bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum
Authors: Lima Daniel C. , Nyberg Lena K. , Westerlund Fredrik , Batistuzzo de Medeiros Silvia R. 
Published: March 2018

AbstractChromobacterium violaceumis a ß-proteobacterium found widely worldwide with important biotechnological properties and is associated to lethal sepsis in immune-depressed individuals. In this work, we report the discover, complete sequence and annotation of a plasmid detected inC. violaceumthat has been unnoticed until now. We used DNA single-molecule analysis to confirm that the episome found was a circular molecule and then proceeded with NGS sequencing. After DNA annotation, we found that this extra-chromosomal DNA is probably a defective bacteriophage of approximately 44 kilobases, with 39 ORFs comprising, mostly hypothetical proteins. We also found DNA sequences that ensure proper plasmid replication and partitioning as well as a toxin addiction system. This report sheds light on the biology of this important species, helping us to understand the mechanisms by whichC. violaceumendures to several harsh conditions. This discovery could also be a first step in the development of a DNA manipulation tool in this bacterium.
Local oceanographic variability influences the performance of juvenile abalone under climate change
Authors: Boch C. A. , Micheli F. , AlNajjar M. , Monismith S. G. , Beers J. M. , Bonilla J. C. , Espinoza A. M. , Vazquez-Vera L. , Woodson C. B. 
Published: March 2018

AbstractClimate change is causing warming, deoxygenation, and acidification of the global ocean. However, manifestation of climate change may vary at local scales due to oceanographic conditions. Variation in stressors, such as high temperature and low oxygen, at local scales may lead to variable biological responses and spatial refuges from climate impacts. We conducted outplant experiments at two locations separated by ~2.5 km and two sites at each location separated by ~200 m in the nearshore of Isla Natividad, Mexico to assess how local ocean conditions (warming and hypoxia) may affect juvenile abalone performance. Here, we show that abalone growth and mortality mapped to variability in stress exposure across sites and locations. These insights indicate that management decisions aimed at maintaining and recovering valuable marine species in the face of climate change need to be informed by local variability in environmental conditions.
The seasonal occupancy and diel behaviour of Antarctic sperm whales revealed by acoustic monitoring
Authors: Miller Brian S. , Miller Elanor J. 
Published: March 2018

AbstractThe seasonal occupancy and diel behaviour of sperm whales (Physeter macrocephalus) was investigated using data from long-term acoustic recorders deployed off east Antarctica. An automated method for investigating acoustic presence of sperm whales was developed, characterised, and applied to multi-year acoustic datasets at three locations. Instead of focusing on the acoustic properties of detected clicks, the method relied solely on the inter-click-interval (ICI) for determining presence within an hour-long recording. Parameters for our classifier were informed by knowledge of typical vocal behaviour of sperm whales. Sperm whales were detected predominantly from Dec-Feb, occasionally in Nov, Mar, Apr, and May, but never in the Austral winter or early spring months. Ice cover was found to have a statistically significant negative effect on sperm whale presence. In ice-free months sperm whales were detected more often during daylight hours and were seldom detected at night, and this effect was also statistically significant. Seasonal presence at the three east Antarctic recording sites were in accord with what has been inferred from 20th century whale catches off western Antarctica and from stomach contents of whales caught off South Africa.
A behavioral approach to shared mapping of peripersonal space between oneself and others
Authors: Teramoto Wataru 
Published: March 2018

AbstractRecent physiological studies have showed that some visuotactile brain areas respond to other’s peripersonal spaces (PPS) as they would their own. This study investigates this PPS remapping phenomenon in terms of human behavior. Participants placed their left hands on a tabletop screen where visual stimuli were projected. A vibrotactile stimulator was attached to the tip of their index finger. While a white disk approached or receded from the hand in the participant’s near or far space, the participant was instructed to quickly detect a target (vibrotactile stimulation, change in the moving disk’s color or both). When performing this task alone, the participants exhibited shorter detection times when the disk approached the hand in their near space. In contrast, when performing the task with a partner across the table, the participants exhibited shorter detection times both when the disk approached their own hand in their near space and when it approached the partner’s hand in the partner’s near space but the participants’ far space. This phenomenon was also observed when the body parts from which the visual stimuli approached/receded differed between the participant and partner. These results suggest that humans can share PPS representations and/or body-derived attention/arousal mechanisms with others.
Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis
Authors: Martin Tesmine , Lou Yuan-Chao , Chou Chun-Chi , Wei Shu-Yi , Sadotra Sushant , Cho Chao-Cheng , Lin Meng-Hsuan , Tai Jung-Hsiang , Hsu Chun-Hua , Chen Chinpan 
Published: March 2018

