bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phacoemulsification Cataract Surgery Affects the Discriminative Capacity of Iris Pattern Recognition
Authors: Nigam Ishan , Keshari Rohit , Vatsa Mayank , Singh Richa , Bowyer Kevin 
Published: July 2019

AbstractCataract is a common ophthalmic disorder and the leading cause of blindness worldwide. While cataract is cured via surgical procedures, its impact on iris based biometric recognition has not been effectively studied. The key objective of this research is to assess the effect of cataract surgery on the iris texture pattern as a means of personal authentication. We prepare and release the IIITD Cataract Surgery Database (CaSD) captured from 132 cataract patients using three commercial iris sensors. A non-comparative non-randomized cohort study is performed on the iris texture patterns in CaSD and authentication performance is studied using three biometric recognition systems. Performance is lower when matching pre-operative images to post-operative images (74.69 ± 9.77%) as compared to matching pre-operative images to pre-operative images (93.42 ± 1.76%). 100% recognition performance is observed on a control-group of healthy irises from 68 subjects. Authentication performance improves if cataract affected subjects are re-enrolled in the system, though re-enrollment does not ensure performance at par with pre-operative scenarios (86.67 ± 5.64%). The results indicate that cataract surgery affects the discriminative nature of the iris texture pattern. This finding raises concerns about the reliability of iris-based biometric recognition systems in the context of subjects undergoing cataract surgery.
Daphnia stressor database: Taking advantage of a decade of Daphnia ‘-omics’ data for gene annotation
Authors: Ravindran Suda Parimala , Lüneburg Jennifer , Gottschlich Lisa , Tams Verena , Cordellier Mathilde 
Published: July 2019

AbstractGene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or “hypothetical” gene functions for a large percentage of genomes. This is particularly evident inDaphniagenomes, which contains many regions coding for “hypothetical proteins” and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, theDaphniastressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies onDaphniagene expression. Using a comparative genomics approach, we used the database to annotateD.galeatatranscripts. The extensive body of literature available forDaphniaspecies allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterizedDaphniagenes, thereby increasing our understanding ofDaphnia’s genetic and phenotypic variability.
Sugar alcohol provides imaging contrast in cancer detection
Authors: Bagga Puneet , Wilson Neil , Rich Laurie , Marincola Francesco M. , Schnall Mitchell D. , Hariharan Hari , Haris Mohammad , Reddy Ravinder 
Published: July 2019

AbstractClinical imaging is widely used to detect, characterize and stage cancers in addition to monitoring the therapeutic progress. Magnetic resonance imaging (MRI) aided by contrast agents utilizes the differential relaxivity property of water to distinguish between tumorous and normal tissue. Here, we describe an MRI contrast method for the detection of cancer using a sugar alcohol, maltitol, a common low caloric sugar substitute that exploits the chemical exchange saturation transfer (CEST) property of the labile hydroxyl group protons on maltitol (malCEST). In vitro studies pointed toward concentration and pH-dependent CEST effect peaking at 1 ppm downfield to the water resonance. Studies with control rats showed that intravenously injected maltitol does not cross the intact blood-brain barrier (BBB). In glioma carrying rats, administration of maltitol resulted in the elevation of CEST contrast in the tumor region only owing to permeable BBB. These preliminary results show that this method may lead to the development of maltitol and other sugar alcohol derivatives as MRI contrast agents for a variety of preclinical imaging applications.
A Fiber-Coupled Stimulated Emission Depletion Microscope for Bend-Insensitive Through-Fiber Imaging
Authors: Heffernan Brendan M. , Meyer Stephanie A. , Restrepo Diego , Siemens Mark E. , Gibson Emily A. , Gopinath Juliet T. 
Published: July 2019

AbstractWe present results for a new type of fiber-coupled stimulated emission depletion (STED) microscope which uses a single fiber to transport STED and excitation light, as well as collect the fluorescence signal. Our method utilizes two higher-order eigenmodes of polarization maintaining (PM) fiber to generate the doughnut-shaped STED beam. The modes are excited with separate beams that share no temporal coherence, yielding output that is independent of fiber bending. We measured the resolution using 45 nm fluorescent beads and found a median bead image size of 116 nm. This resolution does not change as function of fiber bending radius, demonstrating robust operation. We report, for the first time, STED images of fixed biological samples collected in the epi-direction through fiber. Our microscope design shows promise for future use in super-resolution micro-endoscopes and in vivo neural imaging in awake and freely-behaving animals.
Prognostic implications of soluble programmed death-ligand 1 and its dynamics during chemotherapy in unresectable pancreatic cancer
Authors: Park Hyunkyung , Bang Ju-Hee , Nam Ah-Rong , Eun Park Ji , Hua Jin Mei , Bang Yung-Jue , Oh Do-Youn 
Published: July 2019

