bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Nasoalveolar Molding Therapy on Alveolar and Palatal Cleft Deformities in Unilateral and Bilateral Cleft Lip and Palate
Authors: Isik Aslan Belma , Gülşen Ayşe , Findikçioğlu Kemal , Uzuner Deniz , Üçüncü Neslihan 
Published: January 2018

Objective:
The purpose of this study was to evaluate and compare the efficacy of nasoalveolar molding (NAM) therapy in the improvement of alveolar and palatal cleft deformity on unilateral (UCLP) versus bilateral (BCLP) cleft lip and palate.

Materials and Methods:
A total of 19 UCLP (14 boys and 5 girls) and 8 BCLP (7 boys and 1 girl) infants completed NAM therapy were included in this study. Standardized parameters of cleft width of alveol and palate were measured on photocopies taken from the pre- and post-treatment plaster casts. To assess the intragroup differences, paired-samples test in UCLP and Wilcoxon test in BCLP groups were used. Mann–Whitney U test was used to evaluate the differences between the groups.

Results:
Significant decreases in alveolar and palatal cleft gaps were achieved in an average period of 3.3 ± 1.9 and 3.7 ± 1.6 months in UCLP and BCLP patients, respectively. The alveolar cleft decreased 7.85 ± 4.59 mm in UCLP and 4.25 ± 3.13 and 3.81 ± 3.50 mm in right and left alveolar cleft sides in BCLP, respectively. The palatal clefts were decreased 4.63 ± 2.44 mm in medial and 3.72 ± 2.62 mm in posterior parts in UCLP. The decrements in BCLP were 3.00 ± 2.75 mm in medial and 2.88 ± 2.75 mm in posterior palatal cleft distances. No significant differences were determined in the amount of alveolar or palatal cleft closure between UCLP and BCLP groups. The only decrease in arch width was 1.39 mm in medial part of palate in UCLP.

Conclusion:
The NAM device provides significant decreases in both alveolar and palatal cleft deformities in UCLP and BCLP infants, as compared with their birth status.
Uvula Abscess in a Newborn Infant
Authors: Tuncer Erkun , Ors Rahmi 
Published: January 2018

Abstract
Abscesses can be found in several places in the oral cavity, most commonly occurring in peritonsillar and periodontal regions. In this report, the authors described a uvula abscess in a 1-month-old term newborn who was brought to the pediatric outpatient clinic with the complaints of difficulty in sucking-swallowing and refusal to suck at the breast. To the best of the authors’ knowledge this is the first report of a uvula abscess in the literature.
Usefulness of Early Plate Removal in Patients With Occlusal Discrepancies After Sagittal Split Ramus Osteotomy
Authors: Kawase-Koga Yoko , Fujii Yasuyuki , Ikehata Mikiko , Ikehata Naoki , Kono Michihide , Kimoto Akira , Watanabe Masato , Chikazu Daichi 
Published: January 2018

Abstract
The aim of this study was to evaluate the effects of early removal of fixed plates in patients with occlusal discrepancies after sagittal split ramus osteotomy (SSRO) with a focus on the positional relationship of the temporomandibular joint (TMJ). Sagittal split ramus osteotomy with/without Le Fort I osteotomy was performed on 98 patients with mandibular prognathism. Of these 98 patients, 15 with occlusal discrepancies and/or TMJ symptoms underwent early plate removal after SSRO. Finally, 12 consecutive patients were evaluated in this study: 7 underwent bilateral SSRO, 1 underwent unilateral SSRO, and 4 underwent bilateral SSRO with maxillary advancement. The axiolateral TMJ Schuller method was used to evaluate the TMJ position. The authors measured 3 spaces (anterior, superior, and posterior joint spaces) between the condyle and glenoid fossa in the sagittal plane. The anterior and superior joint spaces were significantly larger immediately after the operation than before the operation. After early plate removal, these spaces significantly decreased in size. The posterior joint space increased, but with no significant difference. Three months after SSRO, the size of each of the 3 spaces was closely related to its preoperative size. In conclusion, these results suggest that early removal of fixed plates is 1 treatment option for postoperative occlusal discrepancies after SSRO.
Management of Temporomandibular Joint Ankylosis With Dentofacial Deformities in Children
Authors: Jiang Yangmei , Huang Yuanjin , Ye Bin , Li Yunfeng , Zhu Songsong 
Published: January 2018

