bluuebunny/crossref_metadata_2025_split huggingface dataset:
Image-based siRNA screen to identify kinases regulating Weibel-Palade body size control using electroporation
Authors: Ketteler Robin , Freeman Jamie , Stevenson Nicola , Ferraro Francesco , Bata Nicole , Cutler Dan F. , Kriston-Vizi Janos 
Published: March 2017

AbstractHigh-content screening of kinase inhibitors is important in order to identify biogenesis and function mechanisms of subcellular organelles. Here, we present a human kinome siRNA high-content screen on primary human umbilical vein endothelial cells, that were transfected by electroporation. The data descriptor contains a confocal fluorescence, microscopic image dataset. We also describe an open source, automated image analysis workflow that can be reused to perform high-content analysis of other organelles. This dataset is suitable for analysis of morphological parameters that are linked to human umbilical vein endothelial cell (HUVEC) biology.
Genome-wide siRNA screen of genes regulating the LPS-induced TNF-α response in human macrophages
Authors: Sun Jing , Katz Samuel , Dutta Bhaskar , Wang Ze , Fraser Iain D.C. 
Published: March 2017

AbstractThe mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the human macrophage TNF-α response to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits. We also provide microarray data from the same LPS-treated macrophage cells to facilitate downstream data analysis. Tertiary screening with multiple TLR ligands and a microbial extract demonstrate that novel screen hits have broad effects on the innate inflammatory response to microbial stimuli. These data provide a resource for analyzing gene function in the predominant pathway driving inflammatory cytokine expression in human macrophages.
Genome-wide siRNA screen of genes regulating the LPS-induced NF-κB and TNF-α responses in mouse macrophages
Authors: Li Ning , Katz Samuel , Dutta Bhaskar , Benet Zachary L. , Sun Jing , Fraser Iain D.C. 
Published: March 2017

AbstractThe mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the mouse macrophage TNF-α and NF-κB responses to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits. We also provide microarray data from the same LPS-treated macrophage cells to facilitate downstream data analysis. These data provide a resource for analyzing gene function in the predominant pathway driving inflammatory signaling and cytokine expression in mouse macrophages.
The Impact of Clinical History on the Threshold Estimation of Auditory Brainstem Response Results for Infants
Authors: Zaitoun Maha , Cumming Steven , Purcell Alison , O'Brien Katie 
Published: March 2017

Purpose
This study assesses the impact of patient clinical history on audiologists' performance when interpreting auditory brainstem response (ABR) results.

Method
Fourteen audiologists' accuracy in estimating hearing threshold for 16 infants through interpretation of ABR traces was compared on 2 occasions at least 5 months apart. On the 1st occasion, ABR traces were presented to the audiologists with no clinical information except for the age of the child. On the 2nd occasion, audiologists were given a full clinical history for the ABR cases.

Results
The addition of clinical history information had no statistically significant impact on sensitivity, specificity, or accuracy of diagnosis. Although the mean numbers of true-negative and true-positive diagnoses were higher when audiologists were given clinical information, the difference was again not statistically significant.

Conclusion
This study suggests that if there are circumstances in which case material is incomplete or unavailable, audiologists have no cause for concern regarding the accuracy of their interpretation of ABR traces. In a clinical manner, this may help audiologists with large caseloads or audiologists who need to provide a diagnosis of hearing loss in a short time by allowing them to focus on conducting ABR without the need for case history information.
Exploring Use of the Coordinate Response Measure in a Multitalker Babble Paradigm
Authors: Humes Larry E. , Kidd Gary R. , Fogerty Daniel 
Published: March 2017

Purpose
Three experiments examined the use of competing coordinate response measure (CRM) sentences as a multitalker babble.

Method
In Experiment I, young adults with normal hearing listened to a CRM target sentence in the presence of 2, 4, or 6 competing CRM sentences with synchronous or asynchronous onsets. In Experiment II, the condition with 6 competing sentences was explored further. Three stimulus conditions (6 talkers saying same sentence, 1 talker producing 6 different sentences, and 6 talkers each saying a different sentence) were evaluated with different methods of presentation. Experiment III examined the performance of older adults with hearing impairment in a subset of conditions from Experiment II.

