bluuebunny/crossref_metadata_2025_split huggingface dataset:
Definition of Proteasomal Peptide Splicing Rules for High-Efficiency Spliced Peptide Presentation by MHC Class I Molecules
Authors: Berkers Celia R. , de Jong Annemieke , Schuurman Karianne G. , Linnemann Carsten , Meiring Hugo D. , Janssen Lennert , Neefjes Jacques J. , Schumacher Ton N. M. , Rodenko Boris , Ovaa Huib 
Published: September 2015

Abstract
Peptide splicing, in which two distant parts of a protein are excised and then ligated to form a novel peptide, can generate unique MHC class I–restricted responses. Because these peptides are not genetically encoded and the rules behind proteasomal splicing are unknown, it is difficult to predict these spliced Ags. In the current study, small libraries of short peptides were used to identify amino acid sequences that affect the efficiency of this transpeptidation process. We observed that splicing does not occur at random, neither in terms of the amino acid sequences nor through random splicing of peptides from different sources. In contrast, splicing followed distinct rules that we deduced and validated both in vitro and in cells. Peptide ligation was quantified using a model peptide and demonstrated to occur with up to 30% ligation efficiency in vitro, provided that optimal structural requirements for ligation were met by both ligating partners. In addition, many splicing products could be formed from a single protein. Our splicing rules will facilitate prediction and detection of new spliced Ags to expand the peptidome presented by MHC class I Ags.
Maternal Antibiotic Treatment Protects Offspring from Diabetes Development in Nonobese Diabetic Mice by Generation of Tolerogenic APCs
Authors: Hu Youjia , Peng Jian , Tai Ningwen , Hu Changyun , Zhang Xiaojun , Wong F. Susan , Wen Li 
Published: September 2015

Abstract
Type 1 diabetes (T1D) is a T cell–mediated autoimmune disease that involves the slow, progressive destruction of islet β cells and loss of insulin production, as a result of interaction with environmental factors, in genetically susceptible individuals. The gut microbiome is established very early in life. Commensal microbiota establish mutualism with the host and form an important part of the environment to which individuals are exposed in the gut, providing nutrients and shaping immune responses. In this study, we studied the impact of targeting most Gram-negative bacteria in the gut of NOD mice at different time points in their life, using a combination of three antibiotics—neomycin, polymyxin B, and streptomycin—on diabetes development. We found that the prenatal period is a critical time for shaping the immune tolerance in the progeny, influencing development of autoimmune diabetes. Prenatal neomycin, polymyxin B, and streptomycin treatment protected NOD mice from diabetes development through alterations in the gut microbiota, as well as induction of tolerogenic APCs, which led to reduced activation of diabetogenic CD8 T cells. Most importantly, we found that the protective effect was age dependent, and the most profound protection was found when the mice were treated before birth. This indicates the importance of the prenatal environment and early exposure to commensal bacteria in shaping the host immune system and health.
PREDICTION AND SIMULATION OF TIRE PERFORMANCE CHARACTERISTICS BASED ON DEFORMATION INDEX CONCEPT
Authors: Futamura Shingo , Goldstein Arthur A. 
Published: September 2015

ABSTRACTTire performances such as wear, traction, and rolling resistance have been explained by the hysteretic energy loss of tread compounds under cyclic deformations. Loss factor, tan δ, is often used as the property responsible for energy loss. However, dynamic modulus is also reported to affect energy loss and tire performance. In this review, the modulus effect on energy loss is related to the deformation type through the deformation index. The index can be determined experimentally based on tire performance data or analytically through finite element analysis (FEA). Deformation indices of passenger tire rolling resistance, wet traction, and dry traction were determined experimentally based on tire tests. Using FEA, the energy losses and deformation indices were calculated for all elements of a rolling truck tire. The indices vary widely depending on where the element is located. Deformation indices are summarized on a tire component basis and converted into an Excel spreadsheet. The spreadsheet can be used to compute rolling resistance changes arising from component compound substitutions. The deformation index concept is applied to thermomechanical analysis, where it simplifies the fully coupled iterative FEA method into a noniterative computational method. The novelty of this method is in its application to transient thermomechanical problems. The method's simplicity and accuracy are demonstrated using examples.
Estimation of Internet Node Location by Latency Measurements - The Underestimation Problem
Authors: Komosny Dan , Voznak Miroslav , Ganeshan Kathiravelu , Sathu Hira 
Published: September 2015

