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https://www.readbyqxmd.com/read/28720581/hit-ndrive-patient-specific-multi-driver-gene-prioritization-for-precision-oncology
#1
Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C Collins, Cenk Sahinalp
Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT'nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the "random walk facility location" (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: "multi-hitting time", the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene...
July 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28691918/optical-fingerprint-of-non-covalently-functionalized-transition-metal-dichalcogenides
#2
Maja Feierabend, Ermin Malic, Andreas Knorr, Gunnar Berghäuser
Atomically thin transition metal dichalcogenides (TMDs) hold promising potential for applications in optoelectronics. Due to their direct band gap and the extraordinarily strong Coulomb interaction, TMDs exhibit efficient light-matter coupling and tightly bound excitons. Moreover, large spin orbit coupling in combination with circular dichroism allows for spin and valley selective optical excitation. As atomically thin materials, they are very sensitive to changes in the surrounding environment. This motivates a functionalization approach, where external molecules are adsorbed to the materials surface to tailor its optical properties...
July 10, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28542564/the-pet-and-lim1-2-domains-of-testin-contribute-to-intramolecular-and-homodimeric-interactions
#3
Stefano Sala, Marie Catillon, Ermin Hadzic, Elisabeth Schaffner-Reckinger, Marleen Van Troys, Christophe Ampe
The focal adhesion protein testin is a modular scaffold and tumour suppressor that consists of an N-terminal cysteine rich (CR) domain, a PET domain of unknown function and three C-terminal LIM domains. Testin has been proposed to have an open and a closed conformation based on the observation that its N-terminal half and C-terminal half directly interact. Here we extend the testin conformational model by demonstrating that testin can also form an antiparallel homodimer. In support of this extended model we determined that the testin region (amino acids 52-233) harbouring the PET domain interacts with the C-terminal LIM1-2 domains in vitro and in cells, and assign a critical role to tyrosine 288 in this interaction...
2017: PloS One
https://www.readbyqxmd.com/read/28485387/unconventional-double-bended-saturation-of-carrier-occupation-in-optically-excited-graphene-due-to-many-particle-interactions
#4
Torben Winzer, Martin Mittendorff, Stephan Winnerl, Henry Mittenzwey, Roland Jago, Manfred Helm, Ermin Malic, Andreas Knorr
Saturation of carrier occupation in optically excited materials is a well-established phenomenon. However, so far, the observed saturation effects have always occurred in the strong-excitation regime and have been explained by Pauli blocking of the optically filled quantum states. On the basis of microscopic theory combined with ultrafast pump-probe experiments, we reveal a new low-intensity saturation regime in graphene that is purely based on many-particle scattering and not Pauli blocking. This results in an unconventional double-bended saturation behaviour: both bendings separately follow the standard saturation model exhibiting two saturation fluences; however, the corresponding fluences differ by three orders of magnitude and have different physical origin...
May 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28470501/assessment-of-long-range-transport-potential-of-polychlorinated-naphthalenes-based-on-three-dimensional-qsar-models
#5
Xiaolei Wang, Wenen Gu, Ermin Guo, Chunyue Cui, Yu Li
Experimentally determined octanol-air partition coefficients (K OA) for 43 polychlorinated naphthalene (PCN) congeners and experimentally determined subcooled liquid vapor pressures (P L) for 17 PCN congeners were used with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) to generate three-dimensional quantitative structure-activity relationship (3D-QSAR) models. The data were used to predict K OA values for the other 32 congeners and P L values for the other 58 congeners...
June 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28418035/chronic-social-defeat-reduces-myelination-in-the-mouse-medial-prefrontal-cortex
#6
Michael L Lehmann, Thaddeus K Weigel, Abdel G Elkahloun, Miles Herkenham
The medial prefrontal cortex (mPFC) plays a key role in top-down control of the brain's stress axis, and its structure and function are particularly vulnerable to stress effects, which can lead to depression in humans and depressive-like states in animals. We tested whether chronic social defeat produces structural alterations in the mPFC in mice. We first performed a microarray analysis of mPFC gene expression changes induced by defeat, and biological pathway analysis revealed a dominant pattern of down-regulation of myelin-associated genes...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28394547/influence-of-male-obesity-on-fertility
#7
REVIEW
Miro Kasum, Sonja Anić-Jurica, Ermin Čehić, Tajana Klepac-Pulanić, Josip Juras, Kristina Žužul
The aim of this review is to analyze current diagnostic approaches to obesity in adult men, the potential mechanisms linking obesity to infertility, and treatment options aimed at improving reproductive health. Obesity has become a worldwide epidemic with the estimated prevalence increasing from 28.8% to 36.9% between 1980 and 2013. In terms of diagnosis, numerous simple techniques have been developed including body mass index, waist to hip ratio, waist circumference, bioelectrical impedance analysis, ultrasound and skinfold measurements...