Abstract
This retrospective study described the authors’ experience in the treatment of temporomandibular joint (TMJ) ankylosis with dentofacial deformities in 18 pediatric patients during a 4-year period. These patients underwent different types of arthroplasty with condylar reconstruction, simultaneously with treatment of dentofacial deformities. Re-ankylosis was confirmed if maximal incisal opening (MIO) was <20 mm. Clinical outcomes were evaluated in terms of oral function, radiography, and medical photography. Patients were followed up for a mean time of 24.8 months. No infections, re-ankylosis, or permanent facial nerve damage were found during the hospitalization or follow-up period. All patients achieved significant improvements in MIO and oral function. The dentofacial deformities in most patients were improved to varying degrees. The results provided more useful information for the management of the pediatric patients with TMJ ankylosis and secondary dentofacial deformities. Early treatment and close follow-up play an important role in the management of these patients.
The Measurement of Various Anatomical Structures and Assessment of Morphometric Development of Fetal Skull Base
Authors: Hamzaoglu Vural , Aktekin Mustafa , Ismi Onur , Ozalp Hakan , Karşiyaka Dilan , Baskan Fuat Cem , Vayisoglu Yusuf , Arpaci Rabia Bozdogan , Cayan Filiz , Eti Can Mehmet , Cakir Emine Ecem , Gocer Perihan , Turkegun Merve , Kanik Arzu , Bagdatoglu Celal , Talas Derya Umit 
Published: January 2018

Background:
As the skull base has a complex anatomy, we underline the importance of anomalies for side asymmetry. It is useful to investigate relationship between anatomical structures for the surgical procedure orientations. Dural adherence, enlarged superior petrosal sinus, influence of neural crest cells, and cranial base ossification are among the factors in morphometric growth on skull base.

Material and methods:
Twenty-five fetuses of an estimated gestational age ranging from 17 to 34 weeks were studied in the Anatomy Laboratory of Mersin University Medical Faculty. Craniotomy was made to each fetus and brain hemispheres were dissected. We put plates, passing from the external points of lateral and anterior-posterior borders of fetus heads that are perpendicular to each other. An analytical calculation was formulated for the angle of foraminae to the root of zygoma by using different formulations depending on their posterior or anterior location to the root of zygoma. Statistical method was based on correlation analysis, simple regression, independent 2 group t tests, SPSS20.0, and MedCalc 11.5 (MedicReS, New York, NY).

Results:
Neither side dominance for the jugular foramen, nor the differences of foramen rotundum, spinosum, and ovale to anterior skull wall, root of zygoma, and to midline were found to be significant.

Conclusion:
There is a debate on asymmetry of foramina of the skull base. No certain consensus about the initiation time and the causes of asymmetry in the past was documented. Studies are to be encouraged to further enlighten pre-postnatal factors affecting the fetal skull base morphometrism.
The Sellar Tumor: Metastasis or Chordoma?
Authors: Zhou Lin , Cui Daming , Feng Lijin , Gao Liang 
Published: January 2018

