bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPECTRUM – A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data
Authors: Basharat Abdul Rehman , Iman Kanzal , Khalid Muhammad Farhan , Anwar Zohra , Hussain Rashid , Kabir Humnah Gohar , Tahreem Maria , Shahid Anam , Humayun Maheen , Hayat Hira Azmat , Mustafa Muhammad , Shoaib Muhammad Ali , Ullah Zakir , Zarina Shamshad , Ahmed Sameer , Uddin Emad , Hamera Sadia , Ahmad Fayyaz , Chaudhary Safee Ullah 
Published: August 2019

AbstractTop-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhanced identification of post-translational modifications (PTMs). However, the complexity of TDP spectra poses a significant impediment to protein search and PTM characterization. Furthermore, limited software support is currently available in the form of search algorithms and pipelines. To address this need, we propose ‘SPECTRUM’, an open-architecture and open-source toolbox for TDP data analysis. Its salient features include: (i) MS2-based intact protein mass tuning, (ii)de novopeptide sequence tag analysis, (iii) propensity-driven PTM characterization, (iv) blind PTM search, (v) spectral comparison, (vi) identification of truncated proteins, (vii) multifactorial coefficient-weighted scoring, and (viii) intuitive graphical user interfaces to access the aforementioned functionalities and visualization of results. We have validated SPECTRUM using published datasets and benchmarked it against salient TDP tools. SPECTRUM provides significantly enhanced protein identification rates (91% to 177%) over its contemporaries. SPECTRUM has been implemented in MATLAB, and is freely available along with its source code and documentation athttps://github.com/BIRL/SPECTRUM/.
Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments
Authors: Brailsford Francesca L. , Glanville Helen C. , Golyshin Peter N. , Johnes Penny J. , Yates Christopher A. , Jones Davey L. 
Published: August 2019

AbstractDissolved organic matter (DOM) represents a key component of carbon (C) cycling in freshwater ecosystems. While the behaviour of bulk dissolved organic carbon (DOC) in aquatic ecosystems is well studied, comparatively little is known about the turnover of specific DOC compounds. The aim of this study was to investigate the persistence of 14C-labelled low molecular weight (LMW) DOC at a wide range of concentrations (0.1 µM to 10 mM), in sediments and waters from oligotrophic and mesotrophic rivers within the same catchment. Overall, rates of DOC loss varied between compound groups (amino acids > sugars = organic acids > phenolics). Sediment-based microbial communities contributed to higher DOC loss from river waters, which was attributed, in part, to its greater microbial biomass. At higher DOC compound concentrations, DOC loss was greater in mesotrophic rivers in comparison to oligotrophic headwaters. A lag-phase in substrate use within sediments provided evidence of microbial growth and adaptation, ascribed here to the lack of inorganic nutrient limitation on microbial C processing in mesotrophic communities. We conclude that the higher microbial biomass and available inorganic nutrients in sediments enables the rapid processing of LMW DOC, particularly during high C enrichment events and in N and P-rich mesotrophic environments.
Predictive value of cervical cytokine, antimicrobial and microflora levels for pre-term birth in high-risk women
Authors: Manning Rashmi , James Catherine P. , Smith Marie C. , Innes Barbara A. , Stamp Elaine , Peebles Donald , Bajaj-Elliott Mona , Klein Nigel , Bulmer Judith N. , Robson Stephen C. , Lash Gendie E. 
Published: August 2019

AbstractSpontaneous preterm birth (sPTB, delivery <37 weeks gestation), accounts for approximately 10% of births worldwide; the aetiology is multifactorial with intra-amniotic infection being one contributing factor. This study aimed to determine whether asymptomatic women with a history of sPTB or cervical surgery have altered levels of inflammatory/antimicrobial mediators and/or microflora within cervical fluid at 22–24 weeks gestation. External cervical fluid was collected from women with history of previous sPTB and/or cervical surgery at 22–24 weeks gestation (n = 135). Cytokine and antimicrobial peptides were measured on a multiplex platform or by ELISA. qPCR was performed for detection of 7 potentially pathogenic bacterial species. IL-8 and IL-1β levels were lower in women who delivered preterm compared to those who delivered at term (IL-8 P = 0.02; IL-1β P = 0.04). There were no differences in elafin or human beta defensin-1 protein levels between the two groups. Multiple bacterial species were detected in a higher proportion of women who delivered preterm than in those who delivered at term (P = 0.005). Cervical fluid IL-8 and IL-1β and microflora have the potential to be used as biomarkers to predict sPTB in high risk women.
Assessing genetic diversity and similarity of 435 KPC-carrying plasmids
Authors: Brandt Christian , Viehweger Adrian , Singh Abhijeet , Pletz Mathias W. , Wibberg Daniel , Kalinowski Jörn , Lerch Sandrina , Müller Bettina , Makarewicz Oliwia 
Published: August 2019

