LLukas22/scidocs huggingface dataset:
Inparanoid: a comprehensive database of eukaryotic orthologs

The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.
Operator Valued Hardy Spaces

We give a systematic study on the Hardy spaces of functions with values in the non-commutative L-spaces associated with a semifinite von Neumann algebra M. This is motivated by the works on matrix valued Harmonic Analysis (operator weighted norm inequalities, operator Hilbert transform), and on the other hand, by the recent development on the non-commutative martingale inequalities. Our non-commutative Hardy spaces are defined by the non-commutative Lusin integral function. The main results of this paper include: (i) The analogue in our setting of the classical Fefferman duality theorem between H and BMO. (ii) The atomic decomposition of our non-commutative H. (iii) The equivalence between the norms of the non-commutative Hardy spaces and of the non-commutative L-spaces (1 < p <∞). (iv) The non-commutative Hardy-Littlewood maximal inequality. (v) A description of BMO as an intersection of two dyadic BMO. (vi) The interpolation results on these Hardy spaces. 1
Temporal analysis of clusters of supermarket customers: conventional versus interval set approach

Temporal data mining is the application of data mining techniques to data that takes the time dimension into account. This paper studies changes in cluster characteristics of supermarket customers over a 24 week period. Such an analysis can be useful for formulating marketing strategies. Marketing managers may want to focus on specific groups of customers. Therefore they may need to understand the migrations of the customers from one group to another group. The marketing strategies may depend on the desirability of these cluster migrations. The temporal analysis presented here is based on conventional and modified Kohonen self organizing maps (SOM). The modified Kohonen SOM creates interval set representations of clusters using properties of rough sets. A description of an experimental design for temporal cluster migration studies 0020-0255/$ see front matter 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.ins.2004.12.007 * Corresponding author. Tel.: +1 902 420 5798; fax: +1 902 420 5035. E-mail address: pawan.lingras@smu.ca (P. Lingras). 216 P. Lingras et al. / Information Sciences 172 (2005) 215–240 including, data cleaning, data abstraction, data segmentation, and data sorting, is provided. The paper compares conventional and non-conventional (interval set) clustering techniques, as well as temporal and non-temporal analysis of customer loyalty. The interval set clustering is shown to provide an interesting dimension to such a temporal analysis. 2005 Elsevier Inc. All rights reserved.
Effect of relaxation-breathing training on anxiety and asthma signs/symptoms of children with moderate-to-severe asthma: a randomized controlled trial.

BACKGROUND
Emotional stress triggers and exacerbates asthma in children. Reducing anxiety in adults by relaxation-breathing techniques has been shown in clinical trials to produce good asthma outcomes. However, more evidence is needed on using this intervention with asthmatic children.


OBJECTIVE
To evaluate the effectiveness of combined self-management and relaxation-breathing training for children with moderate-to-severe asthma compared to self-management-only training.


DESIGN
Two-group experimental design.


SETTING AND PARTICIPANTS
Pediatric outpatient clinic of a medical center in central Taiwan. Participants were 48 children, ages 6-14 years, with moderate-to-severe asthma and their parents.


METHODS
Participants were randomly assigned to an experimental or comparison group and matched by gender, age, and asthma severity. Both groups participated in an asthma self-management program. Children in the experimental group were also given 30 min of training in a relaxation-breathing technique and a CD for home practice. Data on anxiety levels, self-perceived health status, asthma signs/symptoms, peak expiratory flow rate, and medication use were collected at baseline and at the end of the 12-week intervention. Effects of group, time, and group-time interaction were analyzed using the Mixed Model in SPSS (12.0).


RESULTS
Anxiety (especially state anxiety) was significantly lower for children in the experimental group than in the comparison group. Differences in the other four physiological variables were also noted between pre- and post-intervention, but these changes did not differ significantly between groups.


CONCLUSIONS
A combination of self-management and relaxation-breathing training can reduce anxiety, thus improving asthmatic children's health. These results can serve as an evidence base for psychological nursing practice with asthmatic children.
Automated Robotic Monitoring and Inspection of Steel Structures and Bridges

This paper presents visual and 3D structure inspection for steel structures and bridges using a developed climbing robot. The robot can move freely on a steel surface, carry sensors, collect data and then send to the ground station in real-time for monitoring as well as further processing. Steel surface image stitching and 3D map building are conducted to provide a current condition of the structure. Also, a computer vision-based method is implemented to detect surface defects on stitched images. The effectiveness of the climbing robot’s inspection is tested in multiple circumstances to ensure strong steel adhesion and successful data collection. The detection method was also successfully evaluated on various test images, where steel cracks could be automatically identified, without the requirement of some heuristic reasoning.
Topic Modeling based on Keywords and Context