AbstractIn pancreatic cancer, acquiring a sufficient amount of tumor tissue is an obstacle. The soluble form of PD-L1 (sPD-L1) may have immunosuppressive activity. Here, we evaluated the prognostic implications of sPD-L1 in unresectable pancreatic cancer. We prospectively enrolled 60 patients treated with first-line FOLFIRINOX chemotherapy. We collected blood samples at diagnosis, first response assessment and disease progression. Serum sPD-L1 levels were measured using enzyme-linked immunosorbent assays. The median sPD-L1 level was 1.7 ng/mL (range, 0.4–5.7 ng/mL). Patients with low sPD-L1 level (<4.6 ng/mL) at diagnosis showed better overall survival (OS) than those with high sPD-L1 level (P = 0.015). Multivariate analysis identified sPD-L1 and the neutrophil-to-lymphocyte ratio as independent prognostic factors for OS. During chemotherapy, more patients achieved complete response (CR)/partial response (PR) as their best response when sPD-L1 was decreased at the first response assessment (P = 0.038). In the patients who achieved CR/PR as their best response, sPD-L1 was significantly higher at the time of disease progression than at the first response assessment (P = 0.025). In conclusion, the sPD-L1 level at diagnosis exhibits a prognostic value in pancreatic cancer. Furthermore, sPD-L1 dynamics correlate with disease course and could be used to understand various changes in the tumor microenvironment during chemotherapy.
Uncovering missed indels by leveraging unmapped reads
Authors: Hasan Mohammad Shabbir , Wu Xiaowei , Zhang Liqing 
Published: July 2019

AbstractIn current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown great accuracy in mapping short reads to the reference genome, a significant number of short reads still remain unmapped and are often excluded from downstream analyses thereby causing nonnegligible information loss in the subsequent variant calling procedure. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the original procedure. Genesis-indel is applied to the unmapped reads of 30 breast cancer patients from TCGA. Results show that the unmapped reads are conserved between the two subtypes of breast cancer investigated in this study and might contribute to the divergence between the subtypes. Genesis-indel identifies 72,997 novel high-quality indels previously not found, among which 16,141 have not been annotated in the widely used mutation database. Statistical analysis of these indels shows significant enrichment of indels residing in oncogenes and tumour suppressor genes. Functional annotation further reveals that these indels are strongly correlated with pathways of cancer and can have high to moderate impact on protein functions. Additionally, some of the indels overlap with the genes that do not have any indel mutations called from the originally mapped reads but have been shown to contribute to the tumorigenesis in multiple carcinomas, further emphasizing the importance of rescuing indels hidden in the unmapped reads in cancer and disease studies.
Considerations related to the use of short neuropeptide promoters in viral vectors targeting hypothalamic neurons
Authors: Kakava-Georgiadou N. , Bullich-Vilarrubias C. , Zwartkruis M. M. , Luijendijk M. C. M , Garner K. M. , Adan R. A. H. 
Published: July 2019

AbstractTargeting specific neuronal cell types is a major challenge for unraveling their function and utilizing specific cells for gene therapy strategies. Viral vector tools are widely used to target specific cells or circuits for these purposes. Here, we use viral vectors with short promoters of neuropeptide genes to target distinct neuronal populations in the hypothalamus of rats and mice. We show that lowering the amount of genomic copies is effective in increasing specificity of a melanin-concentrating hormone promoter. However, since too low titers reduce transduction efficacy, there is an optimal titer for achieving high specificity and sufficient efficacy. Other previously identified neuropeptide promoters as those for oxytocin and orexin require further sequence optimization to increase target specificity. We conclude that promoter-driven viral vectors should be used with caution in order to target cells specifically.
1H NMR-MS-based heterocovariance as a drug discovery tool for fishing bioactive compounds out of a complex mixture of structural analogues
Authors: Grienke Ulrike , Foster Paul A. , Zwirchmayr Julia , Tahir Ammar , Rollinger Judith M. , Mikros Emmanuel 
Published: July 2019