AbstractThe global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over the last decade in the health care setting. blaKPC seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes.
An immortalized cell line derived from renal erythropoietin-producing (REP) cells demonstrates their potential to transform into myofibroblasts
Authors: Sato Koji , Hirano Ikuo , Sekine Hiroki , Miyauchi Kenichiro , Nakai Taku , Kato Koichiro , Ito Sadayoshi , Yamamoto Masayuki , Suzuki Norio 
Published: August 2019

AbstractThe erythroid growth factor erythropoietin (Epo) is produced by renal interstitial fibroblasts, called REP (renal Epo-producing) cells, in a hypoxia-inducible manner. In chronic kidney disease (CKD), REP cells lose their Epo-production ability, leading to renal anaemia. Concurrently, REP cells are suggested to be transformed into myofibroblasts, which are the major player of renal fibrosis. Although establishment of cultured cell lines derived from REP cells has been a long-term challenge, we here successfully established a REP-cell-derived immortalized and cultivable cell line (Replic cells) by using a genetically modified mouse line. Replic cells exhibited myofibroblastic phenotypes and lost their Epo-production ability, reflecting the situation in renal fibrosis. Additionally, we found that cell-autonomous TGFβ signalling contributes to maintenance of the myofibroblastic features of Replic cells. Furthermore, the promoters of genes for Epo and HIF2α, a major activator of Epo gene expression, were highly methylated in Replic cells. Thus, these results strongly support our contention that REP cells are the origin of myofibroblasts in fibrotic kidneys and demonstrate that cell-autonomous TGFβ signalling and epigenetic silencing are involved in renal fibrosis and renal anaemia, respectively, in CKD. The Replic cell line is a useful tool to further investigate the molecular mechanisms underlying renal fibrosis.
Canine parvovirus (CPV) phylogeny is associated with disease severity
Authors: Franzo Giovanni , Tucciarone Claudia Maria , Casagrande Sira , Caldin Marco , Cortey Martí , Furlanello Tommaso , Legnardi Matteo , Cecchinato Mattia , Drigo Michele 
Published: August 2019

AbstractAfter its first identification in 1978, canine parvovirus (CPV) has been recognized all around the world as a major threat for canine population health. This ssDNA virus is characterized by a high substitution rate and several genetic and phenotypic variants emerged over time. Overall, the definition of 3 main antigenic variants was established based on specific amino acid markers located in a precise capsid position. However, the detection of several minor variants and incongruence observed between the antigenic classification and phylogeny have posed doubts on the reliability of this scheme. At the same time, CPV heterogeneity has favored the hypothesis of a differential virulence among variants, although no robust and consistent demonstration has been provided yet. The present study rejects the antigenic variant concept and attempts to evaluate the association between CPV strain phylogeny, reconstructed using the whole information contained in the VP2 coding gene, and several clinical and hemato-biochemical parameters, assessed from 34 CPV infected dogs at admission. By using different statistical approaches, the results of the present study show an association between viral phylogeny and host parameters ascribable to immune system, coagulation profile, acute phase response and, more generally, to the overall picture of the animal response. Particularly, a strong and significant phylogenetic signal was proven for neutrophil count and WBC. Therefore, despite the limited sample size, a relation between viral phylogeny and disease severity has been observed for the first time, suggesting that CPV virulence is an inherited trait. The likely existence of clades with different virulence highlights once more the relevance of intensive epidemiological monitoring and research on CPV evolution to better understand the virulence determinants, their epidemiology and develop adequate countermeasures.
Effect of protracted dexamethasone exposure and its withdrawal on rocuronium-induced neuromuscular blockade and sugammadex reversal: an ex vivo rat study
Authors: Oh Seok Kyeong , Lim Byung Gun , Park Sungsoo , Yang Hong Seuk , In Junyong , Kim Yong Beom , Choi Hey-ran , Lee Il Ok 
Published: August 2019

AbstractStudies have reported that protracted dexamethasone treatment induces resistance to nondepolarizing neuromuscular blocking agents (NMBAs) and the association with nicotinic acetylcholine receptors in the diaphragm of rats. Here, we investigated the effect of protracted dexamethasone administration on the sensitivity to rocuronium and the recovery profile when reversed by sugammadex; additionally, we observed the recovery period of pharmacodynamic change after withdrawal. Sprague-Dawley rats received daily intraperitoneal injections of dexamethasone or saline for 14 days. On days 1, 3, and 7 after the last dexamethasone treatment (Dexa1, Dexa3, and Dexa7, respectively) or 1 day after saline (control group), the phrenic nerve-hemidiaphragm preparation was dissected for assay. The dose-response curve of rocuronium in Dexa1 was shifted to the right compared to controls, but curves in Dexa3 and Dexa7 were not significantly different. Groups were not significantly different in attaining the train-of-four ratio ≥ 0.9, but the recovery index in Dexa7 was shorter than that in control and Dexa1. Recovery profiles (period of sugammadex reversal) were not correlated with resistance properties but rather with total administered drugs (binding capacity of NMBAs and sugammadex). Protracted dexamethasone exposure induced resistance to rocuronium but seemed to have no effect on sugammadex reversal in the rat diaphragm.
Adaptive colour change and background choice behaviour in peppered moth caterpillars is mediated by extraocular photoreception
Authors: Eacock Amy , Rowland Hannah M. , van’t Hof Arjen E. , Yung Carl J. , Edmonds Nicola , Saccheri Ilik J. 
Published: August 2019

AbstractLight sensing by tissues distinct from the eye occurs in diverse animal groups, enabling circadian control and phototactic behaviour. Extraocular photoreceptors may also facilitate rapid colour change in cephalopods and lizards, but little is known about the sensory system that mediates slow colour change in arthropods. We previously reported that slow colour change in twig-mimicking caterpillars of the peppered moth (Biston betularia) is a response to achromatic and chromatic visual cues. Here we show that the perception of these cues, and the resulting phenotypic responses, does not require ocular vision. Caterpillars with completely obscured ocelli remained capable of enhancing their crypsis by changing colour and choosing to rest on colour-matching twigs. A suite of visual genes, expressed across the larval integument, likely plays a key role in the mechanism. To our knowledge, this is the first evidence that extraocular colour sensing can mediate pigment-based colour change and behaviour in an arthropod.
Incidence and Outcomes of Hypernatremia in Adult Neurological Non–Brain-Dead Patients Admitted to Tertiary Care Neurologic Institute: A Retrospective Study
Authors: Jena Sritam S. , Venkatapura Ramesh J. , Christopher Rita , Shukla Dhaval , Chakrabarti Dhritiman 
Published: August 2019

Abstract
Background Hypernatremia is known to have high mortality and morbidity in patients with neurological disorders. However, in most studies, it is not clear whether hypernatremia associated with brain death has been excluded. Including brain-dead patients will spuriously give a very high mortality rate. Therefore, in this study, we have evaluated the mortality of hypernatremic patients after excluding the brain-dead patients on the first day of hypernatremia.
Methods All neurological patients admitted to the hospital who developed hypernatremia (serum Na > 150 mEq/L) were included in the study. Brain-dead patients and patients with Glasgow coma score (GCS) 3 on the first day of detection of hypernatremia were excluded. Demographic variables, clinical variables, and outcome variables were collected from the case files retrospectively.
Results In total, 100 patients developed hypernatremia during the study period. Among them, 14 patients were excluded because of GCS 3 or unavailability of GCS data on the day of detection of hypernatremia. There were 37 mild, 28 moderate, and 21 severe hypernatremic patients. The mortality was 32%, 39%, and 52% in the mild, moderate, and severe hypernatremic patients, respectively. Patients with traumatic brain injury had higher mortality in comparison to all other disease conditions (56% vs. 29.6%, p < 0.02).
Conclusion The mortality is high even in mild cases of hypernatremia. Very high mortality (52%) is seen in severe hypernatremic patients. Therefore, it is important to monitor, identify, and treat these patients aggressively.
Liquid-crystalline phase transitions in lipid droplets are related to cellular states and specific organelle association
Authors: Mahamid Julia , Tegunov Dimitry , Maiser Andreas , Arnold Jan , Leonhardt Heinrich , Plitzko Jürgen M. , Baumeister Wolfgang 
Published: August 2019

Significance
Lipids have essential roles in cellular energy homeostasis and are key structural components of membranes and thereby provide the basis of cellular compartmentalization. The maintenance of lipid homeostasis is of fundamental importance to cellular physiology. Lipid droplets (LDs) are central organelles orchestrating lipid fluxes inside cells. By examining pristinely preserved frozen-hydrated HeLa cells with cryoelectron microscopy, we show that LDs exhibit different internal organizations, as well as organelle associations, depending on cellular states. We demonstrate the presence of a liquid-crystalline phase under certain conditions, which are likely to impact the physiological functions of LDs. Furthermore, crystalline droplets are a major component of atherosclerotic lesions in human arteries. Crystalline LDs secreted by cells may therefore have a direct link to pathologies.
A General Review on Methods of Sediment Sampling and Mineral Content Analysis
Authors: Awal R. , Sapkota P. , Chitrakar S. , Thapa B.S. , Neopane H.P. , Thapa B. 
Published: August 2019

Abstract
Sediment erosion is a major problem in hydropower plants of Himalayan and Andes region which causes frequent breakdown of electromechanical parts in contact with sediment laden water demanding regular maintenance. Sediment suspended in water with high velocity has higher potential to erosion of the turbine parts. Studies show that sediment erosion can be minimized to some extent if modifications in the design, use of erosion resistant material as well as application of erosion resistant paints are carried out on those components. Besides, thorough understanding of sediment by proper analysis is important for designing and making components less prone to sediment erosion. The efficiency of sediment analysis depends on the sampling method and the method used for particle size distribution (PSD) analysis and mineral content (MC) analysis. Depending on the nature of the stream, a different method should be adopted. This paper presents a general overview of the method of sampling, method of PSD and MC analysis.
Opportunities and Challenges of introducing Francis Turbine in Nepalese Micro Hydropower Projects
Authors: Ghimire A. , Dahal D. R. , Pokharel N. , Chitrakar S. , Thapa B. S. , Thapa B. 
Published: August 2019

Abstract
Despite the initiation of the master plan, envisioned by the government of Nepal, complete electrification of rural Nepal still seems over ambitious for quite a long time. Thus Micro Hydropower Plants (MHP) can still be very effective for rural electrification. Decades of manufacturing of same type turbines have saturated the turbine manufacturing industries of Nepal, which demands for some new innovations and that could be the introduction of Francis turbine in Nepalese MHP. It’s undeniable that there are umpteen opportunities for the turbine manufacturers to manufacture and install the Francis turbines in Nepalese MHP. The feasibility studies performed by different institutions and the government policy strengthen the claim. In addition to that, data received from, NMHDA and a local turbine manufacturing industry suggest that there are abundant sites suitable for installation of Francis turbine. This paper illustrates the need of introducing the Francis turbine in Nepalese MHP and discusses about the opportunities available for the turbine manufacturers to enter into the market of Francis turbines for micro hydro and subsequently for larger hydropower projects in the near future. The challenges associated with the introduction of Francis turbine in MHP are highlighted.
Application of ‘Structure from Motion’ (SfM) technique in physical hydraulic modelling
Authors: Kumar Karmacharya Sanat , Bishwakarma Meg , Shrestha Ujjwal , Rüther Nils 
Published: August 2019

Abstract
There are many methods available for measurement of bed morphology in physical hydraulic model studies considering mobile bed sediment. Among which, there are sophisticated instrumentations which provide quality results in shorter time but are vastly expensive and requires special training for execution. Whereas the conventional surveying methodology, which is simple and inexpensive, requires plenty of time for the measurement and processing of the data. That is why the recent developments in ‘Structure from Motion’ (SfM) technique have made it a potential candidate for an inexpensive and efficient tool for measurement of bed morphology in physical hydraulic model studies. SfM method allows to simultaneously determine both the parameters of the camera and the 3D structure of a scene by combining 2D images taken from multiple viewpoints. SfM tools can create a dense point cloud out of a set of partially overlapping photographs taken even by a budget friendly digital camera. The SfM method have already been used as an alternative for topographic surveying to create high-resolution digital elevation models (DEM). Some researchers had also used it for measurement of bed morphology in laboratory experiments. In this study, different freely available SfM tools were used to create a dense point cloud from a set of photographs representing a short reach in a river model in the hydraulic laboratory at Hydro Lab. The selected tools were compared with each other and against a commercial software, based on the methodologies used, processing time and quality of the output. Then the results from SfM method were compared with actual measurements in the physical model done with a conventional surveying technique using a theodolite and a level machine. The results showed that free SfM tools can also produce efficient results compared to commercial tools and SfM method can be used as an inexpensive and efficient alternative for bed morphology measurements in physical hydraulic models.
Physical modelling of pressurized flushing of non-cohesive sediment using lightweight material
Authors: Kumar Karmacharya Sanat , Henry Pierre-Yves , Bishwakarma Meg , Aberle Jochen , Rüther Nils 
Published: August 2019

Abstract
In this study, pressurized flushing of non-cohesive reservoir sediment through a bottom orifice was simulated in laboratory experiments using lightweight material as model sediment. The experiments were carried out by varying flushing discharge, reservoir water level, thickness of sediment deposit layer and opening height of bottom orifice. The volumes of flushing cones formed with lightweight material were compared with volumes calculated using empirical relations proposed by past studies. The good trend observed in variation of dimensionless flushing cone volume against different dimensionless parameters justified the possibility of using the lightweight material as model sediment.