LLukas22/scidocs huggingface dataset:
Insightful classification of crystal structures using deep learning

Computational methods that automatically extract knowledge from data are critical for enabling data-driven materials science. A reliable identification of lattice symmetry is a crucial first step for materials characterization and analytics. Current methods require a user-specified threshold, and are unable to detect average symmetries for defective structures. Here, we propose a machine learning-based approach to automatically classify structures by crystal symmetry. First, we represent crystals by calculating a diffraction image, then construct a deep learning neural network model for classification. Our approach is able to correctly classify a dataset comprising more than 100,000 simulated crystal structures, including heavily defective ones. The internal operations of the neural network are unraveled through attentive response maps, demonstrating that it uses the same landmarks a materials scientist would use, although never explicitly instructed to do so. Our study paves the way for crystal structure recognition of—possibly noisy and incomplete—three-dimensional structural data in big-data materials science. Classifying crystal structures using their space group is important to understand material properties, but the process currently requires user input. Here, the authors use machine learning to automatically classify more than 100,000 simulated perfect and defective crystal structures.
Improved imaging for X-ray inspection systems

A number of advancements for X-ray inspection systems have recently been implemented in the image presented to the operator. Advances in the use of color and image fusion techniques have been developed to maximize the information available in the initial view shown on the monitor. Different techniques are appropriate depending upon the size of the inspection item. Inspection of checked and carry-on baggage requires imaging methods that would not be appropriate for use on larger, more complex objects such as cargo containers or whole trucks. Color-coded presentation of CT images of baggage imposes yet other demands. Comparative images and analyses are presented to support choices for imaging on L-3 Communications systems in terms of the conflicting requirements of cost, sensitivity, resolution, and penetration. A number of enhancements are available to the operator and their influence on system performance is explored. Some experimental enhancements are demonstrated and their trade-offs discussed. The imaging system is ultimately based on hardware, and the choice of detectors, amplifiers, and sampling methods plays an important role in overall performance. Image degradation can be caused by deficiencies in the imaging hardware. Effects such as detector cross-talk and afterglow will negatively impact system performance. Recognition of these factors and steps to mitigate them are discussed. The effect of X-ray source choices such as beam voltage, milliamps, and sampling rate has a direct influence on the image quality and bag dose. Results of theoretical modeling as well as results on actual systems are presented. For a given bag dose, the trade-off between sensitivity, resolution, and penetration are considered. Possibilities for future advancements in imaging for X-ray inspection systems are explored.
Blood Coagulation and Asthma Exacerbation in Children.

BACKGROUND
Recent studies have demonstrated the activation of coagulation pathways in asthmatic airways. This study aimed to determine systemic blood coagulation during asthma exacerbation compared with the stable state in children.


METHODS
Pediatric patients (aged between 5 and 15 years) suffering from asthma exacerbation were enrolled. von Willebrand factor (vWF), plasminogen activator inhibitor type-1 (PAI-1), protein C, D-dimer, prothrombin fragment 1 + 2 (F1 + 2), thrombin-antithrombin complex (TAT), and C-reactive protein (CRP) levels were measured during asthma exacerbation and stable state.


RESULTS
A total of 22 patients were enrolled. The median vWF, PAI-1, and CRP during asthma exacerbation were significantly higher than those of the stable state: 147.5% (interquartile range, IQR: 111.05-196.57) versus 94% (IQR: 69.72-109.62, p < 0.001), 41.9 ng/ml (IQR: 21.91-48.61) versus 26.17 ng/ml (IQR: 15.89-34.44, p < 0.03), and 4.46 mg/l (IQR: 2.15-16.23) versus 0.87 mg/l (IQR: 0.20-3.89, p < 0.015), respectively. However, the median protein C during asthma exacerbation was significantly lower than that of the stable state: 99.5% (IQR: 86.75-117) versus 113% (IQR: 94-115.25), p = 0.01. No significant difference was found between the levels of D-dimer, F1 + 2, and TAT during asthma exacerbation and stable state. Ultimately, D-dimer was positively correlated with asthma exacerbation score (R = 0.466, p = 0.027). A significant correlation was observed between vWF and CRP (R = 0.527, p = 0.012).


