bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression
Authors: Stupnikov Alexey , O’Reilly Paul G. , McInerney Caitriona E. , Roddy Aideen C. , Dunne Philip D. , Gilmore Alan , Ellis Hayley P. , Flannery Tom , Healy Estelle , McIntosh Stuart A. , Savage Kienan , Kurian Kathreena M. , Emmert-Streib Frank , Prise Kevin M. , Salto-Tellez Manuel , McArt Darragh G. 
Published: September 2018

Purpose Gene expression profiling can uncover biologic mechanisms underlying disease and is important in drug development. RNA sequencing (RNA-seq) is routinely used to assess gene expression, but costs remain high. Sample multiplexing reduces RNA-seq costs; however, multiplexed samples have lower cDNA sequencing depth, which can hinder accurate differential gene expression detection. The impact of sequencing depth alteration on RNA-seq–based downstream analyses such as gene expression connectivity mapping is not known, where this method is used to identify potential therapeutic compounds for repurposing. Methods In this study, published RNA-seq profiles from patients with brain tumor (glioma) were assembled into two disease progression gene signature contrasts for astrocytoma. Available treatments for glioma have limited effectiveness, rendering this a disease of poor clinical outcome. Gene signatures were subsampled to simulate sequencing alterations and analyzed in connectivity mapping to investigate target compound robustness. Results Data loss to gene signatures led to the loss, gain, and consistent identification of significant connections. The most accurate gene signature contrast with consistent patient gene expression profiles was more resilient to data loss and identified robust target compounds. Target compounds lost included candidate compounds of potential clinical utility in glioma (eg, suramin, dasatinib). Lost connections may have been linked to low-abundance genes in the gene signature that closely characterized the disease phenotype. Consistently identified connections may have been related to highly expressed abundant genes that were ever-present in gene signatures, despite data reductions. Potential noise surrounding findings included false-positive connections that were gained as a result of gene signature modification with data loss. Conclusion Findings highlight the necessity for gene signature accuracy for connectivity mapping, which should improve the clinical utility of future target compound discoveries.
Safety Outcomes During Pediatric GH Therapy: Final Results From the Prospective GeNeSIS Observational Program
Authors: Child Christopher J , Zimmermann Alan G , Chrousos George P , Cummings Elisabeth , Deal Cheri L , Hasegawa Tomonobu , Jia Nan , Lawrence Sarah , Linglart Agnès , Loche Sandro , Maghnie Mohamad , Pérez Sánchez Jacobo , Polak Michel , Predieri Barbara , Richter-Unruh Annette , Rosenfeld Ron G , Yeste Diego , Yorifuji Tohru , Blum Werner F 
Published: September 2018

Abstract

Context
Safety concerns have been raised regarding premature mortality, diabetes, neoplasia, and cerebrovascular disease in association with GH therapy.

Objective
To assess incidence of key safety outcomes.

Design
Prospective, multinational, observational study (1999 to 2015).

Setting
A total of 22,311 GH-treated children from 827 investigative sites in 30 countries.

Patients
Children with growth disorders.

Interventions
GH treatment.

Main outcome measures
Standardized mortality ratio (SMR) and standardized incidence ratio (SIR) with 95% CIs for mortality, diabetes, and primary cancer using general population registries.

Results
Predominant short stature diagnoses were GH deficiency (63%), idiopathic short stature (13%), and Turner syndrome (8%), with mean ± SD follow-up of 4.2 ± 3.2 years (∼92,000 person-years [PY]). Forty-two deaths occurred in patients with follow-up, with an SMR (95% CI) of 0.61 (0.44, 0.82); the SMR was elevated for patients with cancer-related organic GH deficiency [5.87 (3.21, 9.85)]. Based on 18 cases, type 2 diabetes mellitus (T2DM) risk was elevated [SIR: 3.77 (2.24, 5.96)], but 72% had risk factors. In patients without cancer history, 14 primary cancers were observed [SIR: 0.71 (0.39, 1.20)]. Second neoplasms occurred in 31 of 622 cancer survivors [5.0%; 10.7 (7.5, 15.2) cases/1000 PY] and intracranial tumor recurrences in 67 of 823 tumor survivors [8.1%; 16.9 (13.3, 21.5) cases/1000 PY]. All three hemorrhagic stroke cases had risk factors.