June 2016: Acta Clinica Croatica
https://www.readbyqxmd.com/read/28393578/kisspeptin-as-a-promising-oocyte-maturation-trigger-for-in-vitro-fertilisation-in-humans
#8
Miro Kasum, Daniela Franulić, Ermin Čehić, Slavko Orešković, Albert Lila, Emina Ejubović
The aim of this review is to analyse the effectiveness of exogenous kisspeptin administration as a novel alternative of triggering oocyte maturation, instead of currently used triggers such as human chorionic gonadotropin (hCG) or gonadotropin releasing hormone (GnRH) agonist, in women undergoing in vitro fertilisation (IVF) treatment. Kisspeptin has been considered a master regulator of two modes of GnRH and hence gonadotropin secretion, pulses and surges. Administration of kisspeptin-10 and kisspeptin-54 induces the luteinising hormone (LH) surge required for egg maturation and ovulation in animal investigations and LH release during the preovulatory phase of the menstrual cycle and hypothalamic amenorrhoea in humans...
April 10, 2017: Gynecological Endocrinology
https://www.readbyqxmd.com/read/28294110/proposal-for-dark-exciton-based-chemical-sensors
#9
Maja Feierabend, Gunnar Berghäuser, Andreas Knorr, Ermin Malic
The rapidly increasing use of sensors throughout different research disciplines and the demand for more efficient devices with less power consumption depends critically on the emergence of new sensor materials and novel sensor concepts. Atomically thin transition metal dichalcogenides have a huge potential for sensor development within a wide range of applications. Their optimal surface-to-volume ratio combined with strong light-matter interaction results in a high sensitivity to changes in their surroundings...
March 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28194406/curcumin-ameliorates-diabetic-nephropathy-by-suppressing-nlrp3-inflammasome-signaling
#10
Miaomiao Lu, Nanchang Yin, Wei Liu, Xiangfei Cui, Shuo Chen, Ermin Wang
Diabetic nephropathy (DN) is the leading cause of end-stage renal disease, partly because of the lack of effective treatments for DN. Curcumin has been shown to exert strong antifibrotic effects in DN, but the underlying mechanisms are not well characterized. In this study, we sought to determine the effects of curcumin on diabetic renal disease in db/db mice and characterize the underlying mechanism of action. We administered curcumin to db/db mice for 16 weeks. In comparison to mock-treated db/db mice, curcumin-treated mice showed diminished renal hypertrophy, reduced mesangial matrix expansion, and a lower level of albuminuria...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28131443/fulminant-pneumococcal-pericarditis-in-a-previously-healthy-patient
#11
Cvetan Trpkov, Ermin Nath, Michael Moon, Jonathan Windram, Michelle M Graham
Purulent pericarditis is a rare acutely life-threatening condition. Initial symptoms, signs, and investigations can be nonspecific. Echocardiography is invaluable for establishing the diagnosis and initial management. We present a case of a previously healthy patient with purulent pericarditis caused by Streptococcus pneumoniae in the absence of a primary focus of infection. The patient deteriorated rapidly with cardiac tamponade and septic shock and was managed successfully by a combined medical and surgical approach...
November 17, 2016: Canadian Journal of Cardiology
https://www.readbyqxmd.com/read/27966297/the-role-of-apelin-in-the-assessment-of-response-to-chemotherapyand-prognosis-in-stage-4-nonsmall-cell-lung-cancer
#12
Sinem Ermin, Gürsel Çok, Ali Veral, Timur Köse
BACKGROUND/AIM: Prediction of response to chemotherapy and prognosis bears clinical significance in patients with lung cancer. The aim of the study was to examine the association between apelin expression in tumor tissues and overall survival, progression-free survival, chemoresistance, and treatment response in stage 4 nonsmall cell lung cancer (NSCLC) patients undergoing chemotherapy. MATERIALS AND METHODS: A total of 81 patients who received chemotherapy due to a biopsy-documented diagnosis of NSCLC between 2004 and 2011 were retrospectively studied...
November 17, 2016: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/27819288/excitonic-linewidth-and-coherence-lifetime-in-monolayer-transition-metal-dichalcogenides
#13
Malte Selig, Gunnar Berghäuser, Archana Raja, Philipp Nagler, Christian Schüller, Tony F Heinz, Tobias Korn, Alexey Chernikov, Ermin Malic, Andreas Knorr
Atomically thin transition metal dichalcogenides are direct-gap semiconductors with strong light-matter and Coulomb interactions. The latter accounts for tightly bound excitons, which dominate their optical properties. Besides the optically accessible bright excitons, these systems exhibit a variety of dark excitonic states. They are not visible in the optical spectra, but can strongly influence the coherence lifetime and the linewidth of the emission from bright exciton states. Here, we investigate the microscopic origin of the excitonic coherence lifetime in two representative materials (WS2 and MoSe2) through a study combining microscopic theory with spectroscopic measurements...