AbstractChemometric methods and correlation of spectroscopic or spectrometric data with bioactivity results are known to improve dereplication in classical bio-guided isolation approaches. However, in drug discovery from natural sources the isolation of bioactive constituents from a crude extract containing close structural analogues remains a significant challenge. This study is a 1H NMR-MS workflow named ELINA (Eliciting Nature’s Activities) which is based on statistical heterocovariance analysis (HetCA) of 1H NMR spectra detecting chemical features that are positively (“hot”) or negatively (“cold”) correlated with bioactivity prior to any isolation. ELINA is exemplified in the discovery of steroid sulfatase (STS) inhibiting lanostane triterpenes (LTTs) from a complex extract of the polypore fungus Fomitopsis pinicola.
Increased Antiangiogenic Effect by Blocking CCL2-dependent Macrophages in a Rodent Glioblastoma Model: Correlation Study with Dynamic Susceptibility Contrast Perfusion MRI
Authors: Cho Hye Rim , Kumari Nisha , Thi Vu Hien , Kim Hyeonjin , Park Chul-Kee , Choi Seung Hong 
Published: July 2019

AbstractWhen glioblastoma multiforme (GBM) is treated with anti-vascular endothelial growth factor (VEGF) agents, it commonly exhibits tumor progression due to the development of resistance, which results in a dismal survival rate. GBM tumors contain a large number of monocytes/macrophages, which have been shown to be resistant to the effects of bevacizumab. It has been reported that tumor-associated macrophages (TAMs) promote resistance to bevacizumab treatment. Therefore, it is important to target TAMs in the GBM microenvironment. TAMs, which depend on chemokine ligand 2 (CCL2) for differentiation and survival, induce the expression of proangiogenic factors such as VEGF. Dynamic susceptibility contrast (DSC)-MR imaging is an advanced technique that provides information on tumor blood volume and can potentially predict the response to several treatments, including anti-angiogenic agents such as bevacizumab, in human GBM. In this study, we used a CCL2 inhibitor, mNOX-E36, to suppress the recruitment of TAMs in a CCL2-expressing rat GBM model and investigated the effect of combination therapy with bevacizumab using DSC-MR imaging. We demonstrated that the inhibition of CCL2 blocked macrophage recruitment and angiogenesis, which resulted in decreased tumor volume and blood volume in CCL2-expressing GBM in a rat model. Our results provide direct evidence that CCL2 expression can increase the resistance to bevacizumab, which can be assessed noninvasively with the DSC-MR imaging technique. This study shows that the suppression of CCL2 can play an important role in increasing the efficacy of anti-angiogenic treatment in GBM by inhibiting the recruitment of CCL2-dependent macrophages.
Colicin Z, a structurally and functionally novel colicin type that selectively kills enteroinvasive Escherichia coli and Shigella strains
Authors: Micenková Lenka , Bosák Juraj , Kucera Jiri , Hrala Matěj , Dolejšová Tereza , Šedo Ondrej , Linke Dirk , Fišer Radovan , Šmajs David 
Published: July 2019

AbstractColicin production in Escherichia coli (E. coli) strains represents an important trait with regard to microbial survival and competition in the complex intestinal environment. A novel colicin type, colicin Z (26.3 kDa), was described as a product of an original producer, extraintestinal E. coli B1356 strain, isolated from the anorectal abscess of a 17 years-old man. The 4,007 bp plasmid (pColZ) was completely sequenced and colicin Z activity (cza) and colicin Z immunity (czi) genes were identified. The cza and czi genes are transcribed in opposite directions and encode for 237 and 151 amino acid-long proteins, respectively. Colicin Z shows a narrow inhibitory spectrum, being active only against enteroinvasive E. coli (EIEC) and Shigella strains via CjrC receptor recognition and CjrB- and ExbB-, ExbD-mediated colicin translocation. All tested EIEC and Shigella strains isolated between the years 1958–2010 were sensitive to colicin Z. The lethal effect of colicin Z was found to be directed against cell wall peptidoglycan (PG) resulting in PG degradation, as revealed by experiments with Remazol Brilliant Blue-stained purified peptidoglycans and with MALDI-TOF MS analyses of treated PG. Colicin Z represents a new class of colicins that is structurally and functionally distinct from previously studied colicin types.
Five main phases of landscape degradation revealed by a dynamic mesoscale model analysing the splitting, shrinking, and disappearing of habitat patches
Authors: Kun Ádám , Oborny Beáta , Dieckmann Ulf 
Published: July 2019

