LLukas22/scidocs huggingface dataset:
An SVM-based system for predicting protein subnuclear localizations

The large gap between the number of protein sequences in databases and the number of functionally characterized proteins calls for the development of a fast computational tool for the prediction of subnuclear and subcellular localizations generally applicable to protein sequences. The information on localization may reveal the molecular function of novel proteins, in addition to providing insight on the biological pathways in which they function. The bulk of past work has been focused on protein subcellular localizations. Furthermore, no specific tool has been dedicated to prediction at the subnuclear level, despite its high importance. In order to design a suitable predictive system, the extraction of subtle sequence signals that can discriminate among proteins with different subnuclear localizations is the key. New kernel functions used in a support vector machine (SVM) learning model are introduced for the measurement of sequence similarity. The k-peptide vectors are first mapped by a matrix of high-scored pairs of k-peptides which are measured by BLOSUM62 scores. The kernels, measuring the similarity for sequences, are then defined on the mapped vectors. By combining these new encoding methods, a multi-class classification system for the prediction of protein subnuclear localizations is established for the first time. The performance of the system is evaluated with a set of proteins collected in the Nuclear Protein Database (NPD). The overall accuracy of prediction for 6 localizations is about 50% (vs. random prediction 16.7%) for single localization proteins in the leave-one-out cross-validation; and 65% for an independent set of multi-localization proteins. This integrated system can be accessed at http://array.bioengr.uic.edu/subnuclear.htm . The integrated system benefits from the combination of predictions from several SVMs based on selected encoding methods. Finally, the predictive power of the system is expected to improve as more proteins with known subnuclear localizations become available.
Signature Hole Blast Vibration Control - Twenty Years Hence and Beyond

In the early 1980s, a method for controlling blast vibrations other than by modifying the Scaled Distance came into use. Research studies had indicated that blast vibration could be simulated by detonating a signature hole with the vibration monitored at critical locations, and then using a computer to superpose the waveforms with varying delays. By choosing delay times that create destructive interference at frequencies that are favored by the local geology, the “ringing” vibration that excites structural elements in houses and annoys neighbors could be reduced. At that time, pyrotechnic detonator firing times were less accurate than they are today, and electronic detonators were only in the early stages of development. Since accurate delay times are crucial to effective vibration control, scatter in the firing times limited the method severely. As time has gone on, both the tools and the techniques have improved. Electronic detonators now have scatter less than a millisecond. Computers, of course have increased in speed phenomenally, and software keeps pace. In light of all these changes, many researchers and practitioners have extended and modified the original work, finding both limitations and new potential. This paper will review the history of the method, the assumptions made, the impact of increased detonator accuracy, and successes and failures of the method. Implications for future control methods, for both surface and underground blasting, will be discussed, as well as using vibrations to assess the effectiveness of the explosives. Copyright © 2008 International Society of Explosives Engineers 2008G Volume 2 Signature Hole Blast Vibration Control Twenty Years Hence and Beyond 1 of 12 Introduction For as long as the ISEE (and its predecessor SEE) has been around, blast-generated vibration and airblast have captured a lot of attention. Long before the Society’s inception, research and development addressed the fundamental problem of controlling the wasted explosive energy that goes into vibration. Early efforts focused on determining what “level” of vibration would cause annoyance or damage, and what methods could be used to assure a blaster that he or she could work effectively without worrying about neighbor problems. Simple solutions to engineering problems are generally preferred; to reach a simple solution, it helps to first simplify the problem. In the US, research by the Bureau of Mines from the 1940s and later developed simple methods to classify and address the problem of damaging vibrations. As we all know, peak particle velocity (PPV) was chosen as a descriptor that could be related to damage occurrences. Research elsewhere came to similar conclusions, though the details varied. Regulations followed from recommendations, which in turn followed from the research. The research showed that by knowing distance D and charge weight per delay W, (Scaled Distance W D / = ), one could reasonably predict the resultant vibration through a power law relation:
Robust discrete optimization and network flows