In this paper we deal with discovering a geographic location of a node in the Internet. Knowledge of location is a fundamental element for many location based applications and web services. We focus on location finding without any assistance of the node being located - client-independent estimation. We estimate a location using communication latency measurements between nodes in the Internet. The latency measured is converted into a geographic distance which is used to derive a location by the multilateration (triangulation) principle. We analyse the latency-to-distance conversion with a consideration of location underestimation which is a product of multilateration failure. We demonstrate that location underestimations do not appear in experimental conditions. However with a real-world scenario, a number of devices cannot be located due to underestimations. Finally, we propose a modification to reduce the number of underestimations in real-world scenarios.DOI: http://dx.doi.org/10.5755/j01.itc.44.3.8353
Internal Carotid Artery Hypoplasia
Authors: Chen Pei-Ya , Liu Hung-Yu , Lim Kun-Eng , Lin Shinn-Kuang 
Published: September 2015

ObjectivesThe purpose of this study was to determine the role of color‐coded carotid duplex sonography for diagnosis of internal carotid artery hypoplasia.MethodsWe retrospectively reviewed 25,000 color‐coded carotid duplex sonograms in our neurosonographic database to establish more diagnostic criteria for internal carotid artery hypoplasia.ResultsA definitive diagnosis of internal carotid artery hypoplasia was made in 9 patients. Diagnostic findings on color‐coded carotid duplex imaging include a long segmental small‐caliber lumen (52% diameter) with markedly decreased flow (13% flow volume) in the affected internal carotid artery relative to the contralateral side but without intraluminal lesions. Indirect findings included markedly increased total flow volume (an increase of 133%) in both vertebral arteries, antegrade ipsilateral ophthalmic arterial flow, and a reduced vessel diameter with increased flow resistance in the ipsilateral common carotid artery. Ten patients with distal internal carotid artery dissection showed a similar color‐coded duplex pattern, but the reductions in the internal and common carotid artery diameters and increase in collateral flow from the vertebral artery were less prominent than those in hypoplasia. The ipsilateral ophthalmic arterial flow was retrograde in 40% of patients with distal internal carotid artery dissection. In addition, thin‐section axial and sagittal computed tomograms of the skull base could show the small diameter of the carotid canal in internal carotid artery hypoplasia and help distinguish hypoplasia from distal internal carotid artery dissection.ConclusionsColor‐coded carotid duplex sonography provides important clues for establishing a diagnosis of internal carotid artery hypoplasia. A hypoplastic carotid canal can be shown by thin‐section axial and sagittal skull base computed tomography to confirm the final diagnosis.
Transcranial Parenchymal Sonographic Findings in Patients With Cerebral Small Vessel Disease
Authors: Pavlović Aleksandra M. , Pekmezović Tatjana , Jovanović Zagorka , Medjedović Tamara Svabic , Veselinović Nikola , Norton Melanie C. , Sternić Nada 
Published: September 2015

ObjectivesPatients with cerebral small vessel disease often present with various motor, cognitive, and emotional changes, including gait disturbances, parkinsonism, and depression. Substantia nigra hyperechogenicity, brain stem raphe hypoechogenicity, ventricle diameters, and sonographic characteristics of other brain structures on transcranial sonography have been increasingly used as biomarkers in a range of neurologic diseases. We aimed to explore the frequency and clinical correlates of transcranial sonographic findings in symptomatic patients with small vessel disease.MethodsIn a cross‐sectional study, neurologic, cognitive, and emotional statuses and transcranial sonographic and magnetic resonance imaging findings were compared between 102 patients with small vessel disease and 45 healthy age‐ and sex‐matched control participants.ResultsCompared to healthy controls, small vessel disease cases had more frequent brain stem raphe hypoechogenicity (55.9% versus 11.1%; P < .0001), substantia nigra hyperechogenicity (30.4% versus 11.1%; P = .022), and enlarged third ventricles (P < .0001). Substantia nigra hyperechogenicity correlated with gait disturbances, extrapyramidal features, and cognitive impairment. Brain stem raphe hypoechogenicity was associated with the diagnosis of depression. Enlargement of the third and lateral ventricles was more frequent in patients with cognitive impairment. Pathologic substantia nigra hyperechogenicity and enlarged ventricles were associated with the severity of cerebral ischemic lesions.ConclusionsTranscranial sonography shows pathologic findings in a substantial number of patients with small vessel disease, probably reflecting disruption of frontostriatal pathways.
Evaluation of a Standardized Program for Training Practicing Anesthesiologists in Ultrasound‐Guided Regional Anesthesia Skills
Authors: Mariano Edward R. , Harrison T. Kyle , Kim T. Edward , Kan Jack , Shum Cynthia , Gaba David M. , Ganaway Toni , Kou Alex , Udani Ankeet D. , Howard Steven K. 
Published: September 2015