CONCLUSION
Evidence was found of increased endothelial activation and increased PAI-1 during asthma exacerbation. This may emphasize the potential role of blood coagulation in asthma exacerbation.
Effectiveness of antiepileptic therapy in patients with PCDH19 mutations

PURPOSE
PCDH19 mutations cause epilepsy and mental retardation limited to females (EFMR) or Dravet-like syndromes. Especially in the first years of life, epilepsy is known to be highly pharmacoresistant. The aim of our study was to evaluate the effectiveness of antiepileptic therapy in patients with PCDH19 mutations.


METHODS
We report a retrospective multicenter study of antiepileptic therapy in 58 female patients with PCDH19 mutations and epilepsy aged 2-27 years (mean age 10.6 years).


RESULTS
The most effective drugs after 3 months were clobazam and bromide, with a responder rate of 68% and 67%, respectively, where response was defined as seizure reduction of at least 50%. Defining long-term response as the proportion of responders after 12 months of treatment with a given drug in relation to the number of patients treated for at least 3 months, the most effective drugs after 12 months were again bromide and clobazam, with a long-term response of 50% and 43%, respectively. Seventy-four percent of the patients became seizure-free for at least 3 months, 47% for at least one year.


SIGNIFICANCE
The most effective drugs in patients with PCDH19 mutations were bromide and clobazam. Although epilepsy in PCDH19 mutations is often pharmacoresistant, three quarters of the patients became seizure-free for at least for 3 months and half of them for at least one year. However, assessing the effectiveness of the drugs is difficult because a possible age-dependent spontaneous seizure remission must be considered.
Internet Banking : Market Developments and Regulatory Issues May 2001 ( Revised )

*The opinions expressed in this article are those of the authors alone, and do not necessarily represent those of the Office of the Comptroller of the Currency or the United States Treasury Department. Abstract Internet banking is a subject receiving great attention in the banking industry and the regulatory community. As with other areas of e-commerce, discussions about Internet banking often proceed without reference to the actual state of market developments. This paper describes the current state of Internet banking and discusses its implications for the banking industry and regulatory policy. At the end of 2000, a minority of banks offered Internet banking, but analysis of data collected by Office of the Comptroller of the Currency bank examiners shows that over half of all banks will offer Internet banking by year-end 2001. As a group, large banks are more likely to offer Internet banking, although a growing number of small banks offer it, or plan to. Nevertheless, large banks appear to have an advantage over small banks in the range of services they offer over the Internet. An empirical examination of bank profitability indicates that, at this point in time, Internet banking is not having an independent impact on bank profitability. This result may of course change as the use of Internet banking grows. Use of Internet banking, while forecast to grow significantly, is still relatively modest. We argue that the modest use of Internet banking by consumer customers of banks is due in large part to a lack of a compelling value-added proposition. This problem is less severe for Internet banking customers and may explain why some banks are targeting their Internet strategies toward business customers. Nevertheless, since most consumers have accounts at banks that offer Internet banking, consumer usage patterns could change suddenly. Internet banking's impact on consolidation in the banking industry is uncertain. The economics of Internet banking may favor large institutions, either because of economies of scale and scope, or because of the need to advertise heavily to be successful. Alternatively, Internet banking could offer entry and expansion opportunities that small banks traditionally lacked. Internet banking presents policy makers and regulatory authorities with a set of significant challenges. Changes to the structure and functioning of financial institutions are challenging a regulatory structure that was developed based on increasingly outdated lines of demarcation among types of financial institutions. In addition, existing regulatory policies have to be adapted …
Automatically Recommending Peer Reviewers in Modern Code Review