Abstract. We propose an approach to address data uncertainty for discrete optimization and network flow problems that allows controlling the degree of conservatism of the solution, and is computationally tractable both practically and theoretically. In particular, when both the cost coefficients and the data in the constraints of an integer programming problem are subject to uncertainty, we propose a robust integer programming problem of moderately larger size that allows controlling the degree of conservatism of the solution in terms of probabilistic bounds on constraint violation. When only the cost coefficients are subject to uncertainty and the problem is a 0 − 1 discrete optimization problem on n variables, then we solve the robust counterpart by solving at most n + 1 instances of the original problem. Thus, the robust counterpart of a polynomially solvable 0 − 1 discrete optimization problem remains polynomially solvable. In particular, robust matching, spanning tree, shortest path, matroid intersection, etc. are polynomially solvable. We also show that the robust counterpart of an NP -hard α-approximable 0 − 1 discrete optimization problem, remains α-approximable. Finally, we propose an algorithm for robust network flows that solves the robust counterpart by solving a polynomial number of nominal minimum cost flow problems in a modified network.
Causes of blindness and visual impairment in Nigeria: the Nigeria national blindness and visual impairment survey.

PURPOSE
Determine causes of blindness and visual impairment among adults aged >or=40 years.


METHODS
Multistage, stratified, cluster random sampling with probability proportional to size procedures were used to identify a nationally representative sample of 15,027 persons >or=40 years of age. Distance vision was measured with a reduced logMAR tumbling E-chart. Clinical examination included a basic eye examination of all subjects and a more detailed examination of those who had presenting vision <6/12 in either eye. Cause for vision loss was assigned to all subjects with presenting vision <6/12 in any eye.


RESULTS
Of the 15,122 persons aged >or=40 years who were enumerated, 13,599 (89.9%) were examined. In 84%, blindness was avoidable. Uncorrected refractive errors were responsible for 57.1% of moderate (<6/18-6/60) visual impairment. Cataract (43%) was the commonest cause of blindness (<3/60). Prevalence of cataract-related blindness was 1.8% (95% CI: 1.57-2.05) and glaucoma-related blindness was 0.7% (95% CI: 0.55-0.88). Increasing age was associated with increasing prevalence of all major blinding conditions. Females, illiterate persons, and residents in the North East geopolitical zone had significantly higher odds of cataract-induced blindness and severe visual impairment.


CONCLUSIONS
The high proportion of avoidable blindness, with half being attributable to cataract alone and uncorrected refractive errors being responsible for 57% of moderate visual impairment, means that appropriate and accessible refraction and surgical services need to be provided. If priority attention is not given, the number of blind and severely visually impaired adults in Nigeria will increase by >40% over the next decade.
Beyond concern - a privacy-trust-behavioral intention model of electronic commerce

Despite the recent economic downturn in the Internet and telecommunication sectors, electronic commerce (EC) will continue to grow and corporate Web sites will remain an important communication channel. However, legitimate concerns regarding privacy and trust remain potential obstacles to growth and important issues to both individuals and organizations. This study proposed and tested a theoretical model that considers an individual’s perceptions of privacy and how it relates to his or her behavioral intention to make an online transaction. An experiment that included over 200 subjects was conducted using two EC sites that differed only by the privacy dimensions of their notice, access, choice, and security. The results of this study suggested strong support for the model. # 2003 Published by Elsevier B.V.
Password Mistyping in Two-Factor-Authenticated Key Exchange

