bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immobilization of Trametes hirsuta D7 in Light Expanded Clay Aggregate for Decolorization of Synthetic Dye
Authors: Ardiati F C , Yanto D H Y , Anita S H , Watanabe T 
Published: September 2019

Abstract
Light Expanded Clay Aggregate (LECA) in a granular form was used for the immobilization of fungus Trametes hirsuta D7 to decolorize Remazol Brilliant Blue R (RBBR) dye. The efficacy of LECA as a media for immobilization was assessed using steam activation, contact time, immobilization method and dosage of sorbent. Batch experiments were carried out for decolorization and the results showed that activated LECA has the capability to remove 35% RBBR for 24 h of contact time. Non-freeze dry immobilization process demonstrated a higher decolorization than that of freeze dry process with maximum 88% and 22% removal, respectively. Different dosage of activated and non-freeze dry-LECA was tested to achieve optimum decolorization and it was found that 0.2 g/ml dye could remove 76% dye for 3 hours and reached the maximum removal for 94% at 24 hours with high laccase activities (460 U L− 1). This study found that fungus T. hirsuta D7 and LECA could be used to decolorize RBBR and LECA had the potential to be an alternative matrix for fungi immobilization.
Floating treatment wetlands and submerged vegetation for water quality improvement of an urban lake in megacity Jakarta, Indonesia
Authors: Henny C , Kurniawan R , Akhdiana I 
Published: September 2019

Abstract
Most of urban lakes in Megacity Jakarta have become shallow, polluted and in eutrophic condition due to solids and nutrient pollution which requires urgent handling and management. Aquatic vegetation especially emergent and submerged plants in the lake littoral area have been known to play an important role to reduce the contaminants in the lake water. Floating Treatment Wetlands (FTWs) are cultivated plants growing on buoyant mats in open water. FTWs are an innovative tool that has been widely used for ponds and storm water quality improvement. This study aims to examine the effect of submerged plant and the ability of two different plants grown on Floating Treatment Wetlands (FTWs) system to improve an urban lake water quality. One urban lake has been selected for this study where the lake littoral at the inlet area has been overgrown by the submerged aquatic plant of Myriophillum verticillatum. Two units of Floating Treatment Wetlands (FTWs) (size of 3 m2 each) made of rubber mat and PVC pipes (3 inches) as buoyant material and planted with Heliconia densiflora. and Vetiveria zizanioides. The performance of the FTWs applied and M. vercillatum was assessed by calculating the removal efficiency of nutrients and solids concentrations in the lake water of the coverage area. The observations of several water quality parameters including total nitrogen (TN), total phosphorus (TP) and total suspended solids (TSS) were made at the site before and after the submerged plant and FTWs. Both FTW_ H. densiflora and FTW_V. zizaniodes removed more nutrients and also suspended solids per m2 area than M. vercillatum. Although both submerged vegetation and FTWs can be used as tools to manage a long-term stability for good urban lake water quality, it will require intensive harvesting to control productivity of submerged vegetation.
Effect of C/N ratio variations on the capability of microbes from Muara Karang river sediment in the production of biogas and identification using VITEK 2
Authors: Widadri L M , Mangunwardoyo W , Ambarsari H 
Published: September 2019

Abstract
Gas is one form of microbial metabolism products that can be identified as biogas, one example of biogas is methane gas. The production of methane gas by bacteria occurs through methanogenesis with three stages, namely hydrolysis, acetogenesis, and methanogenesis. These processes are generally performed by bacteria in an anaerobic environment. The Muara Karang River sediments contaminated with organic matters and having low oxygen are potential as the habitat for anaerobic microbes with methanogenesis ability. The ability of such sediment microbes in biogas production was tested by inoculating Muara Karang sediment in a Methanogen Enrichment Barker broth medium with variations of C/N ratio using glucose as the carbon source to analyze the biogas production. The parameters measured were the total carbon, the total nitrogen, and the biogas volume. Two isolates were obtained, namely isolate I and isolate II. These isolates were then identified by the VITEK 2 compact equipment. The result showed that C/N ratio of 25:1 could produce the highest biogas volume. Isolate I was identified by the VITEK 2 equipment as Methylobacterium spp. from methanotroph group bacteria and isolate II was identified as Dermacoccus nishinomiyaensis.
Structural and Optical Studies of Zinc doped BiFeO3 on the Bi-site
Authors: Notonegoro Hamdan Akbar , Soegijono Bambang , Rafsanjani Rifqi Almusawi , Mudzakir Isom , Raksa Teguh Yoga 
Published: September 2019