Results
In Experiment I, performance declined with increasing numbers of talkers and improved with asynchronous sentence onsets. Experiment II identified conditions under which an increase in the number of talkers led to better performance. In Experiment III, the relative effects of the number of talkers, messages, and onset asynchrony were the same for young and older listeners.

Conclusions
Multitalker babble composed of CRM sentences has masking properties similar to other types of multitalker babble. However, when the number of different talkers and messages are varied independently, performance is best with more talkers and fewer messages.
Immunohistochemical Expression of the Tumor Suppressor Protein p16INK4a in Cervical Adenocarcinoma
Authors: Lima Thiago Silva , Cunha Maria do Perpétuo Socorro , Cavalcante Diane Isabelle Magno , Silva Angélica Maria Holanda , Eleutério Jr José 
Published: March 2017

Objective To evaluate the diagnostic utility of the p16ink4a protein expression as a marker for adenocarcinoma of the cervix.
Methods In a cross-sectional study, p16ink4a expression was evaluated in 30 cervical biopsies from patients diagnosed with invasive adenocarcinoma from 2 reference clinics in Brazil, and compared with 18 biopsies of endocervical polyps (control cases). The performance of the tests for p16ink4a was evaluated using a conventional contingency table, and the Kappa (κ) index was used to evaluate the agreement of the marker with the tissue diagnosis.
Results In total, 66% of the invasive adenocarcinoma cases were positive for p16ink4a. All of the adenomatous polyps cases used as negative controls were shown to be negative for p16ink4a. The marker showed a high sensitivity and a high negative predictive value. The Kappa index was good for p16ink4a (κ = 0.6).
Conclusion Considering the strong association between the p16ink4a marker and the cervical adenocarcinoma, its use represents an important tool for reducing incorrect diagnoses of adenocarcinoma and thereby avoiding overtreatment.
Prevalence of Hypertrophic Cardiomyopathy in Fetuses of Mothers with Gestational Diabetes before Initiating Treatment
Authors: Simões Mona Adalgisa , Silva Jean Carl , Santos Anelise Darabas dos , Silva Mariana Ribeiro e , Ferreira Bruna , Palmieri Carolina Rossi 
Published: March 2017

Objective To evaluate the prevalence of hypertrophic cardiomyopathy (HCM) in fetuses of pregnant women with gestational diabetes mellitus (GDM) in the beginning of the treatment.
Methods A cross-sectional study was performed between July 1, 2013, and December 20, 2013, in a public maternity clinic in southern Brazil. The subjects were 63 fetuses of mothers with gestational diabetes, with a single pregnancy and no other associated pathologies. We diagnosed HCM through a fetal echocardiography before treatment and evaluated the maternal and fetal characteristics.
Results The average age of the pregnant women was 32.32 (±6.2) years, and the average gestational age at the time of the evaluation was 30.59 (±2.27) weeks. The interventricular septum thickness showed a standard deviation of more than two in 50.8% of the fetuses (95% confidence interval [95%CI]: 38.1–63.5%). The left ventricular wall thickness showed a standard deviation of more than 2 in 13 (20.6%) fetuses (95%CI: 11.1–30.2%). The HCM was confirmed in 54% of the fetuses (95%CI: 41.3–65.1%). The fetal abdominal circumference was normal in 46 (73%) fetuses, and 50% of these fetuses had HCM.
Conclusion The prevalence of hypertrophic cardiomyopathy in fetuses of pregnant women with GDM before treatment was of 54% (95%CI: 41.3–65.1%).
Recombinant Human Acidic Fibroblast Growth Factor (aFGF) Expressed in Nicotiana benthamiana Potentially Inhibits Skin Photoaging
Authors: Ha Jang-Ho , Kim Ha-Neul , Moon Ki-Beom , Jeon Jae-Heung , Jung Dai-Hyun , Kim Su-Jung , Mason Hugh , Shin Seo-Yeon , Kim Hyun-Soon , Park Kyung-Mok 
Published: March 2017

AbstractResponding to the need for recombinant acidic fibroblast growth factor in the pharmaceutical and cosmetic industries, we established a scalable expression system for recombinant human aFGF using transient and a DNA replicon vector expression in Nicotiana benthamiana. Recombinant human-acidic fibroblast growth factor was recovered following Agrobacterium infiltration of N. benthamiana. The optimal time point at which to harvest recombinant human acidic fibroblast growth factor expressing leaves was found to be 4 days post-infiltration, before necrosis was evident. Commassie-stained SDS-PAGE gels of His-tag column eluates, concentrated using a 10 000 molecular weight cut-off column, showed an intense band at the expected molecular weight for recombinant human acidic fibroblast growth factor. An immunoblot confirmed that this band was recombinant human acidic fibroblast growth factor. Up to 10 µg recombinant human-acidic fibroblast growth factor/g of fresh leaves were achieved by a simple affinity purification protocol using protein extract from the leaves of agroinfiltrated N. benthamiana. The purified recombinant human acidic fibroblast growth factor improved the survival rate of UVB-irradiated HaCaT and CCD-986sk cells approximately 89 and 81 %, respectively. N. benthamiana-derived recombinant human acidic fibroblast growth factor showed similar effects on skin cell proliferation and UVB protection compared to those of Escherichia coli-derived recombinant human acidic fibroblast growth factor. Additionally, N. benthamiana-derived recombinant human acidic fibroblast growth factor increased type 1 procollagen synthesis up to 30 % as well as reduced UVB-induced intracellular reactive oxygen species generation in fibroblast (CCD-986sk) cells.UVB is a well-known factor that causes various types of skin damage and premature aging. Therefore, the present study demonstrated that N. benthamiana-derived recombinant human acidic fibroblast growth factor effectively protects skin cell from UVB, suggesting its potential use as a cosmetic or therapeutic agent against skin photoaging.
Metabolic origins of spatial organization in the tumor microenvironment
Authors: Carmona-Fontaine Carlos , Deforet Maxime , Akkari Leila , Thompson Craig B. , Joyce Johanna A. , Xavier Joao B. 
Published: March 2017

Significance
Cancers appear as disordered mixtures of different cells, which is partly why they are hard to treat. We show here that despite this chaos, tumors show local organization that emerges from cellular processes common to most cancers: the altered metabolism of cancer cells and the interactions with stromal cells in the tumor microenvironment. With a multidisciplinary approach combining experiments and computer simulations we revealed that the metabolic activity of cancer cells produces gradients of nutrients and metabolic waste products that act as signals that cells use to know their position with respect to blood vessels. This positional information orchestrates a modular organization of tumor and stromal cells that resembles embryonic organization, which we could exploit as a therapeutic target.
Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy
Authors: Megjhani Murad , Correa de Sampaio Pedro , Leigh Carstens Julienne , Kalluri Raghu , Roysam Badrinath 
Published: March 2017

Abstract

Motivation
Current spectral unmixing methods for multiplex fluorescence microscopy have a limited ability to cope with high spectral overlap as they only analyze spectral information over individual pixels. Here, we present adaptive Morphologically Constrained Spectral Unmixing (MCSU) algorithms that overcome this limitation by exploiting morphological differences between sub-cellular structures, and their local spatial context.

Results
The proposed method was effective at improving spectral unmixing performance by exploiting: (i) a set of dictionary-based models for object morphologies learned from the image data; and (ii) models of spatial context learned from the image data using a total variation algorithm. The method was evaluated on multi-spectral images of multiplex-labeled pancreatic ductal adenocarcinoma (PDAC) tissue samples. The former constraint ensures that neighbouring pixels correspond to morphologically similar structures, and the latter constraint ensures that neighbouring pixels have similar spectral signatures. The average Mean Squared Error (MSE) and Signal Reconstruction Error (SRE) ratio of the proposed method was 39.6% less and 8% more, respectively, compared to the best of all other algorithms that do not exploit these spatial constraints.

Availability and Implementation
Open source software (MATLAB).

Supplementary information
Supplementary data are available at Bioinformatics online.
ctsGE—clustering subgroups of expression data
Authors: Sharabi-Schwager Michal , Or Etti , Ophir Ron 
Published: March 2017

AbstractSummaryA pre-requisite to clustering noisy data, such as gene-expression data, is the filtering step. As an alternative to this step, the ctsGE R-package applies a sorting step in which all of the data are divided into small groups. The groups are divided according to how the time points are related to the time-series median. Then clustering is performed separately on each group. Thus, the clustering is done in two steps. First, an expression index (i.e. a sequence of 1, −1 and 0) is defined and genes with the same index are grouped together, and then each group of genes is clustered by k-means to create subgroups. The ctsGE package also provides an interactive tool to visualize and explore the gene-expression patterns and their subclusters. ctsGE proposes a way of organizing and exploring expression data without eliminating valuable information.Availability and ImplementationFreely available as part of the Bioconductor project at https://bioconductor.org/packages/ctsGE/.Supplementary informationSupplementary data are available at Bioinformatics online.
PeptideMapper: efficient and versatile amino acid sequence and tag mapping
Authors: Kopczynski Dominik , Barsnes Harald , Njølstad Pål R , Sickmann Albert , Vaudel Marc , Ahrends Robert 
Published: March 2017

Abstract
The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i.e. up to 1000× faster than state-of-the-art software) in terms of memory footprint and execution speed, with regards to both the indexing and the querying of protein sequence databases.

Availability and Implementation
PeptideMapper is implemented in the open source Java CompOmics framework under the permissive Apache 2.0 license https://github.com/compomics/compomics-utilities.

Supplementary information
Supplementary data are available at Bioinformatics online.
Proton tomography through deeply virtual Compton scattering
Authors: Ji Xiangdong 
Published: March 2017

Abstract
In this prize talk, I recall some of the history surrounding the discovery of deeply virtual Compton scattering, and explain why it is an exciting experimental tool to obtain novel tomographic pictures of the nucleons at Jefferson Lab 12 GeV facility and the planned Electron-Ion Collider in the USA. It is certainly a great honor to have received the 2016 Herman Feshbach Prize in theoretical nuclear physics by the American Physical Society. I sincerely thank my colleagues in the Division of Nuclear Physics to recognize the importance of some of the theoretical works I have done in the past, particularly their relevance to the experimental programs around the world.
Organizational Barriers to Technology Adoption: Evidence from Soccer-Ball Producers in Pakistan*
Authors: Atkin David , Chaudhry Azam , Chaudry Shamyla , Khandelwal Amit K. , Verhoogen Eric 
Published: March 2017

AbstractThis article studies technology adoption in a cluster of soccer-ball producers in Sialkot, Pakistan. We invented a new cutting technology that reduces waste of the primary raw material and gave the technology to a random subset of producers. Despite the clear net benefits for nearly all firms, after 15 months take-up remained puzzlingly low. We hypothesize that an important reason for the lack of adoption is a misalignment of incentives within firms: the key employees (cutters and printers) are typically paid piece rates, with no incentive to reduce waste, and the new technology slows them down, at least initially. Fearing reductions in their effective wage, employees resist adoption in various ways, including by misinforming owners about the value of the technology. To investigate this hypothesis, we implemented a second experiment among the firms that originally received the technology: we offered one cutter and one printer per firm a lump-sum payment, approximately a month’s earnings, conditional on demonstrating competence in using the technology in the presence of the owner. This incentive payment, small from the point of view of the firm, had a significant positive effect on adoption. The results suggest that misalignment of incentives within firms is an important barrier to technology adoption in our setting.
Biomechanical Evaluation of the Depth of Resection During Femoral Neck Osteoplasty for Anterior Impingement Following Slipped Capital Femoral Epiphysis
Authors: Dale Kevin M. , Burns Geoffrey T. , Li Ying 
Published: March 2017

Background:
Femoroacetabular impingement as a result of slipped capital femoral epiphysis (SCFE) has been treated traditionally with a proximal femoral osteotomy, but open and arthroscopic femoral osteoplasty is becoming increasingly popular. Cam lesions result from excess bone primarily at the anterolateral femoral head-neck junction. SCFEs result from posterior and inferior slippage of the femoral epiphysis, causing the metaphysis to move anteriorly. This study’s purpose was to compare fourth-generation sawbones standard femurs with SCFE femurs to determine whether bone resection from the anterior metaphysis results in similar biomechanical properties.

Methods:
A custom fourth-generation composite SCFE sawbone was created with a 30-degree slip angle. Control group consisted of fourth-generation composite standard nondeformed medium femurs. The femoral neck at the head-neck junction was divided into 4 quadrants. All resections were done in the anterolateral quadrant. Twenty SCFE sawbones and 20 standard sawbones were divided into 4 subgroups based on resection depths of 0%, 10%, 30%, and 50% of the metaphysis at the head-neck junction. After resection, all proximal femurs were loaded to failure in an Instron testing machine to determine the ultimate load to failure, stiffness, and energy to failure.

Results:
The standard femurs were significantly stronger than the SCFE femurs (P<0.001) and the strength of the femurs decreased significantly as the resection amount increased (P<0.001). Similarly, the standard femurs withstood significantly more energy before failing than the SCFE femurs (P<0.001) and the energy to failure decreased significantly with varying resection amounts (P<0.001).

Conclusions:
SCFE femurs demonstrate a significant reduction in strength and energy to failure after osteoplasty compared with nondeformed femurs in a sawbone model. Strength and energy to failure are inversely proportional to the depth of bone resection.

Clinical Relevance:
Aggressive femoral neck osteoplasty for treatment of a SCFE deformity may lead to increased risk of fracture. Further studies are necessary to determine the safe depth of resection in a clinical setting.
Usage of Chewing Gum in Posterior Spinal Fusion Surgery for Adolescent Idiopathic Scoliosis
Authors: Chan Chris Yin Wei , Chiu Chee Kidd , Lee Chee Kean , Gani Siti Mariam Abd , Mohamad Siti Mariam , Hasan Mohd Shahnaz , Kwan Mun Keong 
Published: March 2017

Study Design.
Randomized controlled trial.

Objective.
The present study investigated the effectiveness of chewing gum on promoting faster bowel function and its ability to hasten recovery for patients with adolescent idiopathic scoliosis (AIS) after posterior spinal fusion (PSF) surgery.

Summary of Background Data.
Sham feeding with chewing gum had been reported to reduce the incidence of postoperative ileus by accelerating recovery of bowel function.

Methods.
We prospectively recruited and randomized 60 patients with AIS scheduled for PSF surgery into treatment (chewing gum) and control group. The patient-controlled anesthesia usage, wound pain score, abdominal pain score, nausea score, and abdominal girth were assessed and recorded at 12, 24, 36, 48, and 60 hours postoperatively. The timing for the first fluid intake, first oral intake, sitting up, walking, first flatus after surgery, first bowel opening after surgery, and duration of hospital stay were also assessed and recorded.

Results.
We found that there were no significant differences (P > 0.05) in patient-controlled anesthesia usage, wound pain score, abdominal pain score, nausea score, and abdominal girth between treatment (chewing gum) and control groups. We also found that there were no significant difference (P > 0.05) in postoperative recovery parameters, which were the first fluid intake, first oral intake, sitting up after surgery, walking after surgery, first flatus after surgery, first bowel opening after surgery, and duration of hospital stay between both groups. The wound pain was the worst at 12 hours postoperatively, which progressively improved in both groups. The abdominal pain progressively worsened to the highest score at 48 hours in the treatment group and 36 hours in the control group before improving after that. The pattern of severity and recovery of wound pain and abdominal pain was different.

Conclusion.
We found that chewing gum did not significantly reduce the abdominal pain, promote faster bowel function, or hasten patient recovery.

Level of Evidence: 1