bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of genomic signals using dynamic time warping
Authors: Skutkova Helena , Vitek Martin , Babula Petr , Kizek Rene , Provaznik Ivo 
Published: August 2013

Abstract

Background
Classification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a number of imprecisions and requires additional user intervention for exact alignment of the similar segments. The similar segments in DNA represented as a signal are characterized by a similar shape of the curve. The DNA alignment in genomic signals may adjust whole sections not only individual symbols. The dynamic time warping (DTW) is suitable for this purpose and can replace the multiple alignment of symbolic sequences in applications, such as phylogenetic analysis.

Methods
The proposed method is composed of three main parts. The first part represent conversion of symbolic representation of DNA sequences in the form of a string of A,C,G,T symbols to signal representation in the form of cumulated phase of complex components defined for each symbol. Next part represents signals size adjustment realized by standard signal preprocessing methods: median filtration, detrendization and resampling. The final part necessary for genomic signals comparison is position and length alignment of genomic signals by dynamic time warping (DTW).

Results
The application of the DTW on set of genomic signals was evaluated in dendrogram construction using cluster analysis. The resulting tree was compared with a classical phylogenetic tree reconstructed using multiple alignment. The classification of genomic signals using the DTW is evolutionary closer to phylogeny of organisms. This method is more resistant to errors in the sequences and less dependent on the number of input sequences.

Conclusions
Classification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique.
The role of Zic transcription factors in regulating hindbrain retinoic acid signaling
Authors: Drummond Danna L , Cheng Caroline S , Selland Lyndsay G , Hocking Jennifer C , Prichard Lisa B , Waskiewicz Andrew J 
Published: August 2013

Abstract

Background
The reiterated architecture of cranial motor neurons aligns with the segmented structure of the embryonic vertebrate hindbrain. Anterior-posterior identity of cranial motor neurons depends, in part, on retinoic acid signaling levels. The early vertebrate embryo maintains a balance between retinoic acid synthetic and degradative zones on the basis of reciprocal expression domains of the retinoic acid synthesis gene aldhehyde dehydrogenase 1a2 (aldh1a2) posteriorly and the oxidative gene cytochrome p450 type 26a1 (cyp26a1) in the forebrain, midbrain, and anterior hindbrain.

Results
This manuscript investigates the role of zinc finger of the cerebellum (zic) transcription factors in regulating levels of retinoic acid and differentiation of cranial motor neurons. Depletion of zebrafish Zic2a and Zic2b results in a strong downregulation of aldh1a2 expression and a concomitant reduction in activity of a retinoid-dependent transgene. The vagal motor neuron phenotype caused by loss of Zic2a/2b mimics a depletion of Aldh1a2 and is rescued by exogenously supplied retinoic acid.

Conclusion
Zic transcription factors function in patterning hindbrain motor neurons through their regulation of embryonic retinoic acid signaling.
The neurogenic response of cardiac resident nestin(+) cells was associated with GAP43 upregulation and abrogated in a setting of type I diabetes
Authors: Chabot Andreanne , Meus Marc-Andre , Hertig Vanessa , Duquette Natacha , Calderone Angelino 
Published: August 2013