Abstract
Chordomas are uncommon, locally invasive chordate tumors, which are mostly observed in the axial skeleton. Numerous papers have described similar patients around different anatomic locations; however, rare document previously reported that intracranial chordoma was associated with clear cell renal cell carcinoma (ccRCC). The authors report a 51-year-old male patient with a history of right radical nephrectomy for ccRCC presented to us with progressive blurred vision. Ophthalmic examination showed vision loss and visual field defects. Magnetic resonance imaging demonstrated pituitary tumor with hemorrhage, which was compressing the optic chiasm. He underwent a transnasal endoscope resection of the sellar mass. The immediate postoperative pathologic result was simply considered to be pituitary metastasis from ccRCC. After further immunohistochemical study, pathology diagnosis was made the necessary corrections to be the sellar chordoma. The authors summarize this exceptional patient and review the pertinent literature briefly.
Subdural Abnormal Communicating Vessel in Chronic Subdural Hematoma
Authors: Tao Zhiqiang , Ding Shenghong , Hu Maotong , Huang Jianyue , Zu Zhigang , Chen Ruchang 
Published: January 2018

Abstract
Traditionally, lacerations of bridging vessels were surmised to cause chronic subdural hematoma (CSDH), although neither observation studies nor medical research was able to testify this. Nowadays, an inflammatory process is known to take place in the development of CSDH. Of note, post-traumatic angiogenesis at its early stage also features inflammation with immune cell infiltration. The authors found a patient suffering from CSDH with unusual angiogenesis between dura and pia matters. The observation of dura-and-pia angiogenesis may be a piece of evidence to underline compensatory reaction of central nervous system to offset the negative effects produced by CSDH, and points out to a possible approach of bolstering angiogenesis to manage ischemic diseases in cerebral hemispheres.
Condylar Hyperplasia in a Monozygotic Twin Girl: An Argument About Etiology
Authors: Goulart Douglas Rangel , Sigua-Rodriguez Eder Alberto , Fariña Rodrigo , Olate Sergio 
Published: January 2018

Abstract
The diagnosis of unilateral condylar hyperplasia (UCH) requires a combined assessment consisting of clinical, radiological, and histopathological examination. The etiology of this condition is unknown. The purpose of this study is to report a rare case of UCH in a monozygotic twin. A 15-year-old girl was referred to our department complaining of facial asymmetry and malocclusion. Computed tomography and single-photon emission computed tomography imaging reveal enlargement of the left condyle and condylar neck, and an increased uptake that was diagnosed as active UCH. During the investigation of family and co-twin facial profile, no cases of UCH were identified. From the case reported in this study, the authors raise a hypothesis that can exist some environmental factor that is related in the development of condylar hyperplasia given the occurrence of this disease in one of twins.
Evaluation of the Effect of Topical Application of Nigella sativa on Acute Radiation-Induced Nasal Mucositis
Authors: Çanakci Hasan , Yilmaz Ayşe Asli Şahin , Canpolat Mustafa Salih , Şeneldir Hatice , Kir Gözde , Eriş Ali Hikmet , Mayadağli Alpaslan , Oysu Çağatay 
Published: January 2018

Abstract
The goal of this study was to demonstrate the effect of radiotherapy (RT) on nasal mucosa in rats and to evaluate the radioprotective effects of the topical application of black seed oil (Nigella sativa [NS]) to treat acute radiation-induced nasal mucositis.
A total of 18 rats were randomized into 3 groups, with 6 animals per group. The rats in group 1 were topically administered saline in the nasal cavity after sham irradiation. Group 2 received saline at the same dose after irradiation. Group 3 was given NS after irradiation. The rats in groups 2 and 3 were irradiated with a single dose of 40 Gy to the nasal and paranasal area. Only one drop of saline (0.05 mL) was applied to each nostril in the first, second, and third days after RT in groups 1 and 2. One drop of cold press NS (0.05 mL) was applied to each nostril in group 3. Fourteen days after irradiation, the nasal mucosal tissues were excised for histopathological evaluation. Vascular dilatation, inflammatory cell infiltration, superficial erosion, and formation of exudates were classified according to the severity.
No evidence of mucositis was observed in group 1. Of all the parameters the only statistically significant difference between groups 2 and 3 were observed for “superficial erosion" (P < 0.05). Overall microscopic observations in the NS-treated group were better than in group 2.
The preliminary results of our study have shown that local application of NS to the nasal mucosa may be an effective treatment of acute nasal mucositis due to RT.
Polyomavirus BK Nephropathy-Associated Transcriptomic Signatures: A Critical Reevaluation
Authors: Pan Ling , Lyu Zili , Adam Benjamin , Zeng Gang , Wang Zijie , Huang Yuchen , Abedin Zahidur , Randhawa Parmjeet 
Published: January 2018