Conclusions
GeNeSIS (Genetics and Neuroendocrinology of Short Stature International Study) data support the favorable safety profile of pediatric GH treatment. Overall risk of death or primary cancer was not elevated in GH-treated children, and no hemorrhagic strokes occurred in patients without risk factors. T2DM incidence was elevated compared with the general population, but most cases had diabetes risk factors.
Bi-plane and single plane angiography: a study to compare contrast usage and radiation doses for adult cardiac patients in diagnostic studies
Authors: Smith Keith , Crowhurst James , Walters Darren , Starkey Deborah 
Published: September 2018

Objective:
This study compares the performance of bi-plane coronary angiography against single plane angiography in terms of the volume of contrast used (ml) and the total dose–area product (DAP) (μGym2) to the patient measured directly via flat panel detectors.

Methods:
A total of 5176 adult diagnostic cardiac angiograms from a hospital in Brisbane, Australia were retrospectively studied. Patients with aortograms, iliac or femoral artery imaging, and stenting or graft interventions were excluded. Student’s t-tests were used to compare means, and confounding variables were compared using multivariate regression. This quantified the effects of bi-plane system use holding constant other factors (e.g.) body mass index (BMI), age, room, sex, number of digital acquisitions and fluoro time.

Results:
Bi-plane imaging had an average difference in mean contrast use of −15.1 ml [15.5% 95% confidence interval (CI) (–13.2, –17.0) p&lt;0.001], multivariate regression demonstrated a −27.0 ml reduction in contrast use [28% 95% CI (–29.0, –24.83) p&lt;0.0001] when the significant effects of fluoro time, number of digital acquisitions, BMI and sex were held constant. Bi-plane imaging had an average difference in mean DAP of + 887.1 μGym2 [23% 95% CI (+1110.7, +663.4) p &lt; 0.001], whilst multivariate regression found a +628.3 Gym2 increase in DAP [16% 95% CI (+467.5, +789.3) p&lt;0.001] when the significant effects of fluoro time, number of digital acquisitions, BMI and sex were held constant.

Conclusion:
These results demonstrate that bi-plane imaging uses less contrast media than single-plane imaging for coronary angiography at the expense of more radiation. Bi-plane imaging may be preferable in patients with renal impairment, however single plane imaging may be preferable in those without renal impairment.

Advances in knowledge:
This is a large cohort and statistically comprehensive study comparing bi-plane and single plane coronary angiography. Other studies 4, 5, 6, 12 have used Student's t-tests to measure the difference between means, however this provides no causative information on the differences found. This study provides a view of the causative impact of bi-plane usage on DAP and contrast use via multivariate regression modelling.
Colonic distention and patient acceptance of CT colonography: supine/prone vs left/right lateral scanning
Authors: Takahashi Noriaki , Nagata Koichi , Iyama Atsushi , Mikami Teppei , Kanazawa Hidenori , Saito Hiroshi 
Published: September 2018

Objective:
To prospectively evaluate and complete the colonic distention and patient acceptance of CT colonography (CTC) in the supine/prone and left/right lateral positions.

Methods:
A total of 220 consecutive patients were alternately allocated to the supine/prone positioning or left/right lateral positioning group. Two readers scored the degree of colonic distention by segment using a 4-point Likert scale (4 = optimal, 3 = adequate, 2 = inadequate, 1 = collapsed). In addition, patients were asked to rate the discomfort due to positioning during each scan using a 3-point animated face scale (3 = difficult, 2 = somewhat unacceptable, 1 = easy).

Results:
The overall mean colonic distention scores for supine, prone, left lateral, and right lateral positions were 3.16, 3.29, 3.22, and 3.42, respectively. Of all, the right lateral position provided the best colonic distention (p &lt; 0.01). Combined left lateral and right lateral positions provided more adequately distended segments compared with combined supine and prone positions (95.6% vs 90.7 %, respectively, p &lt; 0.01). Patient acceptance was significantly lower in the prone position compared to other positions; however there was no difference in patient acceptance between the supine and left/right lateral positions.

Conclusion:
Right lateral positioning provided the best colonic distention and good patient acceptance.