Current topic models often suffer from discovering topics not matching human intuition, unnatural switching of topics within documents and high computational demands. We address these shortcomings by proposing a topic model and an inference algorithm based on automatically identifying characteristic keywords for topics.
ROS and Rosbridge: Roboticists out of the loop

The advent of ROS, the Robot Operating System, has finally made it possible to implement and use state-of-the-art navigation and manipulation algorithms on widely-available, inexpensive standard robot platforms. With the addition of the Rosbridge application programming interface, interface designers and applications programmers can create robot interfaces and behaviors without venturing into the specialized world of robotics engineers. This tutorial introduces ROS and Rosbridge, and shows how quickly and easily these tools can be used to design and conduct large-scale online HRI experiments, access algorithms for autonomous robot behavior, and leverage the huge ecosystem of general-purpose web-based and application-oriented software engineering for robotics and HRI research. Tutorial attendees will learn the basics of autonomous and teleoperated navigation and manipulation, as well as interface design for online interaction with robots. During the tutorial they will design and write their own remote presence application, as well as develop strategies for incorporating autonomy and dealing with data collection.
Dynamic Load-Balancing via a Genetic Algorithm

We produce a GA scheduling routine, which with often relatively low cost finds well-balanced schedules. Incoming tasks (of varying durations) accumulate, then are periodically scheduled, in small batches, to the available processors. Two important priorities for our scheduling work are that loads on the processors are well balanced, and that scheduling per seremains cheap in comparison to the actual productive work of the processors. We also include experimental results, exploring a variety of distributions of task durations, which show that our scheduler consistently produces well-balanced schedules, and quite often does so at relatively low cost.
Semi-supervised Outlier Detection using Generative And Adversary Framework

In many outlier detection tasks, only training data belonging to one class, i.e., the positive class, is available. The task is then to predict a new data point as belonging either to the positive class or to the negative class, in which case the data point is considered an outlier. For this task, we propose a novel corrupted Generative Adversarial Network (CorGAN). In the adversarial process of training CorGAN, the Generator generates outlier samples for the negative class, and the Discriminator is trained to distinguish the positive training data from the generated negative data. The proposed framework is evaluated using an image dataset and a real-world network intrusion dataset. Our outlier-detection method achieves state-of-the-art performance on both tasks. Keywords—Outlier detection, generative adversary networks, semi-supervised learning.
Low-firing, temperature stable and improved microwave dielectric properties of ZnO TiO2Nb2O5 composite ceramics

Abstract This article presents low-firing, low-loss and temperature stable ZnO TiO 2 Nb 2 O 5 microwave dielectric composite ceramics with the assistance of lithium borosilicate (LBS) and zinc borosilicate (ZBS) glass frits. There is a liquid phase (eutectic mixture) generated by LBS (ZBS) glass, and solid particles could be wetted and dissolved. Therefore, the migrations and rearrangements of particles could be performed. Besides, compared with ceramics undoped with glass frits, lower activation energies (E a ) of ceramics doped with LBS and ZBS glass suggest that the low-temperature sintering behavior is easier to carry out. The results indicated that LBS and ZBS glass both are effective sintering aids to accelerate the sintering process and improve the microwave dielectric properties of composite ceramics by controlling the phase compositions under low temperature. Combination great properties of ZnO TiO 2 Nb 2 O 5 ceramics were obtained when sintered at 900 °C for 4 h: e r  = 36.7, Q × f = 20,000 GHz, τ f  = 7 ppm/ o C.
Pregnancy Outcomes after Treatment for Cervical Cancer Precursor Lesions: An Observational Study

OBJECTIVE
To examine whether surgical procedures involving the uterine cervix were associated with pregnancy outcomes, including preterm birth, low birth weight, cesarean delivery and pregnancy loss.


DESIGN
Population-based observational study nested in retrospective matched cohort.


SETTING
Kaiser Permanente Northwest integrated health plan in Oregon/Washington, U.S.A.


POPULATION
Female health plan members age 14-53 years with documented pregnancies from 1998-2009. Women with prior excisional and ablative cervical surgical procedures (N = 322) were compared to women unexposed to cervical procedures (N = 4,307) and, separately, to those having undergone only diagnostic/biopsy procedures (N = 847).


METHODS
Using log-linear regression models, we examined risk of adverse pregnancy outcomes in relation to prior excisional or ablative cervical surgical procedures. We stratified excisional procedures by excision thickness. We evaluated for confounding by age, body mass index, race, smoking history, previous preterm birth, and parity.


