bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symptom burden in malignant and non-malignant disease on admission to a palliative care unit
Authors: See David , Le Brian , Gorelik Alexandra , Eastman Peter 
Published: February 2019

BackgroundThere is increasing recognition that patients with non-malignant diseases have comparable physical and psychosocial symptom burden to patients with cancer. There is currently limited data directly comparing symptom burden between these patient groups.ObjectiveTo investigate differences in symptom burden between patients with malignant and non-malignant conditions admitted to a palliative care unit (PCU).MethodA cross-sectional study involving 186 patients admitted to a PCU was undertaken. Patients were dichotomised into malignant or non-malignant disease categories. Symptom burden at admission was assessed using the Symptom Assessment Scale and Palliative Care Problem Severity Score. Group differences in symptoms were analysed using univariate and multivariate approaches.ResultsOne hundred patients (53.8%) had cancer, with upper gastrointestinal the most common type (18.0%). Among the 86 patients with non-malignant disease, neurological conditions were most prevalent (40.7%). Patients admitted with non-malignant diseases were older, more functionally impaired and more likely to be deteriorating or terminal. A malignant diagnosis was associated with a higher likelihood of clinician-assessed pain, patient-assessed pain, fatigue, psychological/spiritual symptoms and other symptoms. However, when adjusted for confounders, disease category ceased to be a significant predictor of symptom burden. Younger patients experienced worse pain and patients in terminal phase experienced less symptom burden.ConclusionSymptom burden was similar between patients with malignant and non-malignant disease after adjustment for confounders. Further research is needed to understand the palliative care needs of patients with non-malignant disease.
Age-disparate partnerships and HSV-2 among adolescent girls and young women in South Africa: implications for HIV infection risk
Authors: Maughan-Brown Brendan , George Gavin , Beckett Sean , Evans Meredith , Lewis Lara , Cawood Cherie , Khanyile David , Kharsany Ayesha B M 
Published: February 2019

ObjectiveThere is an urgent need to understand high HIV-infection rates among young women in sub-Saharan Africa. While age-disparate partnerships have been characterised with high-risk sexual behaviours, the mechanisms through which these partnerships may increase HIV-risk are not fully understood. This study assessed the association between age-disparate partnerships and herpes simplex virus type-2 (HSV-2) infection, a factor known to increase HIV-infection risk.MethodsCross-sectional face-to-face questionnaire data, and laboratory HSV-2 and HIV antibody data were collected among a representative sample in the 2014/2015 household survey of the HIV Incidence Provincial Surveillance System in KwaZulu-Natal, South Africa. Among 15–24-year-old women who reported having ever had sex (n=1550), the association between age-disparate partnerships (ie, male partner ≥5 years older) and HSV-2 antibody status was assessed using multivariable Poisson regression models with robust variance. Analyses were repeated among HIV-negative women.ResultsHSV-2 prevalence was 55% among 15–24-year-old women. Women who reported an age-disparate partnership with their most recent partner were more likely to test HSV-2 positive compared with women with age-similar partners (64% vs 51%; adjusted prevalence ratio (aPR):1.19 (95% CI 1.07 to 1.32, p<0.01)). HSV-2 prevalence was also significantly higher among HIV-negative women who reported age-disparate partnerships (51% vs 40 %; aPR:1.25 (95% CI 1.05 to 1.50, p=0.014)).ConclusionsResults indicate that age-disparate partnerships are associated with a greater risk of HSV-2 among young women. These findings point towards an additional mechanism through which age-disparate partnerships could increase HIV-infection risk. Importantly, by increasing the HSV-2 risk, age-disparate partnerships have the potential to increase the HIV-infection risk within subsequent partnerships, regardless of the partner age-difference in those relationships.
ACCURATE DETECTION OF SEIZURE USING NONLINEAR PARAMETERS EXTRACTED FROM EEG SIGNALS
Authors: VICNESH JAHMUNAH , HAGIWARA YUKI 
Published: February 2019

Electroencephalography (EEG) is the graphical recording of electrical activity along the scalp. The EEG signal monitors brain activity noninvasively with a high accuracy of milliseconds and provides valuable discernment about the brain’s state. It is also sensitive in detecting spikes in epilepsy. Computer-aided diagnosis (CAD) tools allow epilepsy to be diagnosed by evading invasive methods. This paper presents a novel CAD system for epilepsy using other linear features together with Hjorth’s nonlinear features such as mobility, complexity, activity and Kolmogorov complexity. The proposed method uses MATLAB software to extract the nonlinear features from the EEG data. The optimal features are selected using the statistical analysis, ANOVA (analysis of variance) test for classification. Once selected, they are fed into the decision tree (DT) for the classification of the different epileptic classes. The proposed method affirms that four nonlinear features, Kolmogorov complexity, singular value decomposition, mobility and permutation entropy are sufficient to provide the highest accuracy of 93%, sensitivity of 97%, specificity of 88% and positive predictive value (PPV) of 94%, with the DT classifier. The mean value is the highest in the ictal stage for the Kolmogorov complexity proving it to have the best variation. It also has the highest [Formula: see text]-value of 300.439 portraying it to be the best parameter that is favourable for the clinical diagnosis of epilepsy, when used together with the DT classifier, for a duration of 23.6[Formula: see text]s of EEG data.
Electro-Steering Tapered Fiber-Optic Device with Liquid Crystal Cladding
Authors: Korec Joanna , Stasiewicz Karol A. , Strzeżysz Olga , Kula Przemysław , Jaroszewicz Leszek R. 
Published: February 2019