Code review is an important part of the software development process. Recently, many open source projects have begun practicing code review through “modern” tools such as GitHub pull-requests and Gerrit. Many commercial software companies use similar tools for code review internally. These tools enable the owner of a source code change to request individuals to participate in the review, i.e., reviewers. However, this task comes with a challenge. Prior work has shown that the benefits of code review are dependent upon the expertise of the reviewers involved. Thus, a common problem faced by authors of source code changes is that of identifying the best reviewers for their source code change. To address this problem, we present an approach, namely cHRev, to automatically recommend reviewers who are best suited to participate in a given review, based on their historical contributions as demonstrated in their prior reviews. We evaluate the effectiveness of cHRev on three open source systems as well as a commercial codebase at Microsoft and compare it to the state of the art in reviewer recommendation. We show that by leveraging the specific information in previously completed reviews (i.e.,quantification of review comments and their recency), we are able to improve dramatically on the performance of prior approaches, which (limitedly) operate on generic review information (i.e., reviewers of similar source code file and path names) or source coderepository data. We also present the insights into why our approach cHRev outperforms the existing approaches.
Till Death Us Do Part and the BBC: Racial Politics and the British Working Classes 1965–75:

Historians have struggled to unpick the complex relationship between the British working classes and heightened Commonwealth immigration to postwar Britain and have tended to explain the developmen...
Report of Working Group 19 on Ecosystem-based Management Science and its Application to the North Pacific

BOOKS – are prepared for PICES Annual Meetings and symposia (co-)organized by PICES. For further information on our publications, visit the PICES website at www.pices.int.
FORMATION OF INTERSTELLAR MOLECULES ON THE SURFACE OF GRAINS

Relative amounts of molecules formed by relaxation type reactions between radicals (atoms) and radicals (atoms) on the grain surfaces are calculated. The result can explain the formation mechanism of observed molecules. A prediction has been made on molecules such as methylamine which are expected to be detectable.
Comparison of the Efficacy and Safety of Aripiprazole Versus Bupropion Augmentation in Patients With Major Depressive Disorder Unresponsive to Selective Serotonin Reuptake Inhibitors: A Randomized, Prospective, Open-Label Study.

PURPOSE
The purpose of this study was to compare the efficacy and safety of aripiprazole versus bupropion augmentation in patients with major depressive disorder (MDD) unresponsive to selective serotonin reuptake inhibitors (SSRIs).


METHODS
This is the first randomized, prospective, open-label, direct comparison study between aripiprazole and bupropion augmentation. Participants had at least moderately severe depressive symptoms after 4 weeks or more of SSRI treatment. A total of 103 patients were randomized to either aripiprazole (n = 56) or bupropion (n = 47) augmentation for 6 weeks. Concomitant use of psychotropic agents was prohibited. Montgomery Asberg Depression Rating Scale, 17-item Hamilton Depression Rating scale, Iowa Fatigue Scale, Drug-Induced Extrapyramidal Symptoms Scale, Psychotropic-Related Sexual Dysfunction Questionnaire scores were obtained at baseline and after 1, 2, 4, and 6 weeks of treatment.


RESULTS
Overall, both treatments significantly improved depressive symptoms without causing serious adverse events. There were no significant differences in the Montgomery Asberg Depression Rating Scale, 17-item Hamilton Depression Rating scale, and Iowa Fatigue Scale scores, and response rates. However, significant differences in remission rates between the 2 groups were evident at week 6 (55.4% vs 34.0%, respectively; P = 0.031), favoring aripiprazole over bupropion. There were no significant differences in adverse sexual events, extrapyramidal symptoms, or akathisia between the 2 groups.


CONCLUSIONS
The present study suggests that aripiprazole augmentation is at least comparable to bupropion augmentation in combination with SSRI in terms of efficacy and tolerability in patients with MDD. Both aripiprazole and bupropion could help reduce sexual dysfunction and fatigue in patients with MDD. Aripiprazole and bupropion may offer effective and safe augmentation strategies in patients with MDD who are unresponsive to SSRIs. Double-blinded trials are warranted to confirm the present findings.
Genetic markers of suicidal ideation emerging during citalopram treatment of major depression.

OBJECTIVE
Suicidal ideation is an uncommon symptom than can emerge during antidepressant treatment. The biological basis of treatment-emergent suicidal ideation is unknown. Genetic markers may shed light on the causes of treatment-emergent suicidal ideation and help identify individuals at high risk who may benefit from closer monitoring, alternative treatments, or specialty care.