ObjectivesPracticing anesthesiologists have generally not received formal training in ultrasound‐guided perineural catheter insertion. We designed this study to determine the efficacy of a standardized teaching program in this population.MethodsAnesthesiologists in practice for 10 years or more were recruited and enrolled to participate in a 1‐day program: lectures and live‐model ultrasound scanning (morning) and faculty‐led iterative practice and mannequin‐based simulation (afternoon). Participants were assessed and recorded while performing ultrasound‐guided perineural catheter insertion at baseline, at midday (interval), and after the program (final). Videos were scored by 2 blinded reviewers using a composite tool and global rating scale. Participants were surveyed every 3 months for 1 year to report the number of procedures, efficacy of teaching methods, and implementation obstacles.ResultsThirty‐two participants were enrolled and completed the program; 31 of 32 (97%) completed the 1‐year follow‐up. Final scores [median (10th–90th percentiles)] were 21.5 (14.5–28.0) of 30 points compared to 14.0 (9.0–20.0) at interval (P < .001 versus final) and 12.0 (8.5–17.5) at baseline (P < .001 versus final), with no difference between interval and baseline. The global rating scale showed an identical pattern. Twelve of 26 participants without previous experience performed at least 1 perineural catheter insertion after training (P < .001). However, there were no differences in the monthly average number of procedures or complications after the course when compared to baseline.ConclusionsPracticing anesthesiologists without previous training in ultrasound‐guided regional anesthesia can acquire perineural catheter insertion skills after a 1‐day standardized course, but changing clinical practice remains a challenge.
Ultrasound Integration in Undergraduate Medical Education: Comparison of Ultrasound Proficiency Between Trained and Untrained Medical Students
Authors: Dinh Vi Am , Dukes William Seth , Prigge Jennifer , Avila Michael 
Published: September 2015

ObjectivesThe benefit of formal ultrasound implementation in undergraduate medical education remains unclear. The goal of this study was to evaluate the effectiveness of ultrasound curriculum implementation during year 1 medical student physical examination teaching on the ultrasound proficiency of medical students.MethodsAn ultrasound curriculum was formally implemented at our institution in August 2012 and since then has successfully trained 2 classes of medical students (year 1 and year 2). Year 3 and year 4 medical students did not receive any formal ultrasound training, as the curriculum had not yet been implemented during their preclinical years. With the use of a 22‐point ultrasound objective structured clinical examination (US‐OSCE), trained medical students were compared to untrained medical students. The US‐OSCE tested image acquisition and interpretation of the following systems: ocular, neck, vascular, pulmonary, cardiovascular, and abdominal. Emergency medicine (EM) residents formally trained in bedside ultrasound were also tested with the US‐OSCE to provide a reference standard.ResultsThere were 174 year 1, 25 year 2, and 19 year 3/year 4 medical students and 30 EM residents tested on the US‐OSCE. Ultrasound‐trained medical students were compared to untrained medical students, and overall US‐OSCE scores ± SD were 91.4% ± 14.0% versus 36.1% ± 21.4% (P < .001), respectively. The EM resident group had an overall score of 99.1% ± 1.8%. The absolute percentage differences were 7.7% between EM resident and ultrasound‐trained medical student scores and 63.0% between EM resident and untrained medical student scores (P < .001).ConclusionsImplementation of an ultrasound curriculum in undergraduate medical education showed a significant increase in trained versus untrained medical student ultrasound capabilities.
Prediction of Left Ventricular Filling Pressure by 3‐Dimensional Speckle‐Tracking Echocardiography in Patients With Coronary Artery Disease
Authors: Ma Hong , Xie Rong-Ai , Gao Li-Jian , Zhang Jin-Ping , Wu Wei-Chun , Wang Hao 
Published: September 2015