Advances in knowledge:
The left/right lateral position should be considered for routine CTC positioning protocols.
Determination of mammographic breast density using a deep convolutional neural network
Authors: Ciritsis Alexander , Rossi Cristina , Vittoria De Martini Ilaria , Eberhard Matthias , Marcon Magda , Becker Anton S. , Berger Nicole , Boss Andreas 
Published: September 2018

Objective:
High breast density is a risk factor for breast cancer. The aim of this study was to develop a deep convolutional neural network (dCNN) for the automatic classification of breast density based on the mammographic appearance of the tissue according to the American College of Radiology Breast Imaging Reporting and Data System (ACR BI-RADS) Atlas.

Methods:
In this study, 20,578 mammography single views from 5221 different patients (58.3 ± 11.5 years) were downloaded from the picture archiving and communications system of our institution and automatically sorted according to the ACR density (a-d) provided by the corresponding radiological reports. A dCNN with 11 convolutional layers and 3 fully connected layers was trained and validated on an augmented dataset. The model was finally tested on two different datasets against: i) the radiological reports and ii) the consensus decision of two human readers. None of the test datasets was part of the dataset used for the training and validation of the algorithm.

Results:
The optimal number of epochs was 91 for medio-lateral oblique (MLO) projections and 94 for cranio-caudal projections (CC), respectively. Accuracy for MLO projections obtained on the validation dataset was 90.9% (CC: 90.1%). Tested on the first test dataset of mammographies (850 MLO and 880 CC), the algorithm showed an accordance with the corresponding radiological reports of 71.7% for MLO and of 71.0% for CC. The agreement with the radiological reports improved in the differentiation between dense and fatty breast for both projections (MLO = 88.6% and CC = 89.9%). In the second test dataset of 200 mammographies, a good accordance was found between the consensus decision of the two readers on both, the MLO-model (92.2%) and the right craniocaudal-model (87.4%). In the differentiation between fatty (ACR A/B) and dense breasts (ACR C/D), the agreement reached 99% for the MLO and 96% for the CC projections, respectively.

Conclusions:
The dCNN allows for accurate classification of breast density based on the ACR BI-RADS system. The proposed technique may allow accurate, standardized, and observer independent breast density evaluation of mammographies.

Advances in knowledge:
Standardized classification of mammographies by a dCNN could lead to a reduction of falsely classified breast densities, thereby allowing for a more accurate breast cancer risk assessment for the individual patient and a more reliable decision, whether additional ultrasound is recommended.
Optical Trapping and Orientation Manipulation of 2D Inorganic Materials Using a Linearly Polarized Laser Beam
Authors: Tominaga Makoto , Higashi Yuki , Kumamoto Takuya , Nagashita Takashi , Nakato Teruyuki , Suzuki Yasutaka , Kawamata Jun 
Published: September 2018

AbstractBecause inorganic nanosheets, such as clay minerals, are anisotropic, the manipulation of nanosheet orientation is an important challenge in order to realize future functional materials. In the present study, a novel methodology for nanosheet manipulation using laser radiation pressure is proposed. When a linearly polarized laser beam was used to irradiate a niobate (Nb6O174-) nanosheet colloid, the nanosheet was trapped at the focal point so that the in-plane direction of the nanosheet was oriented parallel to the propagation direction of the incident laser beam so as to minimize the scattering force. In addition, the trapped nanosheet was aligned along the polarization direction of the linearly polarized laser beam.
Removal of Water-Soluble Polymers from an Aqueous Solution by Adsorption onto an Acidic Clay
Authors: Teepakakorn Aranee (Pleng) , Hayakawa Takayuki , Bureekaew Sareeya , Ogawa Makoto 
Published: September 2018

AbstractDue to the wide range of uses of water-soluble polymers in commercial products, water contamination by polymers has become a serious environmental concern. Adsorption onto an acidic clay, obtained from Tsunagi mine, Niigata, Japan, of water-soluble polymers from aqueous solutions was investigated as a means of purifying water. Poly(vinylpyrrolidone) (PVP) was used as a sample polymer in an attempt to find optimal conditions for extracting the greatest proportion of polymer from the aqueous solution. The adsorption isotherms at lower equilibrium concentrations were of type L, indicating a strong affinity between the acidic clay and PVP. A larger amount of PVP was adsorbed when a higher-molecularweight PVP (comparison between MWs of 160,000 and 10,000) was used. From the Langmuir equation, the adsorption capacity was calculated as 0.029 g/g clay for the adsorption of poly(vinylpyrrolidone) from an aqueous solution. The adsorption of PVP from a NaCl solution (simulated sea water) was also possible though the amount of adsorption was slightly less than from an aqueous solution. A polymer removal efficiency of >90% was achieved when 200 mg of the acidic clay was added to 50 mL of 0.001 wt.% PVP aqueous solution. The acidic clay was also used for adsorption of poly(ethylene glycol), poly(vinyl alcohol), and polyacrylamide from aqueous solutions.
The Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogens Causing Sepsis
Authors: Luethy Paul M , Johnson J Kristie 
Published: September 2018

