LLukas22/scidocs huggingface dataset:
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

UNLABELLED
We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves.


AVAILABILITY AND IMPLEMENTATION
Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at http://joey711.github.io/shiny-phyloseq/.
Evolutionary games on graphs

Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner’s Dilemma, the Rock–Scissors–Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games. © 2007 Published by Elsevier B.V. PACS: 02.50.Le; 89.65.−s; 87.23.Kg; 05.65.+b; 87.23.Ge
A Broadband Dual-Polarized Omnidirectional Antenna Based on Orthogonal Dipoles

A broadband dual-polarized omnidirectional antenna is investigated. The proposed dually polarized antenna consists of four vertical dipoles for vertical polarization (VP) and four horizontal dipoles for horizontal polarization (HP), which are uniformly printed around a dielectric cylindrical barrel for omnidirectional radiation. Two broadband feeding networks are employed to excite the vertical dipoles and the horizontal dipoles, respectively. The dual-polarized omnidirectional antenna achieves a bandwidth of ~ 30% (1.7-2.3 GHz) with an isolation of about 25 dB. The gain variations in the horizontal plane are less than 0.5 dB for VP and 1.5 dB for HP. The cross-polarization levels of VP and HP in horizontal plane are around -20 dB. The proposed antenna has a great potential for mobile communications.
Identifying spam in the iOS app store

Popular apps on the Apple iOS App Store can generate millions of dollars in profit and collect valuable personal user information. Fraudulent reviews could deceive users into downloading potentially harmful spam apps or unfairly ignoring apps that are victims of review spam. Thus, automatically identifying spam in the App Store is an important problem. This paper aims to introduce and characterize novel datasets acquired through crawling the iOS App Store, compare a baseline Decision Tree model with a novel Latent Class graphical model for classification of app spam, and analyze preliminary results for clustering reviews.
Transparent Conducting Oxides—An Up-To-Date Overview

Transparent conducting oxides (TCOs) are electrical conductive materials with comparably low absorption of electromagnetic waves within the visible region of the spectrum. They are usually prepared with thin film technologies and used in opto-electrical apparatus such as solar cells, displays, opto-electrical interfaces and circuitries. Here, based on a modern database-system, aspects of up-to-date material selections and applications for transparent conducting oxides are sketched, and references for detailed information are given. As n-type TCOs are of special importance for thin film solar cell production, indium-tin oxide (ITO) and the reasonably priced aluminum-doped zinc oxide (ZnO:Al), are discussed with view on preparation, characterization and special occurrences. For completion, the recently frequently mentioned typical p-type delafossite TCOs are described as well, providing a variety of references, as a detailed discussion is not reasonable within an overview publication.
Hardware complications in scoliosis surgery

Background: Scoliosis surgery has undergone a dramatic evolution over the past 20 years with the advent of new surgical techniques and sophisticated instrumentation. Surgeons have realized scoliosis is a complex multiplanar deformity that requires thorough knowledge of spinal anatomy and pathophysiology in order to manage patients afflicted by it. Nonoperative modalities such as bracing and casting still play roles in the treatment of scoliosis; however, it is the operative treatment that has revolutionized the treatment of this deformity that affects millions worldwide. As part of the evolution of scoliosis surgery, newer implants have resulted in improved outcomes with respect to deformity correction, reliability of fixation, and paucity of complications. Each technique and implant has its own set of unique complications, and the surgeon must appreciate these when planning surgery. Materials and methods: Various surgical techniques and types of instrumentation typically used in scoliosis surgery are briefly discussed. Though scoliosis surgery is associated with a wide variety of complications, only those that directly involve the hardware are discussed. The current literature is reviewed and several illustrative cases of patients treated for scoliosis at the Connecticut Children's Medical Center and the Newington Children's Hospital in Connecticut are briefly presented. Conclusion: Spine surgeons and radiologists should be familiar with the different types of instrumentation in the treatment of scoliosis. Furthermore, they should recognize the clinical and roentgenographic signs of hardware failure as part of prompt and effective treatment of such complications.
Effects of mometasone furoate administered via a dry powder inhaler once daily in the evening on nocturnal lung function and sleep parameters in patients with moderate persistent asthma: a randomized, double-blind, placebo-controlled pilot study.

BACKGROUND AND OBJECTIVE
Nocturnal symptoms are common in asthma patients and have the potential for considerable clinical effects due to a lack of sleep and persistent daytime symptoms of somnolence and activity impairment. The primary objective of this investigation was to determine the effect of a 14-day course of once-daily evening administration of mometasone furoate 400 microg administered via a dry powder inhaler (MF-DPI 400 microg qd pm) on the overnight decline in pulmonary function observed in patients with nocturnal asthma.