We study the problem of Key Exchange (KE), where authentication is two-factor and based on both electronically stored long keys and human-supplied credentials (passwords or biometrics). The latter credential has low entropy and may be adversarily mistyped. Our main contribution is the first formal treatment of mistyping in this setting. Ensuring security in presence of mistyping is subtle. We show mistypingrelated limitations of previous KE definitions and constructions (of Boyen et al. [7, 6, 10] and Kolesnikov and Rackoff [16]). We concentrate on the practical two-factor authenticated KE setting where servers exchange keys with clients, who use short passwords (memorized) and long cryptographic keys (stored on a card). Our work is thus a natural generalization of Halevi-Krawczyk [15] and Kolesnikov-Rackoff [16]. We discuss the challenges that arise due to mistyping. We propose the first KE definitions in this setting, and formally discuss their guarantees. We present efficient KE protocols and prove their security.
The Sensitivity of Topic Coherence Evaluation to Topic Cardinality

When evaluating the quality of topics generated by a topic model, the convention is to score topic coherence — either manually or automatically — using the top-N topic words. This hyper-parameter N , or the cardinality of the topic, is often overlooked and selected arbitrarily. In this paper, we investigate the impact of this cardinality hyper-parameter on topic coherence evaluation. For two automatic topic coherence methodologies, we observe that the correlation with human ratings decreases systematically as the cardinality increases. More interestingly, we find that performance can be improved if the system scores and human ratings are aggregated over several topic cardinalities before computing the correlation. In contrast to the standard practice of using a fixed value of N (e.g. N = 5 or N = 10), our results suggest that calculating topic coherence over several different cardinalities and averaging results in a substantially more stable and robust evaluation. We release the code and the datasets used in this research, for reproducibility.1
NT-pro-BNP, but not C-reactive protein, is predictive of atrial fibrillation in patients undergoing coronary artery bypass surgery.

OBJECTIVE
Atrial fibrillation (AF) remains the most commonly observed complication following myocardial revascularisation surgery. We aimed to evaluate the clinical utility of N-terminal fragment of the brain natriuretic peptide (NT-pro-BNP), troponin T, transcoronary lactate gradient (TCLG) and C-reactive protein (CRP) as predictors of AF in patients undergoing isolated coronary artery bypass surgery (CABG).


METHODS
This study included 215 consecutive patients in sinus rhythm (SR) undergoing elective CABG between May 2007 and May 2008. The patients were grouped according to their respective postoperative rhythm into SR and AF groups. The data are presented as mean values+/-standard deviation, or medians with quartiles.


RESULTS
Fifty-five patients developed AF (26%). The preoperative NT-pro-BNP values were 273+/-347 and 469+/-629 pg ml(-1) in the SR and AF groups, respectively (p<0.0001). The postoperative NT-pro-BNP values were 3110+/-3600 pg ml(-1) in the SR and 4625+/-5640 pg ml(-1) in the AF groups (p=0.027). The transcoronary lactate gradient rose from the pre-cardiopulmonary bypass values to those observed 5 min after revascularisation in both groups (-0.05+/-0.37 to 0.39+/-0.46 mmol l(-1) (p<0.0001) in the SR group and -0.01+/-0.27 to 0.43+/-0.46 mmol l(-1) (p<0.0001) in the AF group). The CRP values increased from 6+/-13 to 163+/-88 mg l(-1) (p<0.0001) in the SR group, and from 6+/-16 to 163+/-104 mg l(-1) (p<0.0001) in the AF group. The dynamics of TCLG and CRP did not differ between the groups (p=0.71, p=0.44, respectively). The troponin T values on postoperative day 1 were significantly higher in the AF than the SR group (0.86 (0.49-2.1) ng ml(-1) vs 0.67 (0.37-1.16) ng ml(-1), p=0.046). The duration of cardiopulmonary bypass (CPB) was 85+/-24 min in the SR and 93+/-30 min in the AF group (p=0.05). Patients who developed AF were older (66+/-7 years vs 60+/-9 years, p<0.0001) and had a higher EuroSCORE (3.9+/-2.7 vs 2.9+/-2.2, p=0.009). Multivariate analysis identified age (p=0.0043), preoperative NT-pro-BNP (p=0.019) and duration of CPB (p=0.035) as independent predictors of AF.