AbstractCyclophilin 1 (TvCyP1), a cyclophilin type peptidyl-prolyl isomerase present in the human parasite Trichomonas vaginalis, interacts with Myb1 and assists in its nuclear translocation. Myb1 regulates the expression of ap65-1 gene that encodes for a disease causing cytoadherence enzyme. Here, we determined the crystal structures of TvCyP1 and its complex with the minimum TvCyP1-binding sequence of Myb1 (Myb1104–111), where TvCyP1 formed a homodimer, unlike other single domain cyclophilins. In the complex structure, one Myb1104–111 peptide was bound to each TvCyP1 protomer, with G106-P107 and Y105 fitting well into the active site and auxiliary S2 pocket, respectively. NMR data further showed that TvCyP1 can catalyze the cis/trans isomerization of P107 in Myb1104–111. Interestingly, in the well-folded Myb1 protein (Myb135–141), the minimum binding sequence adopted a different conformation from that of unstructured Myb1104–111 peptide, that could make P107 binding to the active site of TvCyP1 difficult. However, NMR studies showed that similar to Myb1104–111 peptide, Myb135–141 also interacted with the active site of TvCyP1 and the dynamics of the Myb135–141 residues near P107 was reduced upon interaction. Together, the structure of TvCyP1 and detailed structural insights on TvCyP1-Myb1 interaction provided here could pave the way for newer drugs to treat drug-resistant strains.
Rule-based modelling provides an extendable framework for comparing candidate mechanisms underpinning clathrin polymerisation
Authors: Sorokin Anatoly , Heil Katharina F. , Armstrong J. Douglas , Sorokina Oksana 
Published: March 2018

AbstractPolymerisation of clathrin is a key process that underlies clathrin-mediated endocytosis. Clathrin-coated vesicles are responsible for cell internalization of external substances required for normal homeostasis and life –sustaining activity. There are several hypotheses describing formation of closed clathrin structures. According to one of the proposed mechanisms cage formation may start from a flat lattice buildup on the cellular membrane, which is later transformed into a curved structure. Creation of the curved surface requires rearrangement of the lattice, induced by additional molecular mechanisms. Different potential mechanisms require a modeling framework that can be easily modified to compare between them. We created an extendable rule-based model that describes polymerisation of clathrin molecules and various scenarios of cage formation. Using Global Sensitivity Analysis (GSA) we obtained parameter sets describing clathrin pentagon closure and the emergence/production and closure of large-size clathrin cages/vesicles. We were able to demonstrate that the model can reproduce budding of the clathrin cage from an initial flat array.
Longterm Reversal of Severe Visual Loss by Mitochondrial Gene Transfer in a Mouse Model of Leber Hereditary Optic Neuropathy
Authors: Yu Hong , Porciatti Vittorio , Lewin Alfred , Hauswirth William , Guy John 
Published: March 2018

AbstractIn many human disorders mitochondrial dysfunction is central to degeneration of retinal ganglion cells. As these cells do not regenerate, vision is irreversibly lost. Here we show reversal of visual dysfunction by a mitochondrially targeted adeno associated virus in transgenic mice harboring a G11778A mutation in the ND4 subunit of complex I persists longterm and it is associated with reduced loss of RGCs and their axons, improved oxidative phosphorylation, persistence of transferred ND4 DNA and transcription of ND4 mRNA.
Stochastic Modeling of Radiation-induced Dendritic Damage on in silico Mouse Hippocampal Neurons
Authors: Cacao Eliedonna , Parihar Vipan K. , Limoli Charles L. , Cucinotta Francis A. 
Published: March 2018

