliability criteria (i.e. alpha = 0.72, test-retest intraclass correlation = 0.79). A consistent finding from item-level evaluations of aggregate endorsement frequencies and skewness suggested that response scales may be improved by reducing the number of response options from five to four.


CONCLUSIONS
Both the ACTS Burdens and ACTS Benefits scales consistently satisfied traditional reliability and validity criteria across multiple language datasets, supporting it as a clinically useful patient-reported instrument of satisfaction with anticoagulant treatment in clinical trials.


TRIAL REGISTRATION NUMBER
NCT00440193.
Multi-Agent Approach for Enhancing Security of Protection Schemes in Cyber-Physical Energy Systems

This paper presents a distributed multiagent scheme to detect and identify cyber threats on the protection systems of power grids. The integration of information and communication technologies into existing power grids builds critical cyber-physical energy systems, in which digital relays are networked cyber-physical components subject to various cyber threats. Cyber attacks on protection systems may mimic real faults, cause component failure, and disable the communication links. Agents utilize both cyber and physical properties to reinforce the detection technique and further distinguish cyber attacks from physical faults. This paper also introduces the problem of secure communication protocols and highlights the comparative studies for enhancing the security of the protection systems. The proposed scheme is validated using a benchmark power system under various fault and cyber attack scenarios.