METHOD
A clinically representative cohort of outpatients with major depressive disorder who enrolled in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) trial were treated with citalopram under a standard protocol for up to 14 weeks. DNA samples from 1,915 participants were genotyped for 768 single-nucleotide polymorphisms in 68 candidate genes. Allele and genotype frequencies were compared between the 120 participants who developed treatment-emergent suicidal ideation and those who did not.


RESULTS
Two markers were significantly associated with treatment-emergent suicidal ideation in this sample (marker rs4825476, p=0.0000784, odds ratio=1.94; permutation p=0.01; marker rs2518224, p=0.0000243, odds ratio=8.23; permutation p=0.003). These markers reside within the genes GRIA3 and GRIK2, respectively, both of which encode ionotropic glutamate receptors.


CONCLUSIONS
Markers within GRIK2 and GRIA3 were associated with treatment-emergent suicidal ideation during citalopram therapy. If replicated, these findings may shed light on the biological basis of this potentially dangerous adverse event and help identify patients at increased risk.
The Effect of Methylphenidate on Fatigue in Advanced Cancer: An Aggregated N-of-1 Trial.

CONTEXT
Fatigue is common in life-limiting cancer. Methylphenidate (MPH), a psychostimulant, may be a useful therapy. Gathering evidence in patients with advanced cancer can be challenging.


OBJECTIVES
To determine if MPH improves cancer-related fatigue in people with advanced cancer.


METHODS
N-of-1 trials are multicycle, double-blind, randomized, controlled crossover trials using standardized measures of effect in individuals. They are normally used to assess treatment effects in individuals. Aggregated N-of-1 trials from participants with end-stage cancer suffering fatigue were used to assess the group effect of MPH, producing an estimate of equivalent power to a parallel-group randomized controlled trial (RCT) but requiring less than half of the sample size. Up to three cycles of MPH 5 mg twice daily (three days) vs. identical placebo (three days) capsules were offered to participants. Primary outcome was improvement in fatigue as measured by the Functional Assessment of Chronic Illness Therapy-Fatigue Scale and the Wu Cancer Fatigue Scale. Analysis used Bayesian statistical methods using intention-to-treat principles.


RESULTS
Forty-three participants completed 84 cycles of MPH and placebo in random order, exceeding sample size estimates. Overall, MPH did not improve fatigue (mean difference 3.2; 95% credible interval -2.0, 9.0; posterior probability of favorable effect 0.890). Eight participants showed important improvement, and one participant showed important worsening of fatigue on MPH. There were no features that distinguished participants whose fatigue responded to MPH compared with those who did not.


CONCLUSION
MPH does not improve fatigue in the population of patients with end-stage cancer. Aggregated N-of-1 trial methodology is feasible and produces population-based sample estimates with less than half the sample size required for the equivalent parallel-group RCT. It also identified individuals who did and did not respond to MPH, which is a feature difficult to achieve in a standard RCT. The study was registered with the Australian Clinical Trials Registry (12609000794202).
Polymorphism of the CYP3A5 gene and its effect on tacrolimus blood level.

OBJECTIVES
Tacrolimus is the cornerstone for immunosuppression in renal transplant and is metabolized by the cytochrome P 450 3A (CYP3A) subfamily of enzymes in the liver and small intestine. A polymorphism in intron 3 of the CYP3A5 gene affects the expression of this enzyme and tacrolimus trough blood levels. The purpose of this study was to identify the proportion of CYP3A5 gene polymorphisms in South Indian renal transplant patients and determine the effect of CYP3A5 gene polymorphisms on tacrolimus trough blood levels in patients with and without CYP3A5 expression.


MATERIALS AND METHODS
We included 25 adult patients who underwent renal transplant at Government Medical College, Trivandrum. All patients received tacrolimus (dose, 0.1 mg/kg/body weight, in 2 divided doses). Tacrolimus trough blood levels were determined on postoperative day 6. The CYP3A5 genotype analysis was performed by polymerase chain reaction amplification of target and detection by restriction fragment length polymorphism analysis.