AbstractCognitive dysfunction associated with radiotherapy for cancer treatment has been correlated to several factors, one of which is changes to the dendritic morphology of neuronal cells. Alterations in dendritic geometry and branching patterns are often accompanied by deficits that impact learning and memory. The purpose of this study is to develop a novel predictive model of neuronal dendritic damages caused by exposure to low linear energy transfer (LET) radiation, such as X-rays, γ-rays and high-energy protons. We establishedin silicorepresentations of mouse hippocampal dentate granule cell layer (GCL) and CA1 pyramidal neurons, which are frequently examined in radiation-induced cognitive decrements. Thein silicorepresentations are used in a stochastic model that describes time dependent dendritic damage induced by exposure to low LET radiation. Changes in morphometric parameters, such as total dendritic length, number of branch points and branch number, including the Sholl analysis for single neurons are described by the model. Our model based predictions for different patterns of morphological changes based on energy deposition in dendritic segments (EDDS) will serve as a useful basis to compare specific patterns of morphological alterations caused by EDDS mechanisms.
Nanoscale High-Tc YBCO/GaN Super-Schottky Diode
Authors: Panna Dmitry , Balasubramanian Krishna , Bouscher Shlomi , Wang Yujia , Yu Pu , Chen Xi , Hayat Alex 
Published: March 2018

AbstractWe demonstrate a high-temperature nanoscale super-Schottky diode based on a superconducting tunnel junction of pulsed-laser-deposited YBCO on GaN thin films. A buffer-free direct growth of nanoscale YBCO thin films on heavily doped GaN was performed to realize a direct high-Tc superconductor-semiconductor junction. The junction shows strongly non-linear I-V characteristics, which have practical applications as a low-voltage super-Schottky diode for microwave mixing and detection. The V-shaped differential conductance spectra observed across the junction are characteristic of the c-axis tunneling into a cuprate superconductor with a certain disorder level. This implementation of the super-Schottky diode, supported by the buffer-free direct growth of nanoscale high-Tc thin films on semiconductors, paves the way for practical large-scale fabrication and integration of high-Tc-superconductor devices in future technologies.
Isolation and characterisation of CD9-positive pituitary adult stem/progenitor cells in rats
Authors: Horiguchi Kotaro , Fujiwara Ken , Yoshida Saishu , Nakakura Takashi , Arae Ken , Tsukada Takehiro , Hasegawa Rumi , Takigami Shu , Ohsako Shunji , Yashiro Takashi , Kato Takako , Kato Yukio 
Published: March 2018

AbstractS100β protein and SOX2-double positive (S100β/SOX2-positive) cells have been suggested to be adult pituitary stem/progenitor cells exhibiting plasticity and multipotency. The aim of the present study was to isolate S100β/SOX2-positive cells from the adult anterior lobes of rats using a specific antibody against a novel membrane marker and to study their characteristics in vitro. We found that cluster of differentiation (CD) 9 is expressed in the majority of adult rat S100β/SOX2-positive cells, and we succeeded in isolating CD9-positive cells using an anti-CD9 antibody with a pluriBead-cascade cell isolation system. Cultivation of these cells showed their capacity to differentiate into endothelial cells via bone morphogenetic protein signalling. By using the anterior lobes of prolactinoma model rats, the localisation of CD9-positive cells was confirmed in the tumour-induced neovascularisation region. Thus, the present study provides novel insights into adult pituitary stem/progenitor cells involved in the vascularisation of the anterior lobe.
MiRNA-142-3p increases radiosensitivity in human umbilical cord blood mononuclear cells by inhibiting the expression of CD133
Authors: Yuan Fang , Liu Lu , Lei Yonghong , Hu Yi 
Published: March 2018

AbstractThis study is to explore the molecular regulation mechanism of CD133 which is associated with malignancy and poor prognosis of blood system diseases. CD133+HUCB-MNC (human umbilical cord blood mononuclear cells) and CD133−HUCB-MNC were isolated and amplificated from umbilical cord blood, and then were exposed to different doses of radiation and subjected to a clonogenic assay. CCK-8 kit was used to detect cell viability, Annexin V-FITC/PI cell apoptosis detection kit was used for the detection of apoptotic cells and the BrdU assay was performed by flow cytometry. The expression of protein was analyzed by western blots. The profile of miRNA expression in response to radiation was examined and validated by RT-PCR. miR-142-3p inhibited the expression of CD133 in umbilical cord blood mononuclear cells to increase radiosensitivity. CD133+HUCB-MNC cells were more radioresistant compared with CD133−HUCB-MNC cells. CD133+HUCB-MNC cells showed higher p-AKT and p-ERK levels after radiation. And miR-142-3p acted on 3′UTR of CD133 mRNA to inhibit CD133 expression. Moreover, miRNA-142-3p mimic increased radiosensitivity in CD133+HUCB-MNC cells. Our results elucidated a novel regulation pathway in hematopoietic stem cells and suggested a potential therapeutic approach for blood system diseases therapy.
Vertical Transport Control of Electrical Charge Carriers in Insulator/Oxide Semiconductor Hetero-structure
Authors: Lee Jinwon , Yoon Kapsoo , Lim Keon-Hee , Park Jun-Woo , Lee Donggun , Cho Nam-Kwang , Kim Youn Sang 
Published: March 2018