AbstractBackgroundCardiac nestin(+)cells exhibit properties of a neural progenitor/stem cell population characterized by thede novosynthesis of neurofilament-M in response to ischemic injury and 6-hydroxydopamine administration. The induction of growth associated protein 43 (GAP43) was identified as an early event of neurogenesis. The present study tested the hypothesis that thede novosynthesis of neurofilament-M by nestin(+)cells was preceded by the transient upregulation of GAP43 during the acute phase of reparative fibrosis in the infarcted male rat heart. Secondly, a seminal feature of diabetes is impaired wound healing secondary to an inadequate neurogenic response. In this regard, an additional series of experiments tested the hypothesis that the neurogenic response of cardiac nestin(+)cells was attenuated in a setting of type I diabetes.MethodsThe neurogenic response of cardiac nestin(+)cells was examined during the early phase of reparative fibrosis following permanent ligation of the left anterior descending coronary artery in the adult male rat heart. The experimental model of type I diabetes was created following a single injection of streptozotocin in adult male rats. The impact of a type I diabetic environment on the neurogenic response of cardiac nestin(+)cells was examined during myocardial infarction and following the administration of 6-hydroxydopamine.ResultsDuring the early phase of scar formation/healing, the density of GAP43/nestin(+)fibres innervating the peri-infarct/infarct region was significantly increased, whereas neurofilament-M/nestin(+)fibres were absent. With ongoing scar formation/healing, a temporal decrease of GAP43/nestin(+)fibre density and a concomitant increase in the density of innervating neurofilament-M/nestin(+)fibres were observed. The neurogenic response of cardiac nestin(+)cells during scar formation/healing was inhibited following the superimposition of type I diabetes. Thede novosynthesis of neurofilament-M by nestin(+)cells after 6-hydroxydopamine administration was likewise attenuated in the heart of type I diabetic rats whereas the density of GAP43/nestin(+)fibres remained elevated.ConclusionThe transient upregulation of GAP43 apparently represents a transition event during the acquisition of a neuronal-like phenotype and a type I diabetic environment attenuated the neurogenic response of cardiac nestin(+)cells to ischemia and 6-hydroxydopamine.
Impaired skin microcirculation in paediatric patients with type 1 diabetes mellitus
Authors: Heimhalt-El Hamriti Mirjam , Schreiver Corinna , Noerenberg Anja , Scheffler Julia , Jacoby Ulrike , Haffner Dieter , Fischer Dagmar-C 
Published: August 2013

Abstract

Aims/hypothesis
We used Laser Doppler Fluximetry (LDF) to define "normal" endothelial function in a large cohort of healthy children and adolescents and to evaluate skin microcirculation in paediatric patients with type 1 diabetes mellitus.

Methods
LDF was performed in 102 healthy children (12.8 ± 3.3 years of age; 48 male) and 68 patients (12.9 ± 3.3 years of age; 33 male). Duration of disease was 5.0 ± 3.97 years. Each participant sequentially underwent three stimulation protocols (localized thermal hyperaemia with localized warming to maximum 40°C, iontophoretic delivery of pilocarpine hydrochloride (PCH) and sodium nitroprusside (SNP)). The maximum relative increase in skin blood flow and the total relative response, i.e. the area under the curve (AUC) to each stimulus (AUCheat, AUCPCH, AUCSNP) was determined. In addition, the area of a right-angled triangle summarizing the time to and the amplitude of the first peak, which represents the axon reflex mediated neurogenic vasodilation (ARR) was calculated.

Results
In healthy controls, AUCheat, AUCPCH, AUCSNP, and ARR turned out to be independent of sex, age, and anthropometric values. Per parameter the 10th percentile generated from data of healthy controls was used as the lower threshold to define normal endothelial function. Diabetic patients showed significantly reduced vasodilatative response to either physical or pharmacological stimulation with SNP, whereas the response to PCH was comparable in both cohorts. In patients compared to controls i) a significantly higher frequency of impaired vasodilatation in response to heat and SNP was noted and ii) vascular response was classified as pathological in more than one of the parameters with significantly higher frequency.

Conclusions/interpretation
Skin microvascular endothelial dysfunction is already present in about 25% of paediatric type 1 diabetic patients suffering from type 1 diabetes for at least one year. Future studies are needed to assess the predictive value of endothelial dysfunction in the development of long-term (cardio)vascular comorbidity in these patients.
The pathologic response of resected synovial sarcomas to hyperthermic isolated limb perfusion with melphalan and TNF-α: a comparison with the whole group of resected soft tissue sarcomas
Authors: Schwindenhammer Benjamin , Podleska Lars Erik , Kutritz Andrea , Bauer Sebastian , Sheu Sien-Yi , Taeger Georg , Schmid Kurt Werner , Grabellus Florian 
Published: August 2013

Abstract

Background
Hyperthermic isolated limb perfusion with tumor necrosis factor-α and melphalan (TM-HILP) has been successfully used to treat limb soft tissue sarcomas (STSs) with high response rates. The data on the effectiveness of HILP-TM for the treatment of STSs are mainly based on various STS types. The aim of this study was to investigate the responses of synovial sarcomas (SS) to TM-HILP.

