LLukas22/scidocs huggingface dataset:
Identification of Birds through DNA Barcodes

Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10x average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.
Representational Power of Restricted Boltzmann Machines and Deep Belief Networks

Deep belief networks (DBN) are generative neural network models with many layers of hidden explanatory factors, recently introduced by Hinton, Osindero, and Teh (2006) along with a greedy layer-wise unsupervised learning algorithm. The building block of a DBN is a probabilistic model called a restricted Boltzmann machine (RBM), used to represent one layer of the model. Restricted Boltzmann machines are interesting because inference is easy in them and because they have been successfully used as building blocks for training deeper models. We first prove that adding hidden units yields strictly improved modeling power, while a second theorem shows that RBMs are universal approximators of discrete distributions. We then study the question of whether DBNs with more layers are strictly more powerful in terms of representational power. This suggests a new and less greedy criterion for training RBMs within DBNs.
Botulinum toxin injection for hypertonicity of the upper extremity within 12 weeks after stroke: a randomized controlled trial.

BACKGROUND
Botulinum neurotoxin type A (BoNT-A) reduces upper-extremity poststroke spasticity when given 6 or more months after stroke. Effects on functional use of the arm and hand are less apparent.


OBJECTIVE
To determine the effect and safety of very early use of BoNT-A for patients with upper-limb spasticity.


METHODS
The Asia Botulinum Toxin-A Clinical Trial


DESIGN
ed for Early Post-stroke Spasticity (ABCDE-S; NCT00234546) was a multicenter, randomized, placebo-controlled trial conducted in patients recruited within 2 -12 weeks of first-ever stroke. Participants with a Modified Ashworth Scale (MAS) score of 1+ or above received BoNT-A (Dysport) 500 U or placebo to one or more wrist and elbow mover muscles, plus unstructured rehabilitation. The primary outcome was the MAS score in the most affected joint 4 weeks after first injection. Follow-up was 24 weeks.


RESULTS
A total of 163 patients were enrolled and assigned to placebo (n = 83) or BoNT-A (n = 80). Mean time since stroke was about 7 weeks. At 4 weeks postinjection, BoNT-A significantly improved MAS scores. Treatment effect-size estimates increased with higher baseline MAS scores from 0.45 (Q1) to 0.70 (Q3). MAS scores for all secondary end points improved with BoNT-A versus placebo at all time points (P < .0001, all visits). The Functional Motor Assessment Scale did not reveal clinically significant differences. No group differences in adverse events were found. Interpretation. BoNT-A 500 U can provide a sustained reduction in poststroke upper-limb spasticity when combined with rehabilitation in Asian patients who have mild-to-moderate hypertonicity and voluntary movement, within 2 -12 weeks of stroke. Functional use of the arm and hand was not affected.
New ZnSnO3-based varistor system

Semiconducting ceramics are widely used in electrical industries involving mobile communications, computers, signal processing, power transport, and control systems, because of their unique and useful electrical characteristics [1]. Varistors which are generally used to protect electronic circuits from voltage shock can sense and limit high transient voltage surges and can repeatedly endure such surges without being destroyed. The most important property of a varistor is its nonlinear voltage–current characteristic. It can be expressed by the equation I = K V α . The α coefficient gives the degree of nonlinearity and the constant K depends on the microstructure and is related to the electrical resistivity of the material. Commercial varistors used in protection systems are based on SiC or on ZnO. Varistors based on SiC have low nonlinearity coefficients [2–4] and ZnO varistors exhibit high nonlinear coefficients, but the degradation problem of ZnO varistors has not been resolved [5–7]. Therefore, the efforts to find new varistor materials have been ongoing. In 1983, N. Yumaka, M. Masuyama found that SrTiO3-based ceramics made by a two-step process had varistor characteristics [8]. In 1995, S. A. Pianaro found a new varistor material [4], (Co,Nb)-doped SnO2, which has only a single phase, rutile structure. In 2000, J. F. Wang found one oxide (Sb2O3)-doped TiO2 ceramic to have varistor behavior [9]. Following Wang, W. B. Su found, in 2002, another TiO2 varistor doped with only one oxide (WO3) [10]. In this work, we found a new varistor material, (Nb,Si)-doped ZnSnO3, and investigated the effects of SiO2 on the properties of the (Nb,Si)-doped ZnSnO3 varistor. The materials used were analytical grades of SnO2 (99.5%), Nb2O5 (99.5%), ZnO (99.5%), and SiO2 (90.0%). The compositions were SnO2 + ZnO + 0.2%Nb2O5 + x%SiO2 in molar terms, where x = 0, 0.25, 0.4, 0.5, 1.0. The varistors were prepared by conventional ceramic processing. The mixed raw chemicals were milled in a nylon kettle with ZrO2 balls and some distilled water, dried, mixed with 0.6% weight of PVA binder and pressed into disks 15 mm in diameter and 1.5 mm in thickness at 160 MPa. The disks were sintered at 1427 ◦C for an hour and cooled to room temperature after burning out the PVA binder at 650 ◦C. To measure the electrical properties, silver electrodes were made on both surfaces of the sintered disks. For microstructure characterization, the surfaces of the samples were observed by scanning electron microscopy (SEM) and the phases were analyzed by X-ray diffraction (XRD). For electrical characterization of current density versus applied electrical field, an I–V grapher (QT2) was used. The complex impedance dependent on frequency is measured using an Agilent 4294A impedance analyzer. According to the XRD analysis (Fig. 1), no apparent second phase was observed and SnO2 and ZnO should be synthesized according to the following reaction [11]:
Comparative Changes of Lipid Levels in Treatment-Naive, HIV-1-Infected Adults Treated with Dolutegravir vs. Efavirenz, Raltegravir, and Ritonavir-Boosted Darunavir-Based Regimens Over 48 Weeks

BACKGROUND AND OBJECTIVES
Long-term use of antiretroviral therapy (ART) to treat HIV infection has been associated with dyslipidemia and metabolic and cardiovascular complications. Available options for patients at risk of cardiovascular disease include antiretroviral drugs with improved lipid profiles. Dolutegravir is one of a new generation of HIV integrase inhibitors recently incorporated into the US Department of Health and Human Services, German, Spanish, and Italian HIV treatment guidelines as a preferred first-line third agent in combination with dual nucleoside reverse transcriptase inhibitor (NRTI) backbone therapies. To understand the lipid profile of dolutegravir in the context of combination ART, we analyzed the lipid outcomes at 48 weeks in ART-naive participants in four phase IIb-IIIb clinical trials.


METHODS
Variables included in this analysis were total cholesterol (TC), low-density lipoprotein (LDL) cholesterol (LDL-C), high-density lipoprotein (HDL) cholesterol (HDL-C), TC/HDL ratio, and triglycerides at baseline and week 48.


RESULTS
In a comparative analysis, dolutegravir demonstrated a broadly neutral effect on lipids versus efavirenz or ritonavir-boosted darunavir; in both comparisons, patients taking dolutegravir exhibited smaller increases in TC, LDL-C, and triglyceride levels. In comparison with raltegravir, dolutegravir exhibited a similar lipid profile, including small increases in TC, LDL-C, and triglyceride levels for both agents. In the pooled dolutegravir analysis, minimal increases in LDL-C and triglycerides were observed but mean values at 48 weeks remained below National Cholesterol Education Program target levels. HDL-C levels increased at 48 weeks, and the mean TC/HDL-C ratio was 0.6 at 48 weeks; these values are associated with a lower risk of cardiovascular disease.


CONCLUSIONS
Together, these data show that dolutegravir has a safer lipid profile in combination ART and provides an important treatment option for older patients who may have other risk factors for metabolic syndrome or cardiovascular disease.
Multiple-pronunciation lexical modeling in a speaker independent speech understanding system

One of the sources of difficulty in speech recognition and understanding is the variability due to alternate pronunciations of words. To address the issue we have investigated the use of multiple-pronunciation models (MPMs) in the decoding stage of a speaker-independent speech understanding system. In this paper we address three important issues regarding MPMs: (a) Model construction: How can MPMs be built from available data without human intervention? (b) Model embedding: How should MPM construction interact with the training of the sub-word unit models on which they are based? (c) Utility: Do they help in speech recognition? Automatic, data-driven MPM construction is accomplished using a structural HMM induction algorithm. The resulting MPMs are trained jointlywith a multi-layer perceptron functioningas a phonetic likelihood estimator. The experiments reported here demonstrate that MPMs can significantly improve speech recognition results over standard single pronunciation models.
Concurrent alcohol and tobacco treatment: Effect on daily process measures of alcohol relapse risk.

OBJECTIVE
The aim of this study was to compare the effects of alcohol treatment along with concurrent smoking treatment or delayed smoking treatment on process measures related to alcohol relapse risk.


METHOD
Alcohol dependent smokers (N = 151) who were enrolled in an intensive outpatient alcohol treatment program and were interested in smoking cessation were randomized to a concurrent smoking cessation (CSC) intervention or to a waiting list for delayed smoking cessation (DSC) intervention scheduled to begin 3 months later. Daily assessments of relapse process measures were obtained using an Interactive Voice Response (IVR) system for 12 weeks after the onset of smoking treatment in the CSC condition, and before beginning smoking treatment in the DSC condition. Smoking outcomes were assessed at 2 and 13 weeks after starting treatment.


RESULTS
Seven-day carbon monoxide (CO) verified smoking abstinence in the CSC condition was 50.5% at 2 weeks and 19.0% at 13 weeks compared with 2.2% abstinence at 2 weeks and 0% abstinence at 13 weeks for those in the DSC condition. Drinking outcomes were not significantly different for CSC versus DSC treatment conditions. On daily IVR assessments, CSC participants had significantly lower positive alcohol outcome expectancies relative to DSC participants. Multilevel modeling (MLM) analyses of within-person effects across the 12 weeks of daily monitoring showed that daily smoking abstinence was significantly associated with same day reports of lower alcohol consumption, lower urge to drink, lower negative affect, lower positive alcohol outcome expectancies, greater alcohol abstinence self-efficacy, greater alcohol abstinence readiness to change, and greater perceived self-control demands.


CONCLUSIONS
Analyses of process measures provide support for recommending smoking intervention concurrent with intensive outpatient alcohol treatment. (PsycINFO Database Record
Sphenoid wing meningiomas: Surgical strategies and evaluation of prognostic factors influencing clinical outcomes

OBJECTIVE
To study microsurgical technique and prognostic factors influencing clinical outcomes in a series of 53 patients with sphenoid wing meningiomas (SWMs).


MATERIALS AND METHODS
The clinical materials of 53 patients with sphenoid wing meningiomas treated microsurgically between January 2008 and January 2012 were analyzed retrospectively. Follow-up period ranged from 6 to 62 months (median, 34 months). Clinical outcomes including postoperative quality of life and recurrence rate were evaluated. Univariate and multivariate statistical analysis were performed among factors that might influence postoperative quality of life.


RESULTS
In our group, the mean age of patients was 49 years. Mean tumor size was 3.9cm. Total tumor resection was achieved in 38 cases (71.7%), subtotal in 10 cases (18.9%) and partial resection in 5 cases (9.4%). Within the follow-up period, ten patients (18.9%) had recurrence and three patients (5.7%) died. In univariate analysis, we found the postoperative Karnofshky Performance Score (KPS) improvement was determined by various factors, including extent of tumor resection, peritumoral edema, tumor blood supply, size, adhesion, encasement and preoperative KPS. However, multivariate analysis showed that complete resection, rich blood supply, adhesion to adjacent structure, encasement of neurovascular were independent predictive factors for worse postoperative KPS.