AbstractThe technology for electrical current passing through an insulator thin-film between two electrodes is newly getting spotlights for substantial potentials toward advanced functional devices including a diode and a resistive switching device. However, depending on an electrode-limited conduction mechanisms of the conventional devices, a narrow processing window for a thickness of the insulator thin-film and an inability to control a magnitude and direction of the currents are challenges to overcome. Herein, we report a new approach to enable electrical charge carriers to pass stably through a relatively-thick insulator layer and to control a magnitude and polarity of the currents by applying an oxide semiconductor electrode in a metal/insulator/metal structure. We reveal that the electrical conduction in our devices follows a space charge-limited conduction mechanism which mainly depends on the charge carriers injected from contacts. Therefore, characteristics of the current including a current value and a rectification ratio of input signal are precisely controlled by electrical properties of the oxide semiconductor electrode. The unique current characteristics in metal/insulator/oxide semiconductor structures give extendable inspirations in electronic materials science, even a prominent solution for various technology areas of electronics.
Investigation of GeSn Strain Relaxation and Spontaneous Composition Gradient for Low-Defect and High-Sn Alloy Growth
Authors: Dou Wei , Benamara Mourad , Mosleh Aboozar , Margetis Joe , Grant Perry , Zhou Yiyin , Al-Kabi Sattar , Du Wei , Tolle John , Li Baohua , Mortazavi Mansour , Yu Shui-Qing 
Published: March 2018

AbstractRecent development of group-IV alloy GeSn indicates its bright future for the application of mid-infrared Si photonics. Relaxed GeSn with high material quality and high Sn composition is highly desirable to cover mid-infrared wavelength. However, its crystal growth remains a great challenge. In this work, a systematic study of GeSn strain relaxation mechanism and its effects on Sn incorporation during the material growth via chemical vapor deposition was conducted. It was discovered that Sn incorporation into Ge lattice sites is limited by high compressive strain rather than historically acknowledged chemical reaction dynamics, which was also confirmed by Gibbs free energy calculation. In-depth material characterizations revealed that: (i) the generation of dislocations at Ge/GeSn interface eases the compressive strain, which offers a favorably increased Sn incorporation; (ii) the formation of dislocation loop near Ge/GeSn interface effectively localizes defects, leading to the subsequent low-defect grown GeSn. Following the discovered growth mechanism, a world-record Sn content of 22.3% was achieved. The experiment result shows that even higher Sn content could be obtained if further continuous growth with the same recipe is conducted. This report offers an essential guidance for the growth of high quality high Sn composition GeSn for future GeSn based optoelectronics.
Ischämischer und hämorrhagischer Schlaganfall
Authors: Schwert Henning , Bäzner Hansjörg 
Published: March 2018

ZusammenfassungSchlaganfälle können entweder durch den Verschluss eines hirnversorgenden Gefäßes (ischämischer Schlaganfall) oder durch eine intrazerebrale Blutung
(hämorrhagischer Schlaganfall) hervorgerufen werden. Zur Unterscheidung eines hämorrhagischen Schlaganfalls von einem ischämischen Schlaganfall ist eine
Bildgebung mittels Computertomografie (CT) oder Magnetresonanztomografie (MRT) erforderlich. Die strikte Trennung von Ischämie und Hämorrhagierisiko wird der
klinischen Problematik häufig nicht gerecht, da das gemeinsame Vorliegen von ischämischen (z. B. im Rahmen massiver mikroangiopathischer Läsionslast) und
hämorrhagischen Ereignissen (ICBs, zerebrale Mikroblutungen) häufig ist. Eingriffe in die Blutgerinnung sind zur Therapie und Vorbeugung ischämischer
Schlaganfälle sinnvoll und geboten, bei hämorrhagischen Ereignissen aber streng kontraindiziert. Daher ist im Vorfeld eine konsequente Abwägung des potentiellen
Nutzens gegenüber möglichen Blutungskomplikationen unabdingbar.
Effect of HIV and Antiretroviral Treatment on Auditory Functions
Authors: Minhas Ravinder , Iyengar Dhanashree , Thakur Jagdeep , Azad Ramesh 
Published: March 2018