Abstract

Background
Sepsis is a life-threatening condition with high rates of morbidity and mortality; effective and appropriate antibiotic therapy is essential for ensuring patient improvement. To aid in the diagnosis of sepsis, blood cultures are drawn and sent to the microbiology laboratory for pathogen growth, identification, and susceptibility testing. The clinical microbiology laboratory can assist the medical team by providing timely identification of the pathogen(s) causing the bloodstream infection through the use of rapid diagnostic technology. One of these rapid diagnostic technologies, MALDI-TOF MS, has been proven to reduce the time required for appropriate antibiotic therapy when used to identify pathogens grown in culture. This technology has also been used to identify pathogens directly from the positive blood cultures with great success.

Content
In this minireview, we summarize the different methods that have been developed to directly identify pathogens from positive blood cultures by use of MALDI-TOF MS and the effect of this technology on patient outcomes. Additionally, we touch on current research in the field, including the identification of antimicrobial resistance directly from positive blood cultures by MALDI-TOF MS.

Summary
Rapid identification of pathogens is important in the survival of patients undergoing a septic event. MALDI-TOF MS technology has played an important role in rapid identification, which has led to a reduction in the time to appropriate antibiotic therapy and contributed to the improvement of patient outcomes. The high sensitivity and specificity of MALDI-TOF MS identification, in combination with MALDI-TOF's rapid function and reduced labor costs, make this technology an attractive choice for clinical laboratories.
Living Hadis dalam Kegiatan Peringatan Maulid Nabi di Pesantren Sunan Ampel Jombang
Authors: Khosyiah Faiqatul 
Published: September 2018

AbstrakPerayaan maulid nabi adalah salah satu tradisi yang banyak dilestarikan oleh masyarakat kita, utamanya di banyak pesantren di Jawa. Tradisi ini memiliki banyak corak cara pelaksanaan yang masing- masing memiliki ciri khas tersendiri. Jika ditinjau dari sejarah pengadaannya, pada dasarnya memang tidak ada suatu tanggal khusus pengadaan maulid nabi, sehingga jika menarik busur sejarah, akan didapati pelaksanaaan maulid digelar pada tanggal yang berbeda- beda di bulan Rabiul Awal. Kenyataan ini ditemukan pula dalam kegiatan pelaksanaan maulid di pondok pesantren Sunan Ampel Jombang yang diadakan selama sepuluh hari lamanya dan dengan berbagai kekhasan di dalamnya. Melalui pendekatan fenomenologi dengan teori fungsional, tulisan ini mencoba memaparkan fenomena di dalam maulid ini dengan hasil bahwa, maulid di tempat tersebut adalah fenomena living hadits. Di samping itu, makna penting dari adanya majelis tersebut, adalah praktek ibadah spiritual yang tidak bisa dihilangkan dari kehidupan masyarakat yang berpartisipasi di dalamnya. AbstractProphet Mohammed birthday’s celebration is one of much tradition sustained by our people, exactly in many boarding schools in Java, Indonesia. This tradition has many implementation variant ways which each way has its specific thing. From historical side, there is no specific date for Prophet Mohammed birthday’s celebration, with result that since for the time being, it took place in various date at Rabiul Awal month. This fact also found in Prophet Mohammed birthday’s celebration at Sunan Ampel Jombang boarding school which happens in ten days with many specific things there. Using phenomenological approach one combined with functionalism theory, this research will explain phenomenon happens in this celebration with the result that celebration is one of living hadith phenomenon. Besides, the important significance by the existence of this tradition is that spiritual aspect which cannot be lost from people tradition.
Peranan Komunikasi Interpersonal Antara Guru Bimbingan Konseling (BK) dengan Siswa dalam Menangani Kenakalan Siswa (Studi Kasus di SMP Kristen 2 Salatiga)
Authors: Timothius Johan Chris 
Published: September 2018