RESULTS
We found a positive association between excisional treatment > = 1.0 cm and the outcomes preterm birth and low birth weight (preterm birth unadjusted risk ratio [RR] = 2.15, 95% confidence interval [CI] 1.16-3.98 for excisions ≥1.0 cm compared to unexposed women), particularly in women who delivered within one year of surgery (RR = 3.26, 95% CI 1.41-7.53). There was no clear association between excisional treatment and cesarean delivery, and treated women did not have a substantially higher risk of dysfunctional labor. Ablative treatment was not associated with low birth weight, preterm birth, or cesarean delivery but was associated with pregnancy loss (RR = 1.43, 95% CI 1.05-1.93 vs. unexposed women). Analyses using the diagnostic procedures comparison group produced similar results.


CONCLUSION
Women with > = 1.0 cm excisional treatment had elevated risk of preterm birth and low birth weight when compared to unexposed women and women with cervical diagnostic procedures. This suggests that increased risk derives from the treatment itself, not from other characteristics. The observed association between pregnancy loss and ablative surgical treatment requires further investigation.
MYO5B and bile salt export pump contribute to cholestatic liver disorder in microvillous inclusion disease.

UNLABELLED
Microvillous inclusion disease (MVID) is a congenital disorder of the enterocyte related to mutations in the MYO5B gene, leading to intractable diarrhea often necessitating intestinal transplantation (ITx). Among our cohort of 28 MVID patients, 8 developed a cholestatic liver disease akin to progressive familial intrahepatic cholestasis (PFIC). Our aim was to investigate the mechanisms by which MYO5B mutations affect hepatic biliary function and lead to cholestasis in MVID patients. Clinical and biological features and outcome were reviewed. Pretransplant liver biopsies were analyzed by immunostaining and electron microscopy. Cholestasis occurred before (n = 5) or after (n = 3) ITx and was characterized by intermittent jaundice, intractable pruritus, increased serum bile acid (BA) levels, and normal gamma-glutamyl transpeptidase activity. Liver histology showed canalicular cholestasis, mild-to-moderate fibrosis, and ultrastructural abnormalities of bile canaliculi. Portal fibrosis progressed in 5 patients. No mutation in ABCB11/BSEP or ATP8B1/FIC1 genes were identified. Immunohistochemical studies demonstrated abnormal cytoplasmic distribution of MYO5B, RAB11A, and BSEP in hepatocytes. Interruption of enterohepatic BA cycling after partial external biliary diversion or graft removal proved the most effective to ensure long-term remission.


CONCLUSION
MVID patients are at risk of developing a PFIC-like liver disease that may hamper outcome after ITx. Our results suggest that cholestasis in MVID patients results from (1) impairment of the MYO5B/RAB11A apical recycling endosome pathway in hepatocytes, (2) altered targeting of BSEP to the canalicular membrane, and (3) increased ileal BA absorption. Because cholestasis worsens after ITx, indication of a combined liver ITx should be discussed in MVID patients with severe cholestasis. Future studies will need to address more specifically the effect of MYO5B dysfunction in BA homeostasis.
Cobalt, nickel, copper and zinc complexes with 1,3-diphenyl-1H-pyrazole-4-carboxaldehyde Schiff bases: antimicrobial, spectroscopic, thermal and fluorescence studies.

Two new Schiff bases of 1,3-diphenyl-1H-pyrazole-4-carboxaldehyde and 4-amino-5-mercapto-3-methyl/H-1,2,4-triazole [HL(1-2)] and their Cobalt, Nickel, Copper and Zinc complexes have been synthesized and characterized by elemental analyses, spectral (UV-vis, IR, (1)H NMR, Fluorescence) studies, thermal techniques and magnetic measurements. A square planar geometry for Cu(II) and octahedral geometry for Co(II), Ni(II) and Zn(II) complexes have been proposed. In order to evaluate the biological activity of Schiff bases and to assess the role of metal ion on biological activity, the pyrazole Schiff bases and their metal complexes have been studied in vitro antibacterial against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa and antifungal against Aspergillus niger, and Aspergillus flavus. In most of the cases higher activity was exhibited upon coordination with metal ions.
Operational semantics of UML activity diagram: An application in project management

With its recent adoption by the International Organization for Standardization, we foresee that UML will be systematically used for object-oriented modeling in industry. UML activity diagrams have been typically used to model software and business processes. Due to its semi-formal semantics and high complexity, its advanced constructs such as expansion regions, interruptible regions, object nodes, time events, and compound activities are rarely used in practice. There has been significant work on formalizing UML activity diagrams in terms of its semantic domain: Petri net. However, none address the recent advanced constructs it offers. In this paper, we define the semantics of UML activity diagram using a rule-based model transformation. Verification and validation of the UML activity diagram model is then achieved by simulating and analyzing the Petri net model. We illustrate our technique by using an extension of UML activity diagram to facilitate project management tasks such as scheduling, cost estimation, and resource allocation.
A Review on the Effects of Soccer Small-Sided Games