METHODS
Eligible enrollees were between the ages of 18 and 60 years and had established mild to moderate asthma, with an improvement in forced expiratory volume in 1 second (FEV(1)) of >15% after administration of inhaled salbutamol (albuterol) 200 microg. All enrolled patients had a history of nocturnal asthma. Enrollees were randomized to receive MF-DPI 400 microg qd pm or placebo administered between 6 pm and 8 pm for 14 days. The primary outcome evaluated in the study was reduction in nocturnal decline in evening (8 pm) to morning (6 am) FEV(1) values. Secondary outcomes included reduction in nocturnal decline in evening to morning peak expiratory flow rate (PEFR), polysomnographic indices of sleep, and psychometric indices (Nocturnal Rhinoconjunctivitis Quality of Life Questionnaire [NRQLQ], 36-item Short Form of the Medical Outcomes Survey [SF-36], and Asthma Quality of Life Questionnaire [AQLQ]).


RESULTS
A total of 20 patients were randomized and completed all phases of the study. No significant differences were observed between treatment groups in the primary outcome of nocturnal decline in FEV(1) from pretreatment to end of treatment. Likewise, there was no significant difference between treatment groups in polysomnographic indices of sleep or quality-of-life assessments. However, there was a trend toward improvement in the activity scale of the AQLQ assessment in the MF-DPI 400 microg qd pm treatment group.


CONCLUSION
No significant treatment effect on nocturnal pulmonary function, sleep indices or quality of life was observed with 14-day administration of MF-DPI 400 microg qd pm. These findings are limited by the small sample size and the short treatment period evaluated. Future studies are warranted to study the effects of MF-DPI therapy in patients with nocturnal asthma.
Revascularization of an immature permanent tooth with periradicular abscess after luxation.

An immature permanent mandibular central incisor with periapical involvement in a 7-year-old boy was treated to promote revascularization. The tooth suffered from acute apical periodontitis after periodontal treatment by a general practitioner. An access cavity was prepared in the tooth and the cavity was left open until the next visit to achieve drainage through the canal. The root canal was not mechanically cleaned during the treatment period, but was irrigated with hydrogen peroxide and sodium hypochlorite. Calcium hydroxide compound was used for disinfection. At the fifth visit vital tissue appeared in the canal near the apical region, and calcium hydroxide compound was placed in contact with the soft tissue in the root canal. The access cavity was sealed with glass-ionomer cement followed by an adhesive composite resin filling. Radiographic examination 30 months after the initial treatment confirmed closure of the apex and thickening of the root wall. The case was observed for up to 13 years and root development was confirmed.
Digital multicarrier-transmission of audio signals over mobile radio channels

This paper presents a systematic overview over different concepts of multicarrier-transmission under the specific aspect of mobile radio transmission. It will be shown that under realistic multipath channel conditions the postulation of ideal bandwidth efficiency has t o be given up. As a consequence sub-optimum multicarrier concepts are regarded and mutually compared under the aspects of intersymbol interference and adjacent channel interference. A specific impuls shaping concept based on time and frequency concentrated impulses (Gaussian shaping) turns out as an appropriate solution since hereby the adjacent channel interference can be largely suppressed at the expense of a small increase in intersymbol inference. The performance of the different multicarrier concepts is illustrated by various simulation results under mobile radio channel conditions.
Functional outcome after repair of proximal hamstring avulsions.

BACKGROUND
Rupture of the proximal origin of the hamstrings leads to pain, weakness, and a debilitating decrease in physical activity. Repair of these injuries should be based on the expectation that these deficits can be addressed. The goal of this study was to objectively evaluate the efficacy of repair of proximal hamstring avulsions.


METHODS
Thirty-four patients were identified retrospectively to have a complete rupture of the proximal origin of the hamstrings based on the presence of a bowstring sign and the results of magnetic resonance imaging (MRI).Patients were contacted for follow-up evaluation to fill out a subjective questionnaire, to undergo functional testing, and to undergo isokinetic testing on a Cybex dynamometer. Twenty-three patients were evaluated.


RESULTS
There were nine acute and fourteen chronic repairs, and the average period of follow-up was 43.3 months. Twenty-one of twenty-three patients reported returning to activity at an average of 95% of their pre-injury activity level at an average of 9.8 months. Eighteen patients reported excellent results; four, good results; and one, fair results. Hamstring strength was an average of 93% and 90% of that in the uninvolved limb at 240° per second and 180° per second, respectively. The hamstrings-to-quadriceps ratio was 56% for 240° per second and 48% at 180° per second. Hamstring endurance was an average of 81% and 91% of the nonoperative limb at 240° per second and 180° per second, respectively. Postoperative quadriceps strength and endurance were positively correlated with return to pre-injury level of activity (r = 0.6, p < 0.05; and r = 0.6, p < 0.05) and negatively correlated with time to return to sport (r = -0.5, p < 0.05; and r = -0.5, p < 0.05). There was no significant effect associated with age or time from injury.