Background
Recent work using DNA microarrays has suggested that genes related to DNA replication, RNA polymerase assembly, and pathogen recognition receptors can serve as surrogate tissue biomarkers for polyomavirus BK nephropathy (BKPyVN).

Methods
We have examined this premise by looking for differential regulation of these genes using a different technology platform (RNA-seq) and an independent set 25 biopsies covering a wide spectrum of diagnoses.

Results
RNA-seq could discriminate T cell–mediated rejection from other common lesions seen in formalin fixed biopsy material. However, overlapping RNA-seq signatures were found among all disease processes investigated. Specifically, genes previously reported as being specific for the diagnosis of BKPyVN were found to be significantly upregulated in T cell–mediated rejection, inflamed areas of fibrosis/tubular atrophy, as well as acute tubular injury.

Conclusions
In conclusion, the search for virus specific molecular signatures is confounded by substantial overlap in pathogenetic mechanisms between BKPyVN and nonviral forms of allograft injury. Clinical heterogeneity, overlapping exposures, and different morphologic patterns and stage of disease are a source of substantial variability in “Omics” experiments. These variables should be better controlled in future biomarker studies on BKPyVN, T cell–mediated rejection, and other forms of allograft injury, before widespread implementation of these tests in the transplant clinic.
Harmonizing semantic annotations for computational models in biology
Authors: Neal ML , König M , Nickerson D , Mısırlı G , Kalbasi R , Dräger A , Atalag K , Chelliah V , Cooling M , Cook DL , Crook S , de Alba M , Friedman SH , Garny A , Gennari JH , Gleeson P , Golebiewski M , Hucka M , Juty N , Le Novère N , Myers C , Olivier BG , Sauro HM , Scharm M , Snoep JL , Touré V , Wipat A , Wolkenhauer O , Waltemath D 
Published: January 2018

AbstractLife science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition, and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current semantic annotation practices among the COmputational Modeling in BIology NEtwork (COMBINE) community and provide a set of recommendations for building a consensus approach to semantic annotation.
Atomic force microscopy of phase separation on ruptured, giant unilamellar vesicles
Authors: Jiang Yanfei , Genin Guy M. , Pryse Kenneth M. , Elson Elliot L. 
Published: January 2018

AbstractGiant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs) are synthetic model systems widely used in biophysical studies of lipid membranes. Phase separation behaviors of lipid species in these two model systems differ due to the lipid-substrate interactions that are present only for SLBs. Therefore, GUVs are believed to resemble natural cell membranes more closely, and a very large body of literature focuses on applying nano-characterization techniques to quantify phase separation on GUVs. However, one important technique, atomic force microscopy (AFM), has not yet been used successfully to study phase separation on GUVs. In the present study, we report that in binary systems, certain phase domains on GUVs retain their original shapes and patterns after the GUVs rupture on glass surfaces. This enabled AFM experiments on phase domains from binary GUVs containing 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) and either 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC). These DLPC/DSPC and DLPC/DPPC GUVs both presented two different gel phases, one of which (bright phase) included a relatively high concentration of DiI-C20but excluded Bodipy-HPC, and the other of which (dark phase) excluded both probes. The bright phases are of interest because they seem to stabilize dark phases against coalescence. Results suggested that the gel phases labeled by DiI-C20in the DLPC/DSPC membrane, which surround the dark gel phase, is an extra layer of membrane, indicating a highly curved structure that might stabilize the interior dark domains. This phenomenon was not found in the DLPC/DPPC membrane. These results show the utility of AFM on collapsed GUVs, and suggest a possible mechanism for stabilization of lipid domains.
HDL-AuNPs-BMS nanoparticle conjugates as molecularly targeted therapy for leukemia
Authors: Shen Na , Yan Fei , Pang Jiuxia , Gao Zhe , Al-Kali Aref , Haynes Christy L. , Litzow Mark R. , Liu Shujun 
Published: January 2018