Abstract
Zinc-doped bismuth ferrite (Bi1-x
Zn
x
FeO3, x = 0, 0.05, 0.1) powdered were synthesized through sol-gel auto combustion methods to investigate the optical properties while maintaining the whole structure of BiFeO3 (BFO). The Zn doped induced the reveal of Bi25FeO40 as a secondary phase and decreased the bond angle of Bi–O–Fe in the BFO phase structure which affect the electron density formation inside of the lattice. The presence of Zn content has also conducted the shifting of optical absorption in the UV-Vis region and increasing the dielectric constant value. This property is potent in visible light photonic applications.
Adsorption Study of Methylene Blue and Eriochrome Black T Dyes on Activated Carbon and Magnetic Carbon Composite
Authors: Fajarwati F I , Anugrahwati M , Yanti I , Safitri R A , Yeni  , Yuanita E 
Published: September 2019

Abstract
Dye is one of the dangerous contaminants because it can interfere with the health of living things and the environment. This research aims to study the comparison of adsorption capacity between activated carbon and its magnetic composite on methylene blue and eriochrome black T, as azo dyes, an organic compound contains a functional group of –N=N-, that are hardly to be degraded in the environment. The activated carbon used in this study was obtained commercially while the composite material was synthesized using activated carbon which was carried by iron species from a solution of Fe2+ and Fe3+ salts. The variables studied in this research were contact periodic time and dye concentration. The adsorption process was evaluated using a kinetics and isotherm model. Furthermore, the characterization of the two adsorbents was conducted using Fourier-transform Infrared (FTIR) spectrometer. The results of FTIR characterization show a functional group that indicates of the proper of magnetic carbon composite preparation as indicated at wave number from the vibration of Fe-O bonds. Adsorption result from activated carbon and magnetic carbon composite on both dyes followed the kinetics model pseudo-second order. Meanwhile, the isotherm adsorption model of the adsorbents against methylene blue follows the Langmuir and Freundlich equations for eriochrome black T.
Localised granulomatosis with polyangiitis in an older patient with rheumatoid arthritis
Authors: Capdevila-Reniu Aina , Rodríguez-Garcia Sebastian De la Cruz , Grafia Ignacio , Sanchez Marcelo , Martínez Daniel , Navarro-López Margarita , Prieto-González Sergio 
Published: September 2019

Abstract
New onset of granulomatosis with polyangiitis (GPA) occurring in patients previously diagnosed with rheumatoid arthritis (RA) is very uncommon. In older individuals, this condition is associated with high mortality, especially in those with renal involvement. We describe the first case of GPA in a patient older than 65 years diagnosed with RA without exposure to biologic disease-modifying anti-rheumatic drugs, presenting with pulmonary nodules due to a limited form of anti-neutrophil cytoplasmic antibody-negative GPA.
Hospitalization Pattern, Inpatient Service Utilization and Quality of Care in Patients With Alcohol Use Disorder: A Sequence Analysis of Discharge Medical Records
Authors: Han Xueyan , Jiang Feng , Zhou Huixuan , Needleman Jack , Guo Moning , Chen Yin , Liu Yuanli , Tang Yilang 
Published: September 2019

Abstract

Aims
To identify and group hospitalization trajectory of alcohol use disorder (AUD) patients and its associations with service utilization, healthcare quality and hospital-level variations.

Methods
Inpatients with AUD as the primary diagnosis from 2012 to 2014 in Beijing, China, were identified. Their discharge medical records were extracted and analyzed using the sequence analysis and the cluster analysis.