Introduction Numerous studies have evaluated auditory functions in human immunodeficiency virus (HIV) patients; however, these studies had a few major limitations in terms of methodology as they used mainly evoked audiometry although this method is expensive, time consuming and not widely available. Therefore, we conducted a study in naïve HIV subjects with routine audiometry.
Objective To determine the effect of HIV and of the drugs used to treat it on the auditory functions.
Methods A prospective observational study was conducted in a medical college with 25 naive HIV-seropositive patients for over a year. Pure tone audiometry (250–8,000 Hz) and CD4 T-lymphocyte count were performed at the time of enrollment and 6 months after commencement of highly active antiretroviral treatment.
Results The subjects had increased hearing thresholds at high frequencies (4 KHz and 8KHz) in both ears at the time of enrollment that persisted at the same level (p > 0.05) on follow-up at 6 months. None of the subjects had any other otological symptom during the 6 months of observation. Seven subjects had sensorineural hearing loss in one or both ears at 0 and 6 months. These observations did not show any significant difference on Wilcoxon-signed-rank test. Spearman correlation did not find a significant correlation (p > 0.05) between CD4 T-lymphocyte counts and pure tone audiometry during the study.
Conclusion We found high-frequency hearing loss in all subjects with no relation with highly active antiretroviral therapy (HAART) and severity of the disease. This study advocates hearing assessment with pure tone audiometry in HIV subjects so that intervention can be initiated in a timely manner.
Percutaneous Transesophageal Gastric Tubes: Indications, Technique, Safety, Efficacy, and Management
Authors: Burns Kevin , Huang Steven 
Published: March 2018

AbstractPercutaneous transesophageal gastric (PTEG) tube placement is an alternative method of gastric access for feeding or decompression in patients with contraindications to conventional gastrostomy tube placement such as peritoneal carcinomatosis, gastric wall tumors, ascites, or intervening organs. PTEG tube placement is safe with a high technical success rate and it can be placed with supplies available in most interventional radiology departments using ultrasound and fluoroscopic guidance. PTEG tubes are highly efficacious at reducing symptoms in patients with malignant bowel obstruction as an alternative to long-term nasogastric decompression.
CDKL5 Gene-Related Encephalopathy: Pathophysiology, Clinical Presentation, Developmental Prognosis, and Treatment
Authors: Takahashi Yoko , Sumit Parikh , Pestana Knight Elia 
Published: March 2018

AbstractThe cyclin-dependent kinase-like 5 gene (CDKL5) plays a crucial role in brain development. Diseases related to mutations in the CDKL5 gene are considered relatively new disorders. Patients with CDKL5-related disease usually present with early-onset refractory epilepsy and severe global developmental delay. Epilepsy is severe and poorly responsive to conventional medical treatment in most of these patients. Other neurological problems include movement disorder, autonomic symptoms, and sleep problems. In addition to neurological problems, patients may have orthopedic and gastrointestinal disease. Arrhythmia and other heart diseases are uncommon, though more information is needed. Management of patients affected with these diseases requires a multidisciplinary team. Seizures in CDKL5-related disease are very refractory, and treatment with antiseizure medications often fails. Some new drugs currently in clinical trials may show benefit. This article reviews the current status of CDKL5 research, highlighting the pathophysiology, clinical presentation, developmental prognosis, and treatment of CDKL5-related diseases, with the goal of increasing disease recognition.
Massive Ileal Bleeding Secondary to a Dieulafoyʼs lesion
Authors: Becq Aymeric , Dray Xavier , Boarini Giulia 
Published: March 2018

AbstractDieulafoyʼs lesions are a rare cause of gastrointestinal bleeding. This article presents the case of a young woman presenting with a massive ileal bleeding, secondary to a Dieulafoyʼs lesion. A computed-tomography angiography scan showed an arterial bleeding in the ileum and the diagnosis was confirmed by an emergency peroperative enteroscopy. Surgical treatment was performed. Dieulafoyʼs lesions account for 1 % to 2 % of acute gastrointestinal bleeding and lesions are mostly located in the upper gastrointestinal tract. This case stresses that Dieulafoyʼs lesions can be located in the lower gastrointestinal tract and that in such cases, diagnostic imaging and surgical treatment are often warranted.