ObjectivesThe purpose of this study was to investigate the diagnostic value of 3‐dimensional (3D) speckle‐tracking echocardiography for estimating left ventricular filling pressure in patients with coronary artery disease (CAD) and a preserved left ventricular ejection fraction.MethodsAltogether, 84 patients with CAD and 30 age‐ and sex‐matched healthy control participants in sinus rhythm were recruited prospectively. All participants underwent conventional and 3D speckle‐tracking echocardiography. Global strain values were automatically calculated by 3D speckle‐tracking analysis. The left ventricular end‐diastolic pressure (LVEDP) was determined invasively by left heart catheterization. Echocardiography and cardiac catheterization were performed within 24 hours.ResultsCompared with the controls, patients with CAD showed lower global longitudinal strain, global circumferential strain, global area strain, and global radial strain. Patients with CAD who had an elevated LVEDP had much lower levels of all 4 3D‐speckle‐tracking echocardiographic variables. Pearson correlation analysis revealed that the LVEDP correlated positively with the early transmitral flow velocity/early diastolic myocardial velocity (E/E′) ratio, global longitudinal strain, global circumferential strain, and global area strain. It correlated negatively with global radial strain. Receiver operating characteristic curve analysis revealed that these 3D speckle‐tracking echocardiographic indices could effectively predict elevated left ventricular filling pressure (LVEDP >15 mm Hg) in patients with CAD (areas under the curve: global longitudinal strain, 0.78; global radial strain, 0.77; global circumferential strain, 0.75; and global area strain, 0.74). These parameters, however, showed no advantages over the commonly used E/E′ ratio (area under the curve, 0.84).ConclusionsThree‐dimensional speckle‐tracking echocardiography was a practical technique for predicting elevated left ventricular filling pressure, but it might not be superior to the commonly used E/E′ ratio in patients with CAD who have a normal left ventricular ejection fraction.
Applying Ultrasound‐Guided Core Needle Biopsy for Diagnosis of Thyroid Masses
Authors: Kim Yong Hee , Kwon Hyeong Ju , Kim Eun-Kyung , Kwak Jin Young , Moon Hee Jung , Yoon Jung Hyun 
Published: September 2015

ObjectivesThe purpose of this study was to investigate the level of conclusive results obtained with ultrasound (US)‐guided core needle biopsy (CNB) and how this method should be applied for diagnosis of thyroid nodules.MethodsFrom January 2013 to November 2014, US‐guided CNB was performed in 84 thyroid lesions of 83 patients. Based on CNB pathologic reports, thyroid nodules were divided into 2 categories: conclusive (nodules reaching a definite pathologic diagnosis suggesting benignity or malignancy) and inconclusive (nodules that were not able to reach a definite diagnosis because of ambiguous results). Medical records and US examinations were reviewed and compared.ResultsThe mean age of the 83 patients ± SD was 49.7 ± 14.1 years. Of the 84 thyroid nodules, 73 (86.9%) were diagnosed as benign or malignant and 11 (13.1%) as inconclusive by CNB pathologic analysis. Among the 11 nodules with inconclusive results, the possibility of a follicular neoplasm was suggested in 8 nodules (72.7%). No significant difference was seen in tumor size and US features when comparing the nodules with conclusive and inconclusive results (all P >.05).ConclusionsUltrasound‐guided CNB may have supplemental roles in addition to US‐guided fine‐needle aspiration for diagnosis of selected cases. A considerable proportion of inconclusive results are seen on US‐guided CNB, especially for diagnosis of follicular lesions, which must be considered when using this method for diagnosis of thyroid nodules.
Antidepressants and suicidality: History, the black-box warning, consequences, and current evidence
Authors: Noel Christopher 
Published: September 2015

Abstract

Introduction
The first published literature on the topic of antidepressants and suicidality dates back to the mid-1950s. Today, 10 years after the black-box warning was issued, this controversial topic is still debated. This article will review the data behind the black-box warning and its revision; address the subsequent impact the warning had on depression diagnoses, prescribing patterns, follow-up visits, and suicide rates in the United States; and summarize meta-analyses on this topic published since the revised warning was issued in 2007.