Over the last years there has been a substantial growth in research related to specific training methods in soccer with a strong emphasis on the effects of small-sided games. The increase of research in this topic is coincident with the increase of popularity obtained by specific soccer conditioning, which involves training players to deal with soccer match situations. Given the limited time available for fitness training in soccer, the effectiveness of small-sided games as a conditioning stimulus needs to be optimized to allow players to compete at the highest level. Available studies indicate that physiological responses (e.g. heart rate, blood lactate concentration and rating of perceived exertion), tactical and technical skill requirements can be modified during small-sided games by altering factors such as the number of players, the size of the pitch, the rules of the game, and coach encouragement. However, because of the lack of consistency in small-sided games design, player fitness, age, ability, level of coach encouragement, and playing rules in each of these studies, it is difficult to make accurate conclusions on the influence of each of these factors separately.
Project Selection by Using a Fuzzy TOPSIS Technique

Selection of a project among a set of possible alternatives is a difficult task that the decision maker (DM) has to face. In this paper, by using a fuzzy TOPSIS technique we propose a new method for a project selection problem. After reviewing four common methods of comparing investment alternatives (net present value, rate of return, benefit cost analysis and payback period) we use them as criteria in a TOPSIS technique. First we calculate the weight of each criterion by a pairwise comparison and then we utilize the improved TOPSIS assessment for the project selection. Keywords—Fuzzy Theory, Pairwise Comparison, Project Selection, TOPSIS Technique.
The negative predictive value of ultrasound-guided 14-gauge core needle biopsy of breast masses: a validation study of 339 cases

PURPOSE
To determine the negative predictive value of sonographically guided 14-gauge core needle biopsy of breast masses, with detailed analysis of any false-negative cases.


MATERIALS AND METHODS
We reviewed 669 cases of sonographically guided 14-gauge core needle biopsies that had benign pathologic findings. Given a benign pathology on core biopsy, true-negatives had either benign pathology on surgical excision or at least 2 years of stable imaging and/or clinical follow-up; false-negatives had malignant histology on surgical excision.


RESULTS
Follow-up was available for 339 breast lesions; 117 were confirmed to be benign via surgical excision, and 220 were stable after 2 years or more of imaging or clinical follow-up (mean follow-up time 33.1 months, range 24-64 months). The negative predictive value was determined to be 99.4%. There were 2 false-negative cases, giving a false-negative rate of 0.1%. There was no delay in diagnosis in either case because the radiologist noted discordance between imaging and core biopsy pathology, and recommended surgical excision despite the benign core biopsy pathology.


CONCLUSIONS
Sonographically guided 14-gauge core needle biopsy provides a high negative predictive value in assessing breast lesions. Radiologic/pathologic correlation should be performed to avoid delay in the diagnosis of carcinoma.
Elton Mayo and Carl Rogers: A Tale of Two Techniques.

Abstract This article examines the simultaneous appearance of nonauthoritarian interviewing and nondirective counseling, two highly similar methods introduced by two different people, Elton Mayo and Carl Rogers. The similarities and differences between the methods and their developers are evaluated against the historical context in which they appear.
BackTap: robust four-point tapping on the back of an off-the-shelf smartphone

We present BackTap, an interaction technique that extends the input modality of a smartphone to add four distinct tap locations on the back case of a smartphone. The BackTap interaction can be used eyes-free with the phone in a user's pocket, purse, or armband while walking, or while holding the phone with two hands so as not to occlude the screen with the fingers. We employ three common built-in sensors on the smartphone (microphone, gyroscope, and accelerometer) and feature a lightweight heuristic implementation. In an evaluation with eleven participants and three usage conditions, users were able to tap four distinct points with 92% to 96% accuracy.
Development of micromanipulator and haptic interface for networked micromanipulation

In this paper, telemicromanipulation systems with haptic feedback, which are connected through network, are proposed. It is based on scaled bilateral teleoperation systems between different structures. These systems are composed of an original 6 degree of freedom (DOF) parallel link manipulator to carry out micromanipulation and a 6-DOF haptic interface with force feedback. A parallel mechanism is adopted as a slave micromanipulator because of its good features of accuracy and stiffness. The system modeling and control of the parallel manipulator system are conducted. Parallel manipulator feasibility as micromanipulator, positioning accuracy and device control characteristics are investigated. The haptic master interface is developed for micromanipulation systems. System modeling and model reference adaptive controller are conducted to compensate friction force, which spoils free motion performance and force response isotropy of the haptic interface. These systems aim to make the micromanipulation more productive constructing a better human interface through the microenvironment force and scale expansion.
UNDERSTANDING FLAVOR MIXING IN QUANTUM FIELD THEORY

We report on recent results showing that a rich non-perturbative vacuum structure is associated with flavor mixing in Quantum Field Theory. 
We treat explicitly the case of mixing among three generations of Dirac fermions. 
Exact oscillation formulas are presented exhibiting new features with respect to the usual ones. CP and T violation are also discussed.