Methods
A total of 125 TM-HILP-treated tumors (STSall), including 14 SSs, were included in the study. The tumors were subdivided into proximal and distal limb localizations. Tumor typing (using the WHO classification), resection status (using the UICC classification), and response to therapy were assessed using light microscopy. The SSs were tested for the SYT-SSX translocation using RT-PCR. The following tests were applied: a chi-squared test, a t test, and the Mann-Whitney U test.

Results
The SSs were localized distally more often than were the STS cohort (STS−SS) (85.7% vs. 32.4%) and were smaller (5.8 cm vs. 10.7 cm). There were no differences in the responder/nonresponder ratios or the mean percentages of pathological regression between the SS and STS−SS cohorts (74.0% vs. 76.0%). A general localization-dependent difference in the tumor responses to TM-HILP could not be detected in the STSall cohort (distal, 72.0% vs. proximal, 78.0%); however, a UICC R0 status was more often observed in proximal tumors (distal, 50.0% vs. proximal, 71.4%). There was no association between the SYT-SSX type and SS responses to TM-HILP.

Conclusions
Because of the high response rates, TM-HILP is recommended for the treatment of SSs. The distal limb localization of TM-HILP-treated STSs was generally (STSall cohort) associated with fewer R0 resections.
Management of distal choroidal artery aneurysms in patients with moyamoya disease: report of three cases and review of the literature
Authors: He Kangmin , Zhu Wei , Chen Liang , Mao Ying 
Published: August 2013

Abstract
Prevention of rebleeding plays an important role in the treatment of hemorrhagic moyamoya disease, because rebleeding results in high mortality and morbidity. We discuss possible treatment for patients with moyamoya disease accompanied with distal choroidal artery aneurysms and review the literature to summarize clinical treatment and mechanisms. The cases of three male patients who suffered from intraventricular hemorrhage are presented. Computed tomography (CT) and digital subtractive angiography (DSA) revealed that bleeding was believed to be caused by ruptured aneurysms originating from distal choroidal artery aneurysms. Two patients successfully underwent superficial temporal artery (STA)-middle cerebral artery (MCA) bypass combined with encephalo-duro-myo-synangiosis (EDMS) and the obliteration of the aneurysm. The follow-up DSA or CT scan demonstrated that the aneurysms completely disappeared with the patency of the reconstructed artery. Neither of the patients experienced rebleeding during the follow-up period (up to 34 months). Given conservative treatment, the third patient experienced recurrent hemorrhages 4 months after the first ictus. This study describes treatment for moyamoya disease accompanied with distal choroidal artery aneurysms. Our experience suggests that cerebral revascularization combined with obliteration of the complicated distal aneurysm in the same session is a possible treatment.
Enhanced interaction between natural killer cells and lung cancer cells: involvement in gefitinib-mediated immunoregulation
Authors: He Sisi , Yin Tao , Li Dan , Gao Xiang , Wan Yang , Ma Xuelei , Ye Tinghong , Guo Fuchun , Sun Jianhong , Lin Ziqiang , Wang Yongsheng 
Published: August 2013

Abstract

Background
Natural killer (NK) cells can kill tumor cells in a non-MHC-restricted manner. However, cancer cells frequently escape from the attack of NK cells by multiple ways. In this study, we investigated the effect of gefitinib on the interaction between NK cells and lung cancer cells.

Methods

51Cr release assay, CD107a assay, and IFN-γ secretion assay were performed to detect the sensitivity of lung cancer cell lines A549 and H1975 to NK cells cytotoxicity in the presence of gefitinib. Human NK cells were co-cultured with A549 and H1975 cell lines in the presence of gefitinib. NKG2D ligands, ULBP1, ULBP2, MICA, and MHC-I on tumor cells, and NKG2D, NKp44 and NKp46 on NK cells were evaluated with flow cytometry. 51Cr release assay was performed when NKG2D antibody were added into the co-culture system. Expressions of stat3 and LC3 I/II on tumor cells were determined with western blot after co-cultured with NK cells. After treated with gefitinib, mannose-6-phosphate receptor (MPR) on H1975 cells was evaluated by flow cytometry. 51Cr release assay were performed when MPR antagonist were used.