CONCLUSIONS
Repair of a symptomatic and displaced ruptured proximal hamstring tendon yields good subjective and objective functional results with minimal complications. Overall, patients are satisfied with surgical repair and experience return of functional activity with minimal postoperative weakness.
The outcomes of glucose abnormalities in pre-diabetic chronic hepatitis C patients receiving peginterferon plus ribavirin therapy.

BACKGROUND/AIMS
Pre-diabetes is a risk factor for type 2 diabetes mellitus (DM) development. This study aimed to elucidate the impact of treatment response on sequential changes in glucose abnormalities in pre-diabetic chronic hepatitis C (CHC) patients.


METHODS
Chronic Hepatitis C patients with a baseline haemoglobin A1C (A1C) range 5.7-6.4% who achieved 80/80/80 adherence were prospectively recruited. All patients received current peginterferon-based recommendations. The primary outcome measurement was their A1C level at the end of follow-up (EOF). The interaction between variants of the IL28B gene and outcomes of glucose metabolism was also measured.


RESULTS
A total of 181 consecutive CHC patients were enrolled. The mean A1C at EOF was 5.82 ± 0.41%, which was significantly lower than the baseline level (5.93 ± 0.21%, P < 0.001). At EOF, 63 (34.8%) patients became normoglycaemic, whereas 10 (5.5%) patients developed DM. The sustained virological response (SVR) rates of 63 normoglycaemics, 108 pre-diabetics and 10 diabetic patients at the EOF were 92.1%, 84.3% and 50% respectively (normoglycaemics vs. diabetics P = 0.003; pre-diabetics vs. diabetics P = 0.02). Achievement of an SVR was the only predictive factor associated with normoglycaemia development at EOF by multivariate logistic regression analysis (Odds ratio = 2.6, P = 0.04). The prevalence of the interleukin 28B rs8099917 TT variant in patients who developed DM (70.0%) at EOF tended to be lower than that in patients with pre-diabetics (87.0%) or normoglycaemics (92.1%).


CONCLUSION
Successful eradication of HCV improves glucose abnormalities in pre-diabetic CHC patients.
On Hilbert's gravitational repulsion (A historical Note)

In the literature on general relativity no mention is made of a remarkable result contained in Hilbert's memoir "Die Grundlagen der Physik", according to which in particular instances and in particular regions the Einsteinian gravity exerts a repulsive action. We give here a concise illustration of this peculiar phenomenon.
Plate tectonics and the Himalayas

Abstract The Himalayas, commonly taken as the type example of continent-continent collision, have developed in two stages. The first stage involves convergence of the northward-drifting Indian subcontinent with a proto-Tibetan landmass during Late Cretaceous and Palaeocene, with collision before Middle Eocene. The second stage involves formation of a fundamental crustal fracture within the Indian block during Late Eocene and Oligocene, and underthrusting of the Indian subcontinent along this fracture from Miocene to Recent. The present elevated Himalayan mountain chain is not a direct result of the continent-continent collision, but of uplift during underthrusting along the deep crustal fracture.
Islam 101: Understanding the Religion and Therapy Implications.

How familiar are you with the religion and cultural aspects of Islam and with Muslim clients? As a psychologist, you likely will work with a Muslim client, given the growing number of Muslims in America. Yet very little psychological research or literature discusses Muslim clients or their experiences. This article provides some foundational information psychologists will need to work effectively with Muslim clients. An overview of the Muslim American community, including cultural values, gender role expectations, behavioral prescriptions, and immigration issues relevant in counseling and therapy, is provided. A case example illustrates how clinicians can effectively incorporate cultural aspects of Islam in their work in order to be culturally competent when working with Muslim clients.
Rationale, design and objectives of ARegPKD, a European ARPKD registry study

BACKGROUND
Autosomal recessive polycystic kidney disease (ARPKD) is a rare but frequently severe disorder that is typically characterized by cystic kidneys and congenital hepatic fibrosis but displays pronounced phenotypic heterogeneity. ARPKD is among the most important causes for pediatric end stage renal disease and a leading reason for liver-, kidney- or combined liver kidney transplantation in childhood. The underlying pathophysiology, the mechanisms resulting in the observed clinical heterogeneity and the long-term clinical evolution of patients remain poorly understood. Current treatment approaches continue to be largely symptomatic and opinion-based even in most-advanced medical centers. While large clinical trials for the frequent and mostly adult onset autosomal dominant polycystic kidney diseases have recently been conducted, therapeutic initiatives for ARPKD are facing the challenge of small and clinically variable cohorts for which reliable end points are hard to establish.