CONCLUSIONS
Preoperative and postoperative NT-pro-BNP as well as TnT values were significantly higher in patients who subsequently developed AF. TCLG and CRP were not useful in identifying patients at higher risk for AF. Multivariate analysis identified age, preoperative NT-pro-BNP and duration of CPB as independent correlates of AF.
The relationship between clinical pharmacokinetics of aripiprazole and CYP2D6 genetic polymorphism: effects of CYP enzyme inhibition by coadministration of paroxetine or fluvoxamine

To investigate the effects of coadministration of paroxetine or fluvoxamine on the pharmacokinetics of aripiprazole in healthy adult Japanese with different CYP2D6 genotypes. Fourteen CYP2D6 extensive metabolizer (EM) and 14 CYP2D6 intermediate metabolizer (IM) subjects were coadministered a single oral dose of aripiprazole 3 mg after steady-state plasma concentrations of the SSRIs paroxetine (20 mg/day) or fluvoxamine (100 mg/day) were reached by repeated oral doses for 6–7 days. The pharmacokinetics of aripiprazole with and without coadministration of SSRIs were compared according to CYP2D6 genotypes. Coadministration of paroxetine, a potent CYP2D6 inhibitor, decreased systemic clearance (CL/F) of aripiprazole by 58 and 23% in CYP2D6 EMs and IMs, respectively, demonstrating that the percentage inhibition of CYP2D6 activity by coadministration of paroxetine was apparently greater in CYP2D6 EMs than in IMs. Coadministration of fluvoxamine, a less potent CYP3A4 inhibitor, decreased the CL/F of aripiprazole by 39% in CYP2D6 EMs and 40% in IMs, indicating the same inhibitory effect on CYP enzymes, regardless of the CYP2D6 genotype. Percent contribution of CYP2D6 to total CL/F (CYP2D6 plus CYP3A4) of aripiprazole estimated as a reduced percentage of CL/F by CYP enzyme inhibition was 62% for CYP2D6 EMs and 24% for IMs in paroxetine coadministration, and 40% for CYP2D6 EMs and 18% for IMs in fluvoxamine coadministration. There were marked differences in the degree of influence of paroxetine coadministration on the pharmacokinetics of aripiprazole between CYP2D6 EMs and IMs, but no apparent differences were found between two CYP2D6 genotypes in fluvoxamine coadministration. Aripiprazole can be used safely in combination with SSRIs that have a CYP enzyme-inhibitory action.
A survey on passive-blind image forgery by doctor method detection

With the huge increasing use of digital photography, and the advent of high-performance commodity hardware and the presence of low-cost image editing softwares over the past few years, finding a credible method to detect digital imagepsilas authenticity and getting the result that which method the tampered image was applied to becomes a very valuable topic. In this paper, associating with the common forge methods, we propose the process of passive-blue detection of digital imagepsilas forging method, and then review the latest development of the passive-blind detection of image forging method, mainly include the detection of copy.move forgery, detection of blur forgery and detection of re-sample forgery.
A Maximum Power Point Tracking of PV System by Scaling Fuzzy Control

Abstract—A scaling fuzzy logic control (FLC) maximum power point tracking (MPPT) algorithm is suggested in this paper. The scaling FLC algorithm is modified from FLC algorithm to achieve MPPT in spite of single or 10 solar PV cells. Here, our solar system is composed of solar penal, boost dc/dc converter and MPPT controller, and then we use OrCAD Pspice for the system simulation. The simulated cases focus on the steady-state response, the dynamic response to the variation of the solar-cell current or load resistance. The simulated results are illustrated to show the efficacy of the proposed algorithm.
Men's voices and women's choices