Results
Gefitinib increased cytotoxicity of NK cells to human lung cancer H1975 cells with EGFR L858R + T790M mutations, while not in A549 cells with wild type EGFR. Gefitinib could block the immune escape by up-regulating the expression of NKG2D ligands ULBP1, ULBP2 or MICA on tumor cells and NKG2D on NK cells in the co-culture system. Gefitinib and NK cells up-regulated MHC-I expression in A549 while not in H1975 cells. NKG2D antibody blocked the enhanced NK cytotoxicity by gefitinib. The combination of NK cells and gefitinib could significantly down-regulate stat3 expression. Furthermore, NK cells-mediated tumor cell autophagy was observed in A549 cells while not in H1975 cells. Notably, gefitinib increased autophagy and MPR expression in H1975 cells, which improved the sensitivity to NK cell-based immunotherapy.

Conclusions
Gefitinib greatly enhanced NK cell cytotoxicity to lung cancer cells with EGFR L858R + T790M resistance mutation. Combination of EGFR tyrokinase inhibitors and NK cells adoptive immunotherapy may represent a potentially effective strategy for patients with non-small cell lung cancer.
Efficient compressive sampling of spatially sparse fields in wireless sensor networks
Authors: Colonnese Stefania , Cusani Roberto , Rinauro Stefano , Ruggiero Giorgia , Scarano Gaetano 
Published: August 2013

Abstract
Wireless sensor networks (WSNs), i.e., networks of autonomous, wireless sensing nodes spatially deployed over a geographical area, are often faced with acquisition of spatially sparse fields. In this paper, we present a novel bandwidth/energy-efficient compressive sampling (CS) scheme for the acquisition of spatially sparse fields in a WSN. The paper contribution is twofold. Firstly, we introduce a sparse, structured CS matrix and analytically show that it allows accurate reconstruction of bidimensional spatially sparse signals, such as those occurring in several surveillance application. Secondly, we analytically evaluate the energy and bandwidth consumption of our CS scheme when it is applied to data acquisition in a WSN. Numerical results demonstrate that our CS scheme achieves significant energy and bandwidth savings with respect to state-of-the-art approaches when employed for sensing a spatially sparse field by means of a WSN.
HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358
Authors: Bichel Katsiaryna , Price Amanda J , Schaller Torsten , Towers Greg J , Freund Stefan MV , James Leo C 
Published: August 2013

Abstract

Background
Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells. Infection of non-dividing cells requires transport through the nuclear pore but how this is mediated is unknown.

Results
Here we present the crystal structure of the N-terminal capsid domain of HIV-1 in complex with the cyclophilin domain of nuclear pore protein NUP358. The structure reveals that HIV-1 is positioned to allow single-bond resonance stabilisation of exposed capsid residue P90. NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid. In contrast, the distantly related feline lentivirus FIV can bind NUP358 but is neither isomerized by it nor requires it for infection.

Conclusion
Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating.
Isolation of midgut escape mutants of two American genotype dengue 2 viruses from Aedes aegypti
Authors: Khoo Cynthia CH , Doty Jeffrey B , Held Nicole L , Olson Ken E , Franz Alexander WE 
Published: August 2013

Abstract

Background
Several studies have shown that American genotype dengue 2 viruses (DENV2) have reduced viral fitness in the mosquito vector, Aedes aegypti, compared to other DENV2 genotypes. Diminished replication efficiency or inability to efficiently traverse membrane barriers encompassing organs such as the midgut or salivary glands are considered major factors negatively impacting viral fitness in the mosquito.

Results
We analyzed the vector competence of Ae. aegypti for two American DENV2 strains, QR94 and PR159 originating from Mexico and Puerto-Rico, respectively. Both strains infected mosquito midguts following acquisition of infectious bloodmeals. However, DENV2-QR94 and DENV2-PR159 poorly disseminated from the midgut at 7 or 14 days post-bloodmeal (pbm). We detected one virus isolate, EM33, among 31 DENV2-QR94 infected mosquitoes, and one isolate, EM41, among 121 DENV2-PR159 infected mosquitoes, generating high virus titers in mosquito carcasses at 7 days pbm. In oral challenge experiments, EM33 and EM41 showed midgut dissemination rates of 40-50%. Replication efficiency of EM41 in secondary mosquito tissue was similar to that of a dissemination-competent control strain, whereas the replication efficiency of EM33 was significantly lower than that of the control virus. The genome sequence of DENV2-QR94 encoded seven unique amino acids (aa), which were not found in 100 of the most closely related DENV2 strains. EM33 had one additional aa change, E202K, in the E protein. DENV2-PR159 encoded four unique aa residues, one of them E202K, whereas EM41 had two additional aa substitutions, Q77E in the E protein and E93D in NS3.