METHODS/DESIGN
ARegPKD is an international, mostly European, observational study to deeply phenotype ARPKD patients in a pro- and retrospective fashion. This registry study is conducted with the support of the German Society for Pediatric Nephrology (GPN) and the European Study Consortium for Chronic Kidney Disorders Affecting Pediatric Patients (ESCAPE Network). ARegPKD clinically characterizes long-term ARPKD courses by a web-based approach that uses detailed basic data questionnaires in combination with yearly follow-up visits. Clinical data collection is accompanied by associated biobanking and reference histology, thus setting roots for future translational research.


DISCUSSION
The novel registry study ARegPKD aims to characterize miscellaneous subcohorts and to compare the applied treatment options in a large cohort of deeply characterized patients. ARegPKD will thus provide evidence base for clinical treatment decisions and contribute to the pathophysiological understanding of this severe inherited disorder.
Hybrid prediction model for Type-2 diabetic patients

A wide range of computational methods and tools for data analysis are available. In this study we took advantage of those available technological advancements to develop prediction models for the prediction of a Type-2 Diabetic Patient. We aim to investigate how the diabetes incidents are affected by patients’ characteristics and measurements. Efficient predictive modeling is required for medical researchers and practitioners. This study proposes Hybrid Prediction Model (HPM) which uses Simple K-means clustering algorithm aimed at validating chosen class label of given data (incorrectly classified instances are removed, i.e. pattern extracted from original data) and subsequently applying the classification algorithm to the result set. C4.5 algorithm is used to build the final classifier model by using the k-fold cross-validation method. The Pima Indians diabetes data was obtained from the University of California at Irvine (UCI) machine learning repository datasets. A wide range of different classification methods have been applied previously by various researchers in order to find the best performing algorithm on this dataset. The accuracies achieved have been in the range of 59.4–84.05%. However the proposed HPM obtained a classification accuracy of 92.38%. In order to evaluate the performance of the proposed method, sensitivity and specificity performance measures that are used commonly in medical classification studies were used. 2010 Elsevier Ltd. All rights reserved.
Synthetic face generation under various operational conditions in video surveillance

In still-to-video face recognition (FR), the faces captured with surveillance cameras are matched against reference stills of target individuals enrolled to the system. FR is a challenging problem in video surveillance due to uncontrolled capture conditions (variations in pose, expression, illumination, blur, scale, etc.), and the limited number of reference stills to model target individuals. This paper introduces a new approach to generate multiple synthetic face images per reference still based on camera-specific capture conditions to deal with illumination variations. For each reference still, a diverse set of faces from non-target individuals appearing in the camera viewpoint are selected based on luminance and contrast distortion. These face images are then decomposed into detail layer and large scale layer using an edge-preserving image decomposition to obtain their illumination dependent component. Finally, the large scale layers of these images are morphed with each reference still image to generate multiple synthetic reference stills that incorporate illumination and contrast conditions. Experimental results obtained with the ChokePoint dataset reveal that these synthetic faces produce an enhanced face model. As the number of synthetic faces grows, the proposed approach provides a higher level of accuracy and robustness across a range of capture conditions.
Association with litter size of new polymorphisms on ESR1 and ESR2 genes in a Chinese-European pig line

The objective of this study was to search for polymorphisms in the coding region of the estrogen receptors 1 and 2 (ESR1 and ESR2 )and to analyze the effects of these variants and the well known intronic ESR1 Pvu II polymorphism on litter size in a Chinese-European pig line. We identified five silent single nucleotide polymorphisms (SNP) in the ESR1 cDNA: c.669T > C (exon 3), c.1227C > T (exon 5), c.1452C > T (exon 7), c.1665T > C and c.1755A > G (exon 8). One pair of these SNP (c.1665T > C and c.1755A > G) co-segregated in the analyzed line, and the SNP c.669T > C showed the same segregation pattern as the Pvu II polymorphism. These polymorphisms were tested in this study, although the c.1452C > T SNP within exon 7 was not analyzed due to its low informativeness. In the ESR2 cDNA, one missense SNP was found within exon 5, which caused an amino acid substitution in the coded protein: "c.949G > A (p.Val317Met)" and was tested on sow litter size. Information on 1622 litter records from 408 genotyped sows was analyzed to determine whether these SNP influenced the total number of piglets born (TNB) or the number of born alive (NBA). The polymorphisms ESR1: [Pvu II; c.669T > C], ESR1: [c.1665T > C; c.1755A > G] and ESR2: c.949G > A showed no statistically significant association with litter size. However, the ESR1: c.1227T allele was significantly associated with TNB. The additive substitution effect was estimated to be 0.40 piglets born per litter (P < 0.03), and no dominance effects were observed. This SNP could be useful in assisted selection for litter size in some pig lines, as a new genetic marker in linkage disequilibrium with the causative mutation.