CONCLUSIONS
With the improved requirement of postoperative quality of life in patients, intentional incomplete resection should be considered as an acceptable treatment option. Multivariate analysis confirmed that incomplete resection, poor blood supply, lack of adhesion or encasement of adjacent structure were independent predictive factors for favorable postoperative quality of life. An individual treatment strategy could help improved quality of life.
A New Characterization of Some Alternating and Symmetric Groups (II)

We suppose that p = 2α3β +1, where α ≥ 1, β ≥ 0, and p ≥ 7 is a prime number. Then we prove that the simple groups An, where n = p,p+1, or p+2, and finite groups Sn, where n = p,p+1, are also uniquely determined by their order components. As corollaries of these results, the validity of a conjecture of J. G. Thompson and a conjecture of Shi and Bi (1990) both on An, where n= p,p+1, or p+2, is obtained. Also we generalize these conjectures for the groups Sn, where n= p,p+1.
Clinical characteristics of patients with acute pulmonary embolism stratified according to their presenting syndromes.

PURPOSE
The purpose of this investigation is to determine the characteristics of the history, physical examination, chest radiograph, and ECG, and the ventilation/perfusion (V/Q) lung scan probability in patients with pulmonary embolism (PE) stratified according to their presenting syndrome.


BACKGROUND
In considering a possible diagnosis of acute PE, it is helpful to consider the patient in terms of the presenting syndrome (pulmonary infarction, isolated dyspnea, or circulatory collapse). In assessing the possibility of acute PE, it would be more useful to know the detailed characteristics of the particular syndrome rather than the clinical characteristics of all patients with PE.


METHODS
Patients described in this investigation participated in the national collaborative trial of the Prospective Investigation of Pulmonary Embolism Diagnosis (PIOPED). All had PE diagnosed by pulmonary angiography. None had prior cardiopulmonary disease. All examinations and laboratory tests were obtained within 24 h of the pulmonary angiogram and most were within 12 h of the pulmonary angiogram.


RESULTS
Among patients with the pulmonary infarction syndrome, 14 of 119 (12%) had neither dyspnea nor tachypnea. Some patients with circulatory collapse did not have dyspnea, tachypnea, or pleuritic pain. A normal ECG was more prevalent among patients with pulmonary infarction syndrome, 45 of 97 (46%), than among patients with isolated dyspnea syndrome, 2 of 21 (10%) (p<0.01). A PaO2 >80 mm Hg was also more prevalent in patients with the pulmonary infarction syndrome, 27 of 99 (27%), than in patients with the isolated dyspnea syndrome, 2 of 19 (11%). A high-probability V/Q lung scan was less prevalent among the pulmonary infarction group, 38 of 119 (32%), than the isolated dyspnea group, 20 of 31 (65%) (p<0.001).


CONCLUSION
Many of the findings in the various syndromes of PE can be understood in terms of the severity of PE as it increases from mild with the pulmonary infarction syndrome to moderate with the isolated dyspnea syndrome to severe with circulatory collapse. The prevalence of various clinical and laboratory characteristics of patients with the syndrome of pulmonary infarction, isolated dyspnea, or circulatory collapse may give clues to the diagnosis or suggest characteristics that may reduce the likelihood of inadvertently discarding the diagnosis of PE.
Colorectal cancer screening : How to help patients comply Strongly recommending that a patient be screened and addressing commonly held fears are among the 7 ways you may be able to improve compliance

Purpose: We elicited patient opinions about how physicians can improve communications about colorectal cancer (CRC) screening. methods: We recruited 15 patients, ages 50 years and older, from an urban family medicine teaching clinic. All patients in the initial pool of candidates had been seen at the university of Arkansas for Medical Sciences Family Medical Center within the past 12 months. The recruits participated in 1 of 3 focus groups to discuss how to enhance the rate of CRC screening. Participants watched a videotape that described the different approaches to CRC screening. We then asked them to comment on how patients could be encouraged to undergo CRC screening. results: using a qualitative analysis of focus group data, we determined the most common reasons participants had not undergone CRC screening: fear, lack of information, and failure of the physician to strongly recommend CRC screening. Participants offered 7 recommendations for how physicians could address their concerns. Participants emphasized the importance of strong physician endorsement of screening, of frank and informative dialogue about patient’s concerns, and of using educational materials to supplement personal advice. conclusion: A physician’s recommendation for screening is the most powerful motivator in patients’ decisions. However, other sources of information such as videotapes, written materials, and even endorsement of CRC screening by the clinic’s office staff can help patients decide to undergo screening. z Focus group recommendations Page E5 Copy right ® Dow den H ealth Med ia For p erson al us e onl y For mass reproduction, content licensing and permissions contact Dowden Health Media.
Variation in detection of ductal carcinoma in situ during screening mammography: a survey within the International Cancer Screening Network.

BACKGROUND
There is concern about detection of ductal carcinoma in situ (DCIS) in screening mammography. DCIS accounts for a substantial proportion of screen-detected lesions but its effect on breast cancer mortality is debated. The International Cancer Screening Network conducted a comparative analysis to determine variation in DCIS detection.


PATIENTS AND METHODS
Data were collected during 2004-2008 on number of screening examinations, detected breast cancers, DCIS cases and Globocan 2008 breast cancer incidence rates derived from national or regional cancer registers. We calculated screen-detection rates for breast cancers and DCIS.


RESULTS
Data were obtained from 15 screening settings in 12 countries; 7,176,050 screening examinations; 29,605 breast cancers and 5324 DCIS cases. The ratio between highest and lowest breast cancer incidence was 2.88 (95% confidence interval (CI) 2.76-3.00); 2.97 (95% CI 2.51-3.51) for detection of breast cancer; and 3.49 (95% CI 2.70-4.51) for detection of DCIS.


CONCLUSIONS
Considerable international variation was found in DCIS detection. This variation could not be fully explained by variation in incidence nor in breast cancer detection rates. It suggests the potential for wide discrepancies in management of DCIS resulting in overtreatment of indolent DCIS or undertreatment of potentially curable disease. Comprehensive cancer registration is needed to monitor DCIS detection. Efforts to understand discrepancies and standardise management may improve care.
Removing Shadows From Images using Retinex

The Retinex Theory first introduced by Edwin Land forty years ago has been widely used for a range of applications. It was first introduced as a model of our own visual processing but has since been used to perform a range of image processing tasks including illuminant correction, dynamic range compression, and gamut mapping. In this paper we show how the theory can be extended to perform yet another image processing task: that of removing shadows from images. Our method is founded on a simple modification to the original, path based retinex computation such that we incorporate information about the location of shadow edges in an image. We demonstrate that when the location of shadow edges is known the algorithm is able to remove shadows effectively. We also set forth a method for the automatic location of shadow edges which makes use of a 1-d illumination invariant image proposed in previous work [1]. In this case the location of shadow edges is imperfect but we show that even so, the algorithm does a good job of removing the shadows.
Biosynthesis, asymmetric synthesis, and pharmacology, including cellular targets, of the pyrrole-2-aminoimidazole marine alkaloids.

The pyrrole-2-aminoimidazole (P-2-AI) alkaloids are a growing family of marine alkaloids, now numbering well over 150 members, with high topographical and biological information content. Their intriguing structural complexity, rich and compact stereochemical content, high N to C ratio (~1 : 2), and increasingly studied biological activities are attracting a growing number of researchers from numerous disciplines world-wide. This review surveys advances in this area with a focus on the structural diversity, biosynthetic hypotheses with increasing, but still rare, verifying experimental studies, asymmetric syntheses, and biological studies, including cellular target receptor isolation studies, of this stimulating and exciting alkaloid family.
Introduction to third international summit on software engineering education (SSEE III: bridging the university/industry gap

Innovative University/Industry interactions are examined in this open event with the aim of providing inputs to an international project that is being funded through the United Kingdom's Teaching Fellowship Scheme. These inputs will support the first stage of the project which is concerned with gaining knowledge of industrial Software Engineering practices and the development of a framework that can be used in the classification and evaluation of such practices.