AbstractThe ecological consequences of habitat loss and fragmentation have been intensively studied on a broad, landscape-wide scale, but have less been investigated on the finer scale of individual habitat patches, especially when considering dynamic turnovers in the habitability of sites. We study changes to individual patches from the perspective of the inhabitant organisms requiring a minimum area for survival. With patches given by contiguous assemblages of discrete habitat sites, the removal of a single site necessarily causes one of the following three elementary local events in the affected patch: splitting into two or more pieces, shrinkage without splitting, or complete disappearance. We investigate the probabilities of these events and the effective size of the habitat removed by them from the population’s living area as the habitat landscape gradually transitions from pristine to totally destroyed. On this basis, we report the following findings. First, we distinguish four transitions delimiting five main phases of landscape degradation: (1) when there is only a little habitat loss, the most frequent event is the shrinkage of the spanning patch; (2) with more habitat loss, splitting becomes significant; (3) splitting peaks; (4) the remaining patches shrink; and (5) finally, they gradually disappear. Second, organisms that require large patches are especially sensitive to phase 3. This phase emerges at a value of habitat loss that is well above the percolation threshold. Third, the effective habitat loss caused by the removal of a single habitat site can be several times higher than the actual habitat loss. For organisms requiring only small patches, this amplification of losses is highest during phase 4 of the landscape degradation, whereas for organisms requiring large patches, it peaks during phase 3.
Quantifying Microsecond Exchange in Large Protein Complexes with Accelerated Relaxation Dispersion Experiments in the Solid State
Authors: Öster Carl , Kosol Simone , Lewandowski Józef R. 
Published: July 2019

AbstractSolid state NMR is a powerful method to obtain information on the structure and dynamics of protein complexes that, due to solubility and size limitations, cannot be achieved by other methods. Here, we present an approach that allows the quantification of microsecond conformational exchange in large protein complexes by using a paramagnetic agent to accelerate 15N R1ρ relaxation dispersion measurements and overcome sensitivity limitations. The method is validated on crystalline GB1 and then applied to a >300 kDa precipitated complex of GB1 with full length human immunoglobulin G (IgG). The addition of a paramagnetic agent increased the signal to noise ratio per time unit by a factor of 5, which allowed full relaxation dispersion curves to be recorded on a sample containing less than 50 μg of labelled material in 5 and 10 days on 850 and 700 MHz spectrometers, respectively. We discover a similar exchange process across the β-sheet in GB1 in crystals and in complex with IgG. However, the slow motion observed for a number of residues in the α-helix of crystalline GB1 is not detected in the complex.
In-parallel resonators to increase the absorption of subwavelength acoustic absorbers in the mid-frequency range
Authors: Aurégan Yves , Farooqui Maaz 
Published: July 2019

AbstractThe acoustic effects of in-parallel resonators is compared to the behavior of a classical single degree of freedom resonator for which the resistance and the mass are in series. In-parallel resonators serve to enhance the acoustic absorption for mid-frequencies thereby extending the active frequency range of perfect acoustic absorbers. Two implementations of these in-parallel absorbers are presented and investigated experimentally as well as numerically. In the first demonstration, the resistance is a perforated plate with a wiremesh and the oscillating mass is the air that fills a tube passing through the plate. The second implementation consists of a thin flexible beam that oscillates and where the resistance is due to the micro-slit resulting from the cutting of the beam.
InGaP electron spectrometer for high temperature environments
Authors: Butera S. , Lioliou G. , Zhao S. , Whitaker M. D. C. , Krysa A. B. , Barnett A. M. 
Published: July 2019

AbstractIn this work, a 200 μm diameter InGaP (GaInP) p+-i-n+ mesa photodiode was studied across the temperature range 100 °C to 20 °C for the development of a temperature-tolerant electron spectrometer. The depletion layer thickness of the InGaP device was 5 μm. The performance of the InGaP detector was analysed under dark conditions and then under the illumination of a 183 MBq 63Ni radioisotope beta particle source. The InGaP photodiode was connected to a custom-made low-noise charge-sensitive preamplifier to realise a particle counting electron spectrometer. Beta spectra were collected at temperatures up to 100 °C with the InGaP device reverse biased at 5 V. The spectrum accumulated at 20 °C was compared with the spectrum predicted using Monte Carlo simulations; good agreement was found between the predicted and experimental spectra. The work is of importance for the development of electron spectrometers that can be used for planetary and space science missions to environments of high temperature or extreme radiation (e.g. Mercury, Jupiter’s moon Europa, near-Sun comets), as well as terrestrial applications.
Ru(II)-thymine complex causes DNA damage and apoptotic cell death in human colon carcinoma HCT116 cells mediated by JNK/p38/ERK1/2 via a p53-independent signaling
Authors: Silva Suellen L. R. , Baliza Ingrid R. S. , Dias Rosane B. , Sales Caroline B. S. , Rocha Clarissa A. Gurgel , Soares Milena B. P. , Correa Rodrigo S. , Batista Alzir A. , Bezerra Daniel P. 
Published: July 2019

AbstractRu(II)-thymine complex [Ru(PPh3)2(Thy)(bipy)]PF6 (where PPh3 = triphenylphosphine, Thy = thyminate and bipy = 2,2′-bipyridine) is a potent cytotoxic agent with ability to bind to DNA, inducing caspase-mediated apoptosis in leukemia cells. In this study, we investigated the mechanism underlying the cell death induction by Ru(II)-thymine complex in human colon carcinoma HCT116 cells, as well as its effect in xenograft tumor model. The Ru(II)-thymine complex increased significantly the percentage of apoptotic HCT116 cells. Co-treatment with a JNK/SAPK inhibitor, p38 MAPK inhibitor and MEK inhibitor, which inhibit the activation of ERK1/2, caused a marked reduction of the percentage of complex-induced apoptotic cells. Moreover, the Ru(II)-thymine complex induced an increase in phospho-JNK2 (T183/Y185), phospho-p38α (T180/Y182) and phospho-ERK1 (T202/Y204) levels in HCT116 cells. Treatment with the Ru(II)-thymine complex increased significantly the phospho-histone H2AX (S139) expression, a DNA damage marker. The expression of phospho-p53 (S15) and MDM2 were not changed, and the co-treatment with a p53 inhibitor (cyclic pifithrin-α) did not reduce the complex-induced apoptosis in HCT116 cells, indicating that the Ru(II)-thymine complex induces DNA damage-mediated apoptosis by JNK/p38/ERK1/2 via a p53-independent signaling. The Ru(II)-thymine complex (1 and 2 mg/kg/day) also inhibited HCT116 cell growth in a xenograft model, reducing the tumor mass at 32.6–40.1%. Altogether, indicate that the Ru(II)-thymine complex is a promising anti-colon cancer drug candidate.
A comprehensive study on genome-wide coexpression network of KHDRBS1/Sam68 reveals its cancer and patient-specific association
Authors: Sumithra B. , Saxena Urmila , Das Asim Bikas 
Published: July 2019

AbstractHuman KHDRBS1/Sam68 is an oncogenic splicing factor involved in signal transduction and pre-mRNA splicing. We explored the molecular mechanism of KHDRBS1 to be a prognostic marker in four different cancers. Within specific cancer, including kidney renal papillary cell carcinoma (KIRP), lung adenocarcinoma (LUAD), acute myeloid leukemia (LAML), and ovarian cancer (OV), KHDRBS1 expression is heterogeneous and patient specific. In KIRP and LUAD, higher expression of KHDRBS1 affects the patient survival, but not in LAML and OV. Genome-wide coexpression analysis reveals genes and transcripts which are coexpressed with KHDRBS1 in KIRP and LUAD, form the functional modules which are majorly involved in cancer-specific events. However, in case of LAML and OV, such modules are absent. Irrespective of the higher expression of KHDRBS1, the significant divergence of its biological roles and prognostic value is due to its cancer-specific interaction partners and correlation networks. We conclude that rewiring of KHDRBS1 interactions in cancer is directly associated with patient prognosis.