AbstractCommunication is one of the most parts in human life. There are several types of communication: interpersonal communication, intrapersonal communication, and mass communication. This study focused on interpersonal communication in education between the teacher and the students. The aim of this study was to know the function of interpersonal communication to solve students’ matter at school. The study conducted in SMP Kristen 2 Salatiga, because the school has had face the problems.The qualitative method was used. Interview and observation were used to collect the data the interview and observation are done with four persons as key respondent: three students and one teacher as counselor. Then, triangulation and content analysis were used to know the respondents’ pattern.The data analysis showed that interpersonal communication gave contribution to solve the students’ matter. The teacher himself should be active by using client center and exchange theory to solve the students’ problem. Furthermore, if there are some matters between teacher and students or students to students, interpersonal communication is the effective way to solve the problems.Keywords: interpersonal communication, education, students’ problem.
FACE WORK SEORANG SPY DALAM GAME ONLINE SUPER ARMADA
Authors: Saptiyono Ami 
Published: September 2018

AbstractOnline media is media that provides a variety of facilities and services for people in activities and meet their needs. This media allows everyone to do various activities such as browsing , blogging , chat , update your status, upload and download data, and even play games . In this article , the researcher discuss how an online game players do face work in the activities of online gaming , especially in the game "Super Armada" , through autoethnography methods , as a method of doing descriptions experience of researcher in this online game , using face work theory as reference in researchKey words: Face work, Autoethnography, Media online.
Emily Wilding Davison Building, Royal Holloway, University of London
Authors: Tuck John , Brooke Matthew 
Published: September 2018

Zusammenfassung
Das Emily Wilding Davison Building ist ein neues Gebäude, das eine Reihe von Services für Studierende an der Royal Holloway, University of London vereinigt. Den größten Teil des Komplexes, der nach sechsjähriger Planungs-, Konstruktions- und Bauzeit im September 2017 eröffnet wurde, bildet die neue Bibliothek, die an 350 Tagen im Jahr rund um die Uhr geöffnet ist. Mit dem Ziel, die Studienbedingungen zu verbessern, sind in dem Gebäude Bibliothek, Studierendenservice, Career Center und Ausstellungs- sowie Veranstaltungsräume, ein Café, ein Geschäft und eine Bank zusammengeführt. Sämtliche Servicebereiche sind über ein Atrium miteinander verbunden.
Sonic Borderscapes: Popular Music, Pirate Radio, and Belonging in Black British Writing in the 1990s
Authors: Nyman Jopi 
Published: September 2018

Abstract
This article addresses the role of music and broadcast radio as elements in the construction of borderscapes, spaces of cultural construction and identity negotiation, in three black British novels published in the 1990 s, namely Diran Adebayo’s Some Kind of Black (1996), Karline Smith’s Moss Side Massive (1994/1998), and Courttia Newland’s Society Within (1999/2000). The article argues that the novels use black popular music and pirate (community) radio stations as means of constructing black identities, belonging, and communities in the conditions of the borderscape where hegemonic and resistant identifications come into contact with each other. Furthermore, the borderscape constructed can be seen as a sonic borderscape owing to the significant role allotted to music and radio in the novels. While music plays a particularly significant role at the level of the individual and contributes to the making of a distinct identity and difference, their becoming, the specific function given to community radio in these novels is to construct communities of belonging.1
The Stixel world – A comprehensive representation of traffic scenes for autonomous driving
Authors: Schneider Lukas , Hafner Michael , Franke Uwe 
Published: September 2018

Abstract
Autonomous vehicles as well as sophisticated driver assistance systems use stereo vision to perceive their environment in 3D. At least two Million 3D points will be delivered by next generation automotive stereo vision systems. In order to cope with this huge amount of data in real-time, we developed a medium level representation, named Stixel world. This representation condenses the relevant scene information by three orders of magnitude. Since traffic scenes are dominated by planar horizontal and vertical surfaces our representation approximates the three-dimensional scene by means of thin planar rectangles called Stixel.
This survey paper summarizes the progress of the Stixel world. The evolution started with a rather simple representation based on a flat world assumption. A major break-through was achieved by introducing deep-learning that allows to incorporate rich semantic information. In its most recent form, the Stixel world encodes geometric, semantic and motion cues and is capable to handle even steepest roads in San Francisco.