RESULTS
The CYP3A5*1/*1 genotype was detected in 5 recipients (20%), *1/*3 genotype in 5 recipients (20%), and *3/*3 genotypes in 15 recipients (60%) of the total 25 graft recipients. Mean tacrolimus level in the CYP3A5*1/*1 group was 5.154 ng/mL (range, 4.42 to 6.5 ng/mL), CYP3A5*1/*3 group was 5.348 ng/mL (range, 3.1 to 9.87 ng/mL), and CYP3A5*3/*3 group was 9.483 ng/mL (range, 4.5 to14.1 ng/mL). Acute rejection episodes were significantly more frequent for CYP3A5*1/*1 homozygous patients (40%) than patients with CYP3A5*1/*3 (20%) or CYP3A5*3/*3 (13%) genotypes.


CONCLUSIONS
Most patients carried the mutant allele CYP3A5*3 (A6986G). Tacrolimus drug level correlated well with presence or absence of CYP3A5 polymorphisms. Acute rejection episodes were more frequent in expressors, and they may require higher doses of tacrolimus. Similarly, tacrolimus nephrotoxicity was more frequent in non-expressors. Therefore, CYP3A5 polymorphism analysis before renal transplant may help determine the optimal dose of tacrolimus in this population and prevent acute rejection episodes or tacrolimus toxicity.
Controlled clinical trial exploring the impact of a brief intervention for prevention of falls in an emergency department.

OBJECTIVE
To establish the effectiveness of a brief intervention to prevent falls in older patients presenting to the ED post-discharge.


METHODS
The present study is a prospective single-centre, quasi-randomised controlled clinical trial of a brief targeted educational intervention to prevent falls. The intervention group received brief scripted education and were advised of their percentage probability of falling in the next 6 months. The key message was to reinforce the importance of falls prevention strategies and the seriousness of falls.


RESULTS
A total of 412 over 65 years old were recruited; 63 (32.1%) patients in the intervention group and 67 (36.8%) in the control group reported falls in the 6 month follow up period (OR 0.81, 95% confidence interval [CI] 0.53-1.25, P = 0.34). No significant differences were noted for mortalities (P = 0.54), ED representations (P = 0.15) and medication changes (P = 0.17). Patients receiving intervention had less hospital admissions (P = 0.002) after adjustment for confounding variables. Intervention patients who presented with a fall had significant (P = 0.007) improvement in function at 6 months, whereas those not presenting with a fall experienced functional decline.


CONCLUSION
A brief intervention was associated with maintenance of function in fallers and reduced hospital admissions, without preventing falls post-discharge.
Improving penetration testing through static and dynamic analysis

Penetration testing is widely used to help ensure the security of web applications. Using penetration testing, testers discover vulnerabilities by simulating attacks on a target web application. To do this efficiently, testers rely on automated techniques that gather input vector information about the target web application and analyze the application’s responses to determine whether an attack was successful. Techniques for performing these steps are often incomplete, which can leave parts of the web application untested and vulnerabilities undiscovered. This paper proposes a new approach to penetration testing that addresses the limitations of current techniques. The approach incorporates two recently developed analysis techniques to improve input vector identification and detect when attacks have been successful against a web application. This paper compares the proposed approach against two popular penetration testing tools for a suite of web applications with known and unknown vulnerabilities. The evaluation results show that the proposed approach performs a more thorough penetration testing and leads to the discovery of more vulnerabilities than both the tools. Copyright q 2011 John Wiley & Sons, Ltd.
The Idea of a Strategist's Education

Abstract 
 
C. P. Snow observed, “the intellectual life of the whole of western society is increasingly split into two polar groups.” As he declared, on one side are the scientists, and on the other, “literary intellectuals.” Within strategic studies, one may compare this to the tensions between social scientist and historical approaches. His observation therefore provides insight into educating young strategists. This paper examines the evolution of the military and strategic studies discipline in an American context, contending the approach is not unique to Americans, but applies generally. Regarding such development, the author contends the role of military culture; the interaction of formal and informal reasoning; and the roles of history and the social sciences are crucial, concluding that a humanistic and scientifically informed interdisciplinary approach steeped by the thoughts of the military and strategic studies expert best prepares young strategists for service.