bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Characteristics and Outcomes of Moraxella Keratitis
Authors: Zafar Hamza , Tan Shi Zhuan , Walkden Andrew , Fullwood Catherine , Au Leon , Brahma Arun , Carley Fiona 
Published: September 2018

Purpose:
Changing trends of infective keratitis have been identified worldwide. The aim of this study was to define the clinical associations, characteristics, and outcomes of patients with culture-proven Moraxella keratitis from a large tertiary corneal unit in the United Kingdom.

Methods:
Patients with confirmed Moraxella isolates presenting between January 2004 and November 2016 were analyzed. Patient-related factors were examined, including patient demographics, date of presentation, clinical presentation, predisposing factors, best-corrected visual acuity (BCVA), treatment plans, and clinical outcomes.

Results:
Eighty-six patients were identified, of whom 61 (70.9%) had at least one recognized predisposing factor. The median BCVA at presentation was 2.60 logarithm of the minimum angle of resolution (logMAR), which improved to median = 0.60 logMAR at final visit (P < 0.001). Visual improvement of more than 2 Snellen lines was achieved in 60.7% of eyes. A significant relationship (P = 0.003) between final vision and the presence of hypopyon was found, where for a fixed BCVA at presentation those with a hypopyon achieved a better final visual acuity of 0.69 logMAR.

Conclusions:
Our study showed that although most patients presented with at least one predisposing factor, some of the more traditionally perceived risk factors may need to be reconsidered. We have shown that with aggressive treatment, favorable visual outcomes can be achieved in most patients. Interestingly, the presence of hypopyon at presentation was linked to a better visual outcome, likely because such patients had more to gain in visual potential.
Development of Cell Analysis Software to Evaluate Fibroblastic Changes in Cultivated Corneal Endothelial Cells for Quality Control
Authors: Okumura Naoki , Kobayashi Keitaro , Ishida Naoya , Kagami Takato , Hiwa Satoru , Hiroyasu Tomoyuki , Koizumi Noriko 
Published: September 2018

Purpose:
To develop software to evaluate the fibroblastic morphological changes in cultured human corneal endothelial cells (HCECs) as a quality control measure for use in tissue engineering therapy.

Methods:
Software was designed to recognize cell borders, to approximate cell shape as an ellipse, and to calculate the aspect ratio of the ellipse as an indicator of severity of the fibroblastic morphological change. Using the designed software, 60 phase contrast images of polygonal HCECs and 60 phase contrast images of fibroblastic HCECs were analyzed. The correlations of the aspect ratio and other parameters (cell density, percentage of cells surrounded by 6 cells, and coefficient of variation) were evaluated.

Results:
Cell shapes were recognized based on phase contrast images and were approximated as ellipses by software. The average aspect ratio was significantly higher (34.9% ± 6.1%) in fibroblastic HCECs than in polygonal HCECs (24.4% ± 2.3%) (P < 0.01). The aspect ratio showed a correlation with cell density, with the percentage of cells surrounded by 6 neighboring cells, and with the coefficient of variation (Pearson correlation coefficients, −0.84, −0.38, and 0.66, respectively).

Conclusions:
We propose that fibroblastic alteration of HCECs can be evaluated by the cell morphology based on the aspect ratio. Software developed in this study, which can analyze the frequency and severity of fibroblastic alteration, will be useful for nondestructive assessment of cells destined for use in cell-based therapy for corneal endothelial decompensation.
Corneal Relapse of Peripheral T-Cell Lymphoma Under Systemic Chemotherapy
Authors: Kiratli Hayyam , Aygün Figen B. , Gedikoğlu Gökhan 
Published: September 2018

Purpose:
To report a patient who developed unilateral corneal stromal infiltration while undergoing systemic chemotherapy for multinodal peripheral T-cell lymphoma not otherwise specified.

Methods:
Clinical, imaging, and immunohistopathological features of a 40-year-old woman who presented with a stromal haze in the right cornea were reviewed.

Results:
At initial presentation, her visual acuity in the right eye was 20/40. Slit-lamp examination showed stromal infiltration located mainly in the inferotemporal peripheral cornea without epithelial or limbal involvement. Immunohistochemical examination of the incisional biopsy specimen revealed CD3+, CD5+, and CD8− neoplastic lymphocytes suggestive of T-cell lymphoma. The corneal lesion and disseminated lymphadenopathy did not respond to various combinations of several cycles of systemic chemotherapy. Remission was achieved only after allogeneic bone marrow transplantation. The corneal infiltrates almost totally regressed within 6 months, and she maintained 20/20 visual acuity thereafter. She did not have any systemic or ocular recurrence during 6 years of posttransplantation follow-up.

Conclusions:
In this rare case of systemic multinodal peripheral T-cell lymphoma, corneal stromal infiltration was the only ocular manifestation. Prompt corneal biopsy enabled the appropriate diagnosis. Development and persistence of corneal infiltration despite systemic chemotherapy may be a warning sign for resistance to treatment.
Central Islands and Visual Outcomes of Phototherapeutic Keratectomy Using the Photorefractive Keratectomy Mode
Authors: Kamiya Kazutaka , Takahashi Masahide , Igarashi Akihito , Shoji Nobuyuki 
Published: September 2018

Purpose:
To compare the rate of central island (CI) and visual acuity after phototherapeutic keratectomy (PTK) with and without the CI program.

Methods:
This retrospective study comprised 147 eyes of 89 consecutive patients (mean age ± SD, 71.1 ± 9.6 years) undergoing PTK with and without the anti-CI program [photorefractive keratectomy (PRK) mode and PTK mode] using the VISX Star S4 excimer laser system (Johnson & Johnson Vision, Santa Ana, US) for treatment of band keratopathy (BK) or granular corneal dystrophy (GCD). The rate of CI formation, defined as a steepening area of 3 D, 1.5 mm in diameter, on each corneal videokeratographer (ATLAS 9000; Carl Zeiss Meditec, Jena), and best spectacle-corrected visual acuity (BSCVA) were assessed 3 months after PTK.

Results:
We found CI formation in 17 eyes (22%) in the PRK mode group and 45 eyes (73%) in the PTK mode group at 3 months postoperatively (P < 0.001, χ2 test). Postoperative logarithm of the minimal angle of resolution BSCVA was 0.10 ± 0.14 in the PRK group and 0.15 ± 0.13 in the PTK group (P = 0.019, Student t test). The rate of CI was 13 eyes (33%) with BK and 6 eyes (15%) with GCD in the PRK mode group and 25 eyes (83%) with BK and 20 eyes (71%) with GCD in the PTK mode group.

Conclusions:
The use of the anti-CI program for PTK significantly decreases the rate of CI formation and significantly improves BSCVA in post-PTK eyes, suggesting its viability for treatment of BK and GCD in clinical setting.
Reconstruction of Temporal Bone Defect Using a Vertically-Oriented Free Muscle-Sparing Rectus Abdominis Musculocutaneous Flap
Authors: Jeong Hyung Hwa , Choi Eun Jeong , Chung Jong Woo , Kim Eun Key 
Published: September 2018

Abstract
Reconstruction of a temporal bone defect after tumor ablation should provide watertight filling and adequate resurfacing. A muscle-sparing rectus abdominis musculocutaneous (ms-RAMC) flap with de-epithelized skin paddle has been used and early experience was reported. Case series enrolled 7 patients who underwent free ms-RAMC flap after tumor ablation for external auditory canal cancer. Vertically oriented flap was harvested with central strip of muscle. Distal skin paddle was de-epithelized to fill the bony defect. Immediate facial nerve reconstruction was performed whenever indicated. The average operation time for reconstruction was 280 minutes. No early complication was reported. An ms-RAMC flap with de-epithelized skin paddle can be used for temporal bone defect reconstruction with its anatomic consistency and technical simplicity. It can provide sufficient bulk for water tight packing that lasts after irradiation. The 11th intercostal nerve can be harvested during pedicle dissection. Muscle sparing technique could minimize donor-site morbidity.
Correlation Between the Existing Classifications of Nasal Bone Fractures and Subjective Patient Satisfaction
Authors: Jeon Minseok , Kim Youngjun 
Published: September 2018

Abstract
Since the nose is at the center of the face, small changes to it can cause a big overall change. Therefore, a nasal fracture needs to be operated on when deformity is expected. Although many taxonomies have been developed for nasal bone fractures, no study has aimed to predict individual patient satisfaction. Herein, the authors tried to determine any correlation between the existing classifications of nasal bone fractures and subjective patient satisfaction. A retrospective study and telephone survey were conducted in 149 patients who underwent closed reduction for a pure nasal bone fracture. Pretraumatic, prereduction, and postoperative patient satisfactions were measured on a numerical scale from 1 to 5. The difference between pretraumatic and prereduction satisfactions was calculated to confirm the change in short-term satisfaction after trauma. The difference between pretraumatic and preoperative satisfactions was measured to determine change in long-term satisfaction postoperatively. The Stranc Robertson classification, modified Murray classification, and the presence of septal fracture were used to classify fractures. Independent and Jonckheere–Terpstra t tests were used in statistical analysis. Only 86 of 149 were included in the study. There was no significant difference in patient satisfaction among frontal/lateral (P = 0.70, 0.56), frontal I/II (P = 1.00, 0.24), and lateral I/II groups (P = 0.57, 0.67) according to the Stranc Robertson classification. Septal fracture (P = 0.21, 0.44) and the modified Murray classification (P = 0.14, 0.47) also had no effect on satisfaction. Existing classification systems have the advantage of reflecting and distinguishing the characteristics of fractures, but there is a limit in their ability to reflect subjective patient satisfaction.
Normative Data of the Interorbital Distance in Thai Population
Authors: Chatdokmaiprai Chalermpong , Kiranantawat Kidakorn , Lertsithichai Panuwat , Taeshineetanakul Patamintita 
Published: September 2018

Abstract
The incidence of the patients with craniofacial anomalies was high in southeast-Asian countries, for example, fronto-ethmoidal encephalo-menigocele or craniosynostosis. These craniofacial anomalies usually involve orbits, so a surgical orbital reconstruction is always required.
Various methods have been used in the past to indirectly analyze the craniofacial region. Plain skull radiography, anthropometry, and cephalometry provided the limited information of interorbital distance in terms of accuracy whereas the interorbital distance is crucial to be reconstructed, increasing or decreasing. The accurate normal interorbital distance which grows by age as other craniofacial structures is the important data in the part of interorbital and orbital reconstruction. To date, the normative data of the bony interorbital distance among Thai population have not been established.
The purpose of this study is to provide normal values and the growth patterns of the bony interorbital distances and other dimensions of the orbit according to age among Thai population through the axial computed tomography. Comparisons can then be made between normal values and those for an individual patient or those for a group of patients, for example, those with front-ethmoidal meningoencephalocele, Crouzon, or Treacher–Collins syndrome, or among values for individual patients at different time intervals.
A retrospective study of computed tomography (CT) scan series of 698 normal orbits from 349 skeletally normal subjects (202 men and 147 women) was enrolled. The age range of the patients was 0 to 21 years (mean, 10.2 years; SD, 5.8 years). A series of 12 measurements were obtained from the CT scans of each subject. All CT images were obtained from patients who underwent CT of the facial bone, brain, and orbits at the Department of Radiology of 3 big hospital in Bangkok–Ramathibodi, Samitivej Srinakarin, and Bangkok hospital–since 2010 to 2015.
The normal measurement values in the orbital region through the CT images, as the normal periorbital growth curve, will help improving diagnostic accuracy, staging of reconstruction, precision of corrective surgery, and follow-up of the Thai patients with craniofacial abnormalities such as front-ethmoidal meningoencephalocele, hypertelorism. These data may also apply to the related population in the southeast-Asian countries.
The ATP-dependent chromatin remodelling enzyme Uls1 prevents Topoisomerase II poisoning
Authors: Swanston Amy , Zabrady Katerina , Ferreira Helder C. 
Published: September 2018

ABSTRACTTopoisomerase II (Top2) is an essential enzyme that decatenates DNA via a transient Top2-DNA covalent intermediate. This intermediate can be stabilised by a class of drugs termed Top2 poisons, resulting in massive DNA damage. Thus, Top2 activity is a double-edged sword that needs to be carefully controlled to maintain genome stability. We show that Uls1, an ATP-dependent chromatin remodelling (Snf2) enzyme, can alter Top2 chromatin binding and prevent Top2 poisoning in yeast. Deletion mutants ofULS1are hypersensitive to the Top2 poison acriflavine (ACF), activating the DNA damage checkpoint. We map Uls1’s Top2 interaction domain and show that this, together with its ATPase activity, is essential for Uls1 function. By performing ChIP-seq, we show that ACF leads to a general increase in Top2 binding across the genome. We map Uls1 binding sites and identify tRNA genes as key regions where Uls1 associates after ACF treatment. Importantly, the presence of Uls1 at these sites prevents ACF-dependent Top2 accumulation. Our data reveal the effect of Top2 poisons on the global Top2 binding landscape and highlights the role of Uls1 in antagonising Top2 function. Remodelling Top2 binding is thus an important new means by which Snf2 enzymes promote genome stability.
Pan-cancer whole genome analyses of metastatic solid tumors
Authors: Priestley Peter , Baber Jonathan , Lolkema Martijn P. , Steeghs Neeltje , de Bruijn Ewart , Shale Charles , Duyvesteyn Korneel , Haidari Susan , van Hoeck Arne , Onstenk Wendy , Roepman Paul , Voda Mircea , Bloemendal Haiko J. , Tjan-Heijnen Vivianne C.G. , van Herpen Carla M.L. , Labots Mariette , Witteveen Petronella O. , Smit Egbert F. , Sleijfer Stefan , Voest Emile E. , Cuppen Edwin 
Published: September 2018

AbstractMetastatic cancer is one of the major causes of death and is associated with poor treatment efficiency. A better understanding of the characteristics of late stage cancer is required to help tailor personalised treatment, reduce overtreatment and improve outcomes. Here we describe the largest pan-cancer study of metastatic solid tumor genomes, including 2,520 whole genome-sequenced tumor-normal pairs, analyzed at a median depth of 106x and 38x respectively, and surveying over 70 million somatic variants. Metastatic lesions were found to be very diverse, with mutation characteristics reflecting those of the primary tumor types, although with high rates of whole genome duplication events (56%). Metastatic lesions are relatively homogeneous with the vast majority (96%) of driver mutations being clonal and up to 80% of tumor suppressor genes bi-allelically inactivated through different mutational mechanisms. For 62% of all patients, genetic variants that may be associated with outcome of approved or experimental therapies were detected. These actionable events were distributed across various mutation types underlining the importance of comprehensive genomic tumor profiling for cancer precision medicine.
Evaluation of correlates of protection against influenza A(H3N2) and A(H1N1)pdm09 infection: Applications to the hospitalized patient population
Authors: Petrie Joshua G. , Martin Emily T. , Truscon Rachel , Johnson Emileigh , Cheng Caroline K. , McSpadden EJ , Malosh Ryan E. , Lauring Adam S. , Lamerato Lois E. , Eichelberger Maryna C. , Ferdinands Jill M. , Monto Arnold S. 
Published: September 2018

ABSTRACTBackgroundInfluenza vaccines are important for prevention of influenza-associated hospitalization. Assessments of serologic correlates of protection can support interpretation of influenza vaccine effectiveness evaluations in hospitalized populations.MethodsSerum specimens collected at admission from adults hospitalized for treatment of acute respiratory illnesses during two influenza seasons were tested in hemagglutination-inhibition (HAI) and neuraminidase-inhibition (NAI) assays. We evaluated the suitability of these specimens as proxies for pre-infection immune status, and measured associations between antibody titers and influenza vaccination and infectionResultsSpecimens were collected within 3 days of illness onset from 65% of participants; geometric mean titers (GMTs) did not vary by day of collection. In both seasons, vaccinated participants had higher HAI and NAI GMTs than unvaccinated participants. HAI titers against the 2014-2015 A(H3N2) vaccine strain did not correlate with protection from infection with antigenically-drifted A(H3N2) viruses that circulated that season. In contrast, higher HAI titers against the A(H1N1)pdm09 vaccine strain were associated with reduced odds of A(H1N1)pdm09 infection in 2015-2016.ConclusionsSerum collected after hospital admission can be used to assess correlates of protection against influenza infection. Broader implementation of similar studies would provide an opportunity to understand the successes and shortcomings of current influenza vaccines.
Predictive Modelling of The Dynamic Patterns of Thinking in Attention-Deficit/Hyperactivity Disorder: Diagnostic Accuracy of Spatiotemporal Fractal Measures
Authors: Labra-Spröhnle F. , Smith G. , Ahammer H. , Postlethwaite C. , Liu I. , Teesdale-Spittle P. , Frean M. 
Published: September 2018

AbstractBackgroundAttention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental condition characterized by executive function (EF) dynamics disturbances. Notwithstanding, current advances in translational neuroscience, no ADHD objective, clinically useful, diagnostic marker is available to date.ObjectivesUsing a customized definition of EF and a new clinical paradigm, we performed a prospective diagnostic accuracy trial to assess the diagnostic value of several fractal measures from the thinking processes or inferences in a cohort of ADHD children and typically developing controls.MethodWe included children from age five to twelve diagnosed with a reference standard based on case history, physical and neurological examination, Conners 3rdEdition, and DSM-V™. The index test consisted of a computer-based inference task with a set of eight different instances of the “Battleships” game to be solved. A consecutive series of 18 cases and 18 controls (n = 36) recruited at the primary paediatrics service from the Nelson Marlborough Health in New Zealand underwent the reference standard and the index test. Several fractal measures were obtained from the inference task to produce supervised classification models.ResultsNotably, the summarized logistic regression’s predicted probabilities from the eight games played by each children yielded a 100% classification accuracy, sensitivity and specificity in both a training and an independent testing/validating cohort.ConclusionsFrom a translational vantage point the expeditious method and the robust results make this technique a promising candidate to develop a screening, diagnostic and monitoring system for ADHD, and may serve to assess other EF disturbances.
Genome-wide active enhancer identification using cell type-specific signatures of epigenomic activity
Authors: Jhanwar Shalu , Ossowski Stephan , Davila-Velderrain Jose 
Published: September 2018

AbstractRecently enhancers have emerged as key players regulating crucial mechanisms such as cell fate determination and establishment of spatiotemporal patterns of gene expression during development. Due to their functional and structural complexity, an accurate in silico identification of active enhancers under specific conditions remain challenging. We present a novel machine learning based method that derives epigenomic patterns exclusively from experimentally characterized active enhancers contrasted with a weighted set of non-enhancer genomic regions. We demonstrate better predictive performance over previous methods, as well as wide generalizability by identifying and annotating active enhancers genome-wide across different tissues/cell types in human and mouse.
Dissecting heterogeneous cell populations across drug and disease conditions with PopAlign
Authors: Chen Sisi , Park Jong H. , Tsou Tiffany , Rivaud Paul , Charles Emeric , Haliburton John , Pichiorri Flavia , Thomson Matt 
Published: September 2018

AbstractSingle-cell measurement techniques can now probe gene expression in heterogeneous cell populations from the human body across a range of environmental and physiological conditions. However, new mathematical and computational methods are required to represent and analyze gene expression changes that occur in complex mixtures of single cells as they respond to signals, drugs, or disease states. Here, we introduce a mathematical modeling platform, PopAlign, that automatically identifies subpopulations of cells within a heterogeneous mixture, and tracks gene expression and cell abundance changes across subpopulations by constructing and comparing probabilistic models. Probabilistic models provide a low-error, compressed representation of single cell data that enables efficient large-scale computations. We apply PopAlign to analyze the impact of 40 different immunomodulatory compounds on a heterogeneous population of donor-derived human immune cells as well as patient-specific disease signatures in multiple myeloma. PopAlign scales to comparisons involving tens to hundreds of samples, enabling large-scale studies of natural and engineered cell populations as they respond to drugs, signals or physiological change.