Methods
A PubMed database search using the MeSH terms Antidepressive Agents and Suicide was conducted from January 2012 through October 2014 to identify articles published on the impact the Food and Drug Administration's black-box warning had on health care at a national level and from January 2007 through October 2014 using the same MeSH terms to identify meta-analyses on the current research regarding the link between antidepressants and suicidality. Search results for both topics were further limited to those articles published in English on human participants with the age criteria Child: Birth – 18 years, Adolescent: 13-18 years, or Young Adult: 19-24 years.

Results
Due to the black-box warning, depression diagnoses and antidepressant prescription issuance rates declined in young patients. It is still debated whether the black-box warning had an untoward effect on suicide rates. Most of the meta-analyses identified a small risk of suicidality in the populations studied. Because of the varying nature of the meta-analyses and the major limitation of the limited availability of prospectively collected suicidality data, an absolute risk is still yet to be determined.

Discussion/Conclusion
More studies on antidepressants conducted to prospectively identify suicidality in patients with Major Depressive Disorder and other varying diagnoses need to be completed to truly identify the incidence of suicidal behavior and ideation when initiating antidepressants. Albeit seemingly low, there is a risk of suicidality when initiating antidepressants; there is also risk in not treating depressed patients with antidepressants in whom they are indicated. Clinicians must be cognizant of this risk and monitor high-risk patients per the Food and Drug Administration–recommended guidelines.
Lithium and clozapine in suicidality: shedding some light to get out of the dark
Authors: Riesselman Amber , Johnson Eric , Palmer Emma 
Published: September 2015

Abstract

Introduction
Suicide is currently on the rise with rates increasing alarmingly during the past decade. There are many risk factors for suicidal behavior, and mental illness is at the top of the list.

Methods
Although a variety of medications have been evaluated in the literature, lithium and clozapine continue to have the most evidence supporting their use in decreasing suicidality.

Results
It is clear that medications are indispensable regarding the reduction of suicidality; however, a holistic approach must be taken when caring for this patient population.

Discussion
This review focuses on the specific role that lithium and clozapine have in the reduction of suicidal behavior.
Black Sea temperature response to glacial millennial‐scale climate variability
Authors: Wegwerth Antje , Ganopolski Andrey , Ménot Guillemette , Kaiser Jérôme , Dellwig Olaf , Bard Edouard , Lamy Frank , Arz Helge W. 
Published: September 2015

AbstractThe Eurasian inland propagation of temperature anomalies during glacial millennial‐scale climate variability is poorly understood, but this knowledge is crucial to understanding hemisphere‐wide atmospheric teleconnection patterns and climate mechanisms. Based on biomarkers and geochemical paleothermometers, a pronounced continental temperature variability between 64,000 and 20,000 years ago, coinciding with the Greenland Dansgaard‐Oeschger cycles, was determined in a well‐dated sediment record from the formerly enclosed Black Sea. Cooling during Heinrich events was not stronger than during other stadials in the Black Sea. This is corroborated by modeling results showing that regular Dansgaard‐Oeschger cycles penetrated deeper into the Eurasian continent than Heinrich events. The pattern of coastal ice‐rafted detritus suggests a strong dependence on the climate background state, with significantly milder winters during periods of reduced Eurasian ice sheets and an intensified meridional atmospheric circulation.
Detection of short‐term response of the low ionosphere on gamma ray bursts
Authors: Nina Aleksandra , Simić Saša , Srećković Vladimir A. , Popović Luka Č. 
Published: September 2015

AbstractIn this paper, we study the possibility of detection of short‐term terrestrial lower ionospheric response to gamma ray bursts (GRBs) using a statistical analysis of perturbations of six very low or low‐frequency (VLF/LF) radio signals emitted by transmitters located worldwide and recorded by VLF/LF receiver located in Belgrade (Serbia). We consider a sample of 54 short‐lasting GRBs (shorter than 1 min) detected by the Swift satellite during the period 2009–2012. We find that a statistically significant perturbation can be present in the low ionosphere, and reactions on GRBs may be observed immediately after the beginning of the GRB event or with a time delay of 60 s–90 s.