Conclusions
Our results indicate that the midgut of Ae. aegypti acts as a selective sieve for DENV2 in which genetically distinct, dissemination-competent virus variants are rapidly selected from the viral quasispecies to be transmitted to vertebrates.
Japanese encephalitis virus infects porcine kidney epithelial PK15 cells via clathrin- and cholesterol-dependent endocytosis
Authors: Yang Songbai , He Minhui , Liu Xiangdong , Li Xinyun , Fan Bin , Zhao Shuhong 
Published: August 2013

Abstract

Background
Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes acute viral encephalitis in humans. Pigs are important amplifiers of JEV. The entry mechanism of JEV into porcine cells remains largely unknown. In this study, we present a study of the internalization mechanism of JEV in porcine kidney epithelial PK15 cells.

Results
We demonstrated that the disruption of the lipid raft by cholesterol depletion with methyl-β-cyclodextrin (MβCD) reduced JEV infection. We also found that the knockdown of clathrin by small interfering RNA (siRNA) significantly reduced JEV-infected cells and JEV E-glycoprotein levels, suggesting that JEV utilizes clathrin-dependent endocytosis. In contrast, the knockdown of caveolin-1, a principal component of caveolae, had only a small (although statistically significant) effect on JEV infection, however, JEV entry was not affected by genistein. These results suggested that JEV entry was independent of caveolae.

Conclusions
Taken together, our results demonstrate that JEV enters porcine kidney epithelial PK15 cells through cholesterol- and clathrin-mediated endocytosis.
Voxel-level comparison of arterial spin-labeled perfusion magnetic resonance imaging in adolescents with internet gaming addiction
Authors: Feng Qi , Chen Xue , Sun Jinhua , Zhou Yan , Sun Yawen , Ding Weina , Zhang Yong , Zhuang Zhiguo , Xu Jianrong , Du Yasong 
Published: August 2013

Abstract

Background
Although recent studies have clearly demonstrated functional and structural abnormalities in adolescents with internet gaming addiction (IGA), less is known about how IGA affects perfusion in the human brain. We used pseudocontinuous arterial spin-labeling (ASL) perfusion functional magnetic resonance imaging (fMRI) to measure the effects of IGA on resting brain functions by comparing resting cerebral blood flow in adolescents with IGA and normal subjects.

Methods
Fifteen adolescents with IGA and 18 matched normal adolescents underwent structural and perfusion fMRI in the resting state. Direct subtraction, voxel-wise general linear modeling was performed to compare resting cerebral blood flow (CBF) between the 2 groups. Correlations were calculated between the mean CBF value in all clusters that survived AlphaSim correction and the Chen Internet Addiction Scale (CIAS) scores, Barratt Impulsiveness Scale-11 (BIS-11) scores, or hours of Internet use per week (hours) in the 15 subjects with IGA.

Results
Compared with control subjects, adolescents with IGA showed significantly higher global CBF in the left inferior temporal lobe/fusiform gyrus, left parahippocampal gyrus/amygdala, right medial frontal lobe/anterior cingulate cortex, left insula, right insula, right middle temporal gyrus, right precentral gyrus, left supplementary motor area, left cingulate gyrus, and right inferior parietal lobe. Lower CBF was found in the left middle temporal gyrus, left middle occipital gyrus, and right cingulate gyrus. There were no significant correlations between mean CBF values in all clusters that survived AlphaSim correction and CIAS or BIS-11 scores or hours of Internet use per week.

Conclusions
In this study, we used ASL perfusion fMRI and noninvasively quantified resting CBF to demonstrate that IGA alters the CBF distribution in the adolescent brain. The results support the hypothesis that IGA is a behavioral addiction that may share similar neurobiological abnormalities with other addictive disorders.