I investigated the relationship between male human vocal characteristics and female judgements about the speaker. Thirty-four males were recorded uttering five vowels and measures were taken, from power spectrums, of the first five harmonic frequencies, overall peak frequency and formant frequencies (emphasized, resonance, frequencies within the vowel). Male body measures were also taken (age, weight, height, and hip and shoulder width) and the men were asked whether they had chest hair. The recordings were then played to female judges, who were asked to rate the males' attractiveness, age, weight and height, and to estimate the muscularity of the speaker and whether he had a hairy chest. Men with voices in which there were closely spaced, low-frequency harmonics were judged as being more attractive, older and heavier, more likely to have a hairy chest and of a more muscular body type. There was no relationship between any vocal and body characteristic. The judges' estimates were incorrect except for weight. They showed extremely strong agreement on all judgements. The results imply that there could be sexual selection through female choice for male vocal characteristics, deeper voices being preferred. However, the function of the preference is unclear given that the estimates were generally incorrect. Copyright 2000 The Association for the Study of Animal Behaviour.
Semantic classifications for detection of verb metaphors

We investigate the effectiveness of semantic generalizations/classifications for capturing the regularities of the behavior of verbs in terms of their metaphoricity. Starting from orthographic word unigrams, we experiment with various ways of defining semantic classes for verbs (grammatical, resource-based, distributional) and measure the effectiveness of these classes for classifying all verbs in a running text as metaphor or non metaphor.
The need for an industrial engineering software library

Abstract There is a real need for an Industrial Engineering Software Library. This need has been specified by previous studies and quantified by a widely distributed questionnaire. This article briefly outlines the work that has been accomplished so far towards the establishment of a clearinghouse to which industrial engineers can turn for available software. The question remaining is: How tto support and implement this project which we believe would be of great value to industrial engineers and others interested in quantitative techniques for decision making?
Women, men, and rheumatoid arthritis: analyses of disease activity, disease characteristics, and treatments in the QUEST-RA Study

INTRODUCTION
Gender as a predictor of outcomes of rheumatoid arthritis (RA) has evoked considerable interest over the decades. Historically, there is no consensus whether RA is worse in females or males. Recent reports suggest that females are less likely than males to achieve remission. Therefore, we aimed to study possible associations of gender and disease activity, disease characteristics, and treatments of RA in a large multinational cross-sectional cohort of patients with RA called Quantitative Standard Monitoring of Patients with RA (QUEST-RA).


METHODS
The cohort includes clinical and questionnaire data from patients who were seen in usual care, including 6,004 patients at 70 sites in 25 countries as of April 2008. Gender differences were analyzed for American College of Rheumatology Core Data Set measures of disease activity, DAS28 (disease activity score using 28 joint counts), fatigue, the presence of rheumatoid factor, nodules and erosions, and the current use of prednisone, methotrexate, and biologic agents.


RESULTS
Women had poorer scores than men in all Core Data Set measures. The mean values for females and males were swollen joint count-28 (SJC28) of 4.5 versus 3.8, tender joint count-28 of 6.9 versus 5.4, erythrocyte sedimentation rate of 30 versus 26, Health Assessment Questionnaire of 1.1 versus 0.8, visual analog scales for physician global estimate of 3.0 versus 2.5, pain of 4.3 versus 3.6, patient global status of 4.2 versus 3.7, DAS28 of 4.3 versus 3.8, and fatigue of 4.6 versus 3.7 (P < 0.001). However, effect sizes were small-medium and smallest (0.13) for SJC28. Among patients who had no or minimal disease activity (0 to 1) on SJC28, women had statistically significantly higher mean values compared with men in all other disease activity measures (P < 0.001) and met DAS28 remission less often than men. Rheumatoid factor was equally prevalent among genders. Men had nodules more often than women. Women had erosions more often than men, but the statistical significance was marginal. Similar proportions of females and males were taking different therapies.


CONCLUSIONS
In this large multinational cohort, RA disease activity measures appear to be worse in women than in men. However, most of the gender differences in RA disease activity may originate from the measures of disease activity rather than from RA disease activity itself.