Results
Eight-hundred thirty-one patients were included, and their hospitalization patterns were grouped into four clusters: short stay (n = 565 (67.99%)), mean psychiatric length of stay in 3 years: (32.25 ± 18.69), repeated short stay (n = 211 (25.39%), 137.76 ± 88.8 days), repeated long stay (n = 41 (4.93%), 405.44 ± 146.54 days), permanent stay (n = 14 (1.68%), 818.14 ± 225.22 days). The latter two clusters (6.61% patients) used 37.26% of the total psychiatric hospital days and 33.65% of the total psychiatric hospitalization expenses. All the patients in the permanent stay cluster and 41.77% of the patients in the short stay cluster were readmitted at least once within 3 years. Two-hundred thirty-four patients (28.16%) were admitted at least once for non-psychiatric reasons, primarily for diseases of circulatory and digestive systems. Cluster composition varied significantly among different hospitals.

Conclusion
Hospitalization pattern of patients with AUD varies greatly, and while most (&gt;2/3) hospitalizations were short stay, those with repeated long stay and permanent stay used more than one third of the hospital days and expenses. Our findings suggest interventions targeting at certain patients may be more effective in reducing resource utilization.
XMAn v2—a database of Homo sapiens mutated peptides
Authors: Flores Marcela Aguilera , Lazar Iulia M 
Published: September 2019

Abstract

Summary
The ‘Unknown Mutation Analysis (XMAn)’ database is a compilation of Homo sapiens mutated peptides in FASTA format, that was constructed for facilitating the identification of protein sequence alterations by tandem mass spectrometry detection. The database comprises 2 539 031 non-redundant mutated entries from 17 599 proteins, of which 2 377 103 are missense and 161 928 are nonsense mutations. It can be used in conjunction with search engines that seek the identification of peptide amino acid sequences by matching experimental tandem mass spectrometry data to theoretical sequences from a database.

Availability and implementation
XMAn v2 can be accessed from github.com/lazarlab/XMAnv2.

Supplementary information
Supplementary data are available at Bioinformatics online.
NERDD: a web portal providing access to in silico tools for drug discovery
Authors: Stork Conrad , Embruch Gerd , Šícho Martin , de Bruyn Kops Christina , Chen Ya , Svozil Daniel , Kirchmair Johannes 
Published: September 2019

Abstract

Summary
The New E-Resource for Drug Discovery (NERDD) is a quickly expanding web portal focused on the provision of peer-reviewed in silico tools for drug discovery. NERDD currently hosts tools for predicting the sites of metabolism (FAME) and metabolites (GLORY) of small organic molecules, for flagging compounds that are likely to interfere with biological assays (Hit Dexter), and for identifying natural products and natural product derivatives in large compound collections (NP-Scout). Several additional models and components are currently in development.

Availability and implementation
The NERDD web server is available at https://nerdd.zbh.uni-hamburg.de. Most tools are also available as software packages for local installation.
Protein–protein interaction site prediction through combining local and global features with deep neural networks
Authors: Zeng Min , Zhang Fuhao , Wu Fang-Xiang , Li Yaohang , Wang Jianxin , Li Min 
Published: September 2019

AbstractMotivationProtein–protein interactions (PPIs) play important roles in many biological processes. Conventional biological experiments for identifying PPI sites are costly and time-consuming. Thus, many computational approaches have been proposed to predict PPI sites. Existing computational methods usually use local contextual features to predict PPI sites. Actually, global features of protein sequences are critical for PPI site prediction.ResultsA new end-to-end deep learning framework, named DeepPPISP, through combining local contextual and global sequence features, is proposed for PPI site prediction. For local contextual features, we use a sliding window to capture features of neighbors of a target amino acid as in previous studies. For global sequence features, a text convolutional neural network is applied to extract features from the whole protein sequence. Then the local contextual and global sequence features are combined to predict PPI sites. By integrating local contextual and global sequence features, DeepPPISP achieves the state-of-the-art performance, which is better than the other competing methods. In order to investigate if global sequence features are helpful in our deep learning model, we remove or change some components in DeepPPISP. Detailed analyses show that global sequence features play important roles in DeepPPISP.Availability and implementationThe DeepPPISP web server is available at http://bioinformatics.csu.edu.cn/PPISP/. The source code can be obtained from https://github.com/CSUBioGroup/DeepPPISP.Supplementary informationSupplementary data are available at Bioinformatics online.
Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies
Authors: Yaxley Keaghan J , Foley Robert A 
Published: September 2019

AbstractOwing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.
Historical biogeography of Trigonostemon and Dimorphocalyx (Euphorbiaceae)
Authors: Yu Ren-Yong , Van Welzen Peter C 
Published: September 2019

AbstractTrigonostemon and Dimorphocalyx are two morphologically similar genera in tropical Asia. We estimated their divergence times through a Bayesian clock analysis and reconstructed the historical biogeography using a likelihood analysis under the dispersal-extinction-cladogenesis (DEC) model and a statistical dispersal-vicariance analysis (S-DIVA). We have found that the two genera differ in their historical biogeography: Trigonostemon originated on the South-East Asian mainland, but one section dispersed to the Malay Peninsula and Borneo, where rapid speciation events occurred during the Pleistocene, whereas Dimorphocalyx originated on and extended to its current distribution from Borneo. The dispersal routes of both genera are well supported by the tectonic history and are comparable to the conclusions in previous case studies. Long-distance dispersals across Wallace’s line are of particular interest in biogeography. We compared the patterns of historical distribution and dispersal of our taxa and other comparable taxa in this area. Our data support the hypothesis that the Philippines is the most common stepping stone for crossing Wallace’s line. Furthermore, we consider that the frequent change of sea levels during the Pleistocene propelled the diversification of Trigonostemon section Trigonostemon in Borneo and the Malay Peninsula.
Sequence-Based Prediction of Olfactory Receptor Responses
Authors: Chepurwar Shashank , Gupta Abhishek , Haddad Rafi , Gupta Nitin 
Published: September 2019

Abstract
Computational prediction of how strongly an olfactory receptor (OR) responds to various odors can help in bridging the widening gap between the large number of receptors that have been sequenced and the small number of experiments measuring their responses. Previous efforts in this area have predicted the responses of a receptor to some odors, using the known responses of the same receptor to other odors. Here, we present a method to predict the responses of a receptor without any known responses by using available data about the responses of other conspecific receptors and their sequences. We applied this method to ORs in insects Drosophila melanogaster (both adult and larva) and Anopheles gambiae and to mouse and human ORs. We found the predictions to be in significant agreement with the experimental measurements. The method also provides clues about the response-determining positions within the receptor sequences.
The Effect of Exposure to Fear-Related Body Odorants on Anxiety and Interpersonal Trust Toward a Virtual Character
Authors: Quintana Pamela , Nolet Kévin , Baus Oliver , Bouchard Stéphane 
Published: September 2019

Abstract
A growing body of literature documents how exposure to another person's fear-related body odorants can increase one's own anxiety and interfere with processing of social information, such as facial expression and impression formation. Building on these results, we aimed to 1) test the hypothesis that exposure to fear-related odorant would affect impression formation through fear contagion and 2) verify whether these effects can be observed in an ecologically valid (i.e., virtual) environment. We proposed that exposure to fear-related odorant would cause receivers to feel more anxious, which in turn would lead them to report less trust toward an unknown virtual character. This study had 2 distinct phases. First, we collected perspiration odorants from the armpits of 12 male senders (i.e., the source of the odorant) during the viewing of either fear or joy inducing film clips. In the second phase, 53 women receivers were exposed to either a fear, joy, or neutral odorant (i.e., between-subjects design) by breathing through a gauze attached to a disposable respirator mask while immersed in a virtual bar. As expected, receivers exposed to fear odorants felt significantly more stressed. Mediation analysis also revealed an indirect effect of exposure on trust through anxiety. More specifically, the more anxious the receiver felt, the less she trusted the virtual character. Our results show for the first time that the impact of exposure to fear-related body odorants on negative interpersonal impression formation is mediated by the anxiety induced in the receiver.
The Invisible Burden: Diagnosing and Combatting Typhoid Fever in Asia and Africa
Authors: Pitzer Virginia E , Meiring James , Martineau Frederick P , Watson Conall H , Kang Gagandeep , Basnyat Buddha , Baker Stephen 
Published: September 2019

Abstract
Measuring the burden of typhoid fever and developing effective strategies to reduce it require a surveillance infrastructure that is currently lacking in many endemic countries. Recent efforts and partnerships between local and international researchers have helped to provide new data on the incidence and control of typhoid in parts of Asia and Africa. Here, we highlight examples from India, Nepal, Vietnam, Fiji, Sierra Leone, and Malawi that summarize past and present experiences with the diagnosis, treatment, and prevention of typhoid fever in different locations with endemic disease. While there is no validated road map for the elimination of typhoid, the lessons learned in studying the epidemiology and control of typhoid in these settings can provide insights to guide future disease control efforts.
Epidemiology and Diagnostics of Carbapenem Resistance in Gram-negative Bacteria
Authors: Nordmann Patrice , Poirel Laurent 
Published: September 2019

Abstract
Carbapenem resistance in gram-negative bacteria has caused a global epidemic that continues to grow. Although carbapenemase-producing Enterobacteriaceae have received the most attention because resistance was first reported in these pathogens in the early 1990s, there is increased awareness of the impact of carbapenem-resistant nonfermenting gram-negative bacteria, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. Moreover, evaluating the problem of carbapenem resistance requires the consideration of both carbapenemase-producing bacteria as well as bacteria with other carbapenem resistance mechanisms. Advances in rapid diagnostic tests to improve the detection of carbapenem resistance and the use of large, population-based datasets to capture a greater proportion of carbapenem-resistant organisms can help us gain a better understanding of this urgent threat and enable physicians to select the most appropriate antibiotics.
Impact of a Telehealth-Based Antimicrobial Stewardship Program in a Community Hospital Health System
Authors: Shively Nathan R , Moffa Matthew A , Paul Kathleen T , Wodusky Eric J , Schipani Beth Ann , Cuccaro Susan L , Harmanos Mark S , Cratty Michael S , Chamovitz Bruce N , Walsh Thomas L 
Published: September 2019

Abstract

Background
Data on antimicrobial stewardship programs (ASPs) facilitated via telehealth in the community hospital setting are limited.

Methods
A telehealth-based ASP was implemented in 2 community hospitals (285 and 176 beds). Local pharmacists without residency or prior antimicrobial stewardship training were trained to conduct prospective audit and feedback. For approximately 60 minutes 3 times weekly at the 285-bed hospital and 2 times weekly at the 176-bed hospital, infectious diseases (ID) physicians remotely reviewed patients on broad-spectrum antibiotics and those admitted with lower respiratory tract infections and skin and soft tissue infections with local pharmacists. Recommendations for ASP interventions made by ID physicians were relayed to primary teams and tracked by local pharmacists. Antimicrobial utilization was collected in days of therapy (DOT) per 1000 patient-days (PD) for a 12-month baseline and 6-month intervention period, and analyzed with segmented linear regression analysis. Local ID consultations were tracked and antimicrobial cost savings were estimated.

Results
During the 6-month intervention period, 1419 recommendations were made, of which 1262 (88.9%) were accepted. Compared to the baseline period, broad-spectrum antibiotic utilization decreased by 24.4% (342.1 vs 258.7 DOT/1000 PD; P &lt; .001) during the intervention period. ID consultations increased by 40.2% (15.4 consultations per 1000 PD vs 21.5 consultations per 1000 PD; P = .001). Estimated annualized savings on antimicrobial expenditures were $142 629.83.

Conclusions
An intense ASP model, facilitated in the community hospital setting via telehealth, led to reduced broad-spectrum antimicrobial utilization, increased ID consultations, and reduced antimicrobial expenditures.