AbstractIn previous work, gold nanoparticles (AuNPs) with adsorbed high-density lipoprotein (HDL) nanoparticles have been utilized to deliver oligonucleotides, yet HDL-AuNPs functionalized with small molecule inhibitors have not been systematically explored. Here, we report an AuNP-based therapeutic system (HDL-AuNPs-BMS) for acute myeloid leukemia (AML) by delivering BMS309403 (BMS), a small molecule that selectively inhibits AML-promoting factor fatty acid binding protein 4 (FABP4). HDL-AuNPs-BMS are synthesized using a gold nanoparticle as template to control conjugate size and ensure a spherical shape to engineer HDL-like nanoparticle containing BMS. The zeta potential and size of the HDL-AuNPs obtained from transmission electron microscopy (TEM) show that the nanoparticles are electrostatically stable and 25 nm in diameter. Functionally, compared to free drug, HDL-AuNPs-BMS conjugates are more readily internalized by AML cells and have more pronounced effect on downregulation of DNA methyltransferase 1 (DNMT1), reduction of global DNA methylation, and restoration of epigenetically-silenced tumor suppressorp15INK4bcoupled with AML growth arrest. Importantly, systemic administration of HDL-AuNPs-BMS conjugates into AML-bearing mice inhibits DNMT1-dependent DNA methylation, induces AML cell differentiation and diminishes AML disease progression without obvious side effects. In summary, these data, for the first time, demonstrate HDL-AuNPs as an effective delivery platform with great potential to attach distinct inhibitors, and HDL-AuNPs-BMS conjugates as a promising therapeutic platform to treat leukemia.
Inference of CRISPR Edits from Sanger Trace Data
Authors: Hsiau Tim , Conant David , Rossi Nicholas , Maures Travis , Waite Kelsey , Yang Joyce , Joshi Sahil , Kelso Reed , Holden Kevin , Enzmann Brittany L , Stoner Rich 
Published: January 2018

AbstractEfficient precision genome editing requires a quick, quantitative, and inexpensive assay of editing outcomes. Here we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs (gRNAs) and then determines which are supported by the data via regression. Additionally, we develop a score called ICE-D (Discordance) that can provide information on large or unexpected edits. We empirically confirm through over 1,800 edits that the ICE algorithm is robust, reproducible, and can analyze CRISPR experiments within days after transfection. We also confirm that ICE strongly correlates with next-generation sequencing of amplicons (Amp-Seq). The ICE tool is free to use and offers several improvements over current analysis tools. For instance, ICE can analyze individual experiments as well as multiple experiments simultaneously (batch analysis). ICE can also detect a wider variety of outcomes, including multi-guide edits (multiple gRNAs per target) and edits resulting from homology-directed repair (HDR), such as knock-ins and base edits. ICE is a reliable analysis tool that can significantly expedite CRISPR editing workflows. It is available online at ice.synthego.com, and the source code is at github.com/synthego-open/ice
Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution
Authors: Munro Catriona , Siebert Stefan , Zapata Felipe , Howison Mark , Damian Serrano Alejandro , Church Samuel H. , Goetz Freya E. , Pugh Philip R. , Haddock Steven H.D. , Dunn Casey W. 
Published: January 2018

AbstractSiphonophores are a diverse group of hydrozoans (Cnidaria) that are found at all depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. Siphonophores play an important role in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups, however there was little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 30 siphonophore species analyzed in combination with 13 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose twice.