November 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/27774297/driving-forces-behind-the-evolution-of-the-aleutian-mink-disease-parvovirus-in-the-context-of-intensive-farming
#14
Marta Canuti, Kimberly E O'Leary, Bruce D Hunter, Grant Spearman, Davor Ojkic, Hugh G Whitney, Andrew S Lang
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography...
January 2016: Virus Evolution
https://www.readbyqxmd.com/read/27631008/altered-clock-and-lipid-metabolism-related-genes-in-atherosclerotic-mice-kept-with-abnormal-lighting-condition
#15
Zhu Zhu, Bingxuan Hua, Zhanxian Shang, Gongsheng Yuan, Lirong Xu, Ermin Li, Xiaobo Li, Ning Sun, Zuoqin Yan, Ruizhe Qian, Chao Lu
Background. The risk of atherosclerosis is elevated in abnormal lipid metabolism and circadian rhythm disorder. We investigated whether abnormal lighting condition would have influenced the circadian expression of clock genes and clock-controlled lipid metabolism-related genes in ApoE-KO mice. Methods. A mouse model of atherosclerosis with circadian clock genes expression disorder was established using ApoE-KO mice (ApoE-KO LD/DL mice) by altering exposure to light. C57 BL/6J mice (C57 mice) and ApoE-KO mice (ApoE-KO mice) exposed to normal day and night and normal diet served as control mice...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27628311/light-conditions-affect-the-performance-of-yponomeuta-evonymellus-on-its-native-host-prunus-padus-and-the-alien-prunus-serotina
#16
A Łukowski, M J Giertych, U Walczak, E Baraniak, P Karolewski
The bird cherry ermine moth, Yponomeuta evonymellus L., is considered an obligatory monophagous insect pest that feeds only on native European Prunus padus L. In recent years, however, increased larval feeding on alien P. serotina Ehrh. has been observed. In both species, general defoliation is extensive for shade grown trees, whereas it is high in P. padus, but very low in P. serotina, when trees are grown in full light conditions. The aim of the present study was to identify how the plant host species and light conditions affect the performance of Y...
April 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/27573929/role-of-salmonella-typhi-vi-antigen-and-secretory-systems-on-immune-response
#17
Ermin Schadich, Petr Džubák, Marián Hajdúch
Virulence capsular polysaccharide (Vi antigen) and Salmonella`s Pathogenicity Island type 1 and 2 (SPI-1 and SPI-2 TTSS) are important membrane virulence factors of human restricted pathogen S. Typhi. The Vi antigen modulates different proinflammatory signaling pathways in infected macrophages, microfold epithelial and dendritic cells. SPI-2 TTSS and its effectors are required for promoting bacterial intracellular survival, replication and apoptosis while SPI-1 and its effectors are associated with invasion of microfold epithelial cells...
August 29, 2016: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/27519674/contributions-of-expected-sensory-and-affective-action-effects-to-action-selection-and-performance-evidence-from-forced-and-free-choice-tasks
#18
Bernhard Hommel, Dominique P Lippelt, Ermine Gurbuz, Roland Pfister
Whereas ideomotor approaches to action control emphasize the importance of sensory action effects for action selection, motivational approaches emphasize the role of affective action effects. We used a game-like experimental setup to directly compare the roles of sensory and affective action effects in selecting and performing reaching actions in forced- and free-choice tasks. The two kinds of action effects did not interact. Action selection and execution in the forced-choice task were strongly impacted by the spatial compatibility between actions and the expected sensory action effects, whereas the free-choice task was hardly affected...
June 2017: Psychonomic Bulletin & Review
https://www.readbyqxmd.com/read/27458346/over-expression-of-meteorin-drives-gliogenesis-following-striatal-injury
#19
Jordan L Wright, Charlotte M Ermine, Jesper R Jørgensen, Clare L Parish, Lachlan H Thompson
A number of studies have shown that damage to brain structures adjacent to neurogenic regions can result in migration of new neurons from neurogenic zones into the damaged tissue. The number of differentiated neurons that survive is low, however, and this has led to the idea that the introduction of extrinsic signaling factors, particularly neurotrophic proteins, may augment the neurogenic response to a level that would be therapeutically relevant. Here we report on the impact of the relatively newly described neurotrophic factor, Meteorin, when over-expressed in the striatum following excitotoxic injury...
2016: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/27426425/fertility-in-men-with-spinal-cord-injury
#20
REVIEW
Ermin Čehić, Miro Kasum, Velimir Šimunić, Slavko Orešković, Goran Vujić, Franjo Grgić
Young men comprise the overwhelming majority of men with spinal cord injury (SCI), the incidence of which has been growing over the years. Due to advances in physical medicine and rehabilitation, remarkable improvements in survival rates have been reported, leading to life expectancies similar to those of the general population. However, many sexual and reproductive functions may be impaired due to erectile or ejaculatory dysfunction and semen abnormalities, characterised by low-sperm motility or viability in SCI males who have not become parents yet...
December 2016: Gynecological Endocrinology
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