The paper presents the results of design, manufacturing, and characterization of a hybrid broad band in-line fiber-optic device. It uses nematic liquid crystal as cladding with electro-steering properties in a biconical optical fiber taper structure. Liquid crystal mixtures denoted as 6CHBT and E7 are designed for electric as well as temperature control of electromagnetic wave propagation in a broad wavelength range. The applied taper with 10±0.5 μm diameters has losses lower than 0.5 dB in whole investigated spectrum range. Three kinds of initial liquid crystal molecules’ orientations (parallel, orthogonal, and twist) in relation to the light beam propagating in a taper were applied. The performance of a tuned cladding was studied at an electric field of the range of 0–190 V and the temperature range from 20°C up to 42°C and 59°C for 6CHBT and E7, respectively. The induced reorientation of liquid crystal molecules was measured at a broad wavelength range (550-1550 nm).
Activated and Exhausted MAIT Cells Foster Disease Progression and Indicate Poor Outcome in Hepatocellular Carcinoma
Authors: Duan Meng , Goswami Shyamal , Shi Jie-Yi , Wu Lin-Jie , Wang Xiao-Ying , Ma Jia-Qiang , Zhang Zhao , Shi Yang , Ma Li-Jie , Zhang Shu , Xi Rui-Bin , Cao Ya , Zhou Jian , Fan Jia , Zhang Xiao-Ming , Gao Qiang 
Published: February 2019

Abstract

Purpose:
Innate immunity is an indispensable arm of tumor immune surveillance, and the liver is an organ with a predominance of innate immunity, where mucosal-associated invariant T (MAIT) cells are enriched. However, little is known about the phenotype, functions, and immunomodulatory role of MAIT cells in hepatocellular carcinoma (HCC).
Experimental Design: The distribution, phenotype, and function of MAIT cells in patients with HCC were evaluated by both flow cytometry (FCM) and in vitro bioassays. Transcriptomic analysis of MAIT cells was also performed. Prognostic significance of tumor-infiltrating MAIT cells was validated in four independent cohorts of patients with HCC.

Results:
Despite their fewer densities in HCC tumor than normal liver, MAIT cells were significantly enriched in the HCC microenvironment compared with other mucosa-associated organs. Tumor-derived MAIT cells displayed a typical CCR7−CD45RA−CD45RO+CD95+ effector memory phenotype with lower costimulatory and effector capabilities. Tumor-educated MAIT cells significantly upregulated inhibitory molecules like PD-1, CTLA-4, TIM-3, secreted significantly less IFNγ and IL17, and produced minimal granzyme B and perforin while shifting to produce tumor-promoting cytokines like IL8. Transcriptome sequencing confirmed that tumor-derived MAIT cells were reprogrammed toward a tumor-promoting direction by downregulating genes enriched in pathways of cytokine secretion and cytolysis effector function like NFKB1 and STAT5B and by upregulating genes like IL8, CXCL12, and HAVCR2 (TIM-3). High infiltration of MAIT cells in HCC significantly correlated with an unfavorable clinical outcome, revealed by FCM, qRT-PCR, and multiplex IHC analyses, respectively.

Conclusions:
HCC-infiltrating MAIT cells were functionally impaired and even reprogrammed to shift away from antitumor immunity and toward a tumor-promoting direction.
See related commentary by Carbone, p. 3199
Mucosa-Associated Microbiota in the Gastrointestinal Tract of Healthy Japanese Subjects
Authors: Kashiwagi Saori , Naito Yuji , Inoue Ryo , Takagi Tomohisa , Nakano Takahiro , Inada Yutaka , Fukui Akifumi , Katada Kazuhiro , Mizushima Katsura , Kamada Kazuhiro , Uchiyama Kazuhiko , Handa Osamu , Ishikawa Takeshi , Itoh Yoshito 
Published: February 2019

Background: The importance of microbiota infiltrating the gut mucus layer has been reported in the pathogenesis of various gastrointestinal and systemic diseases. However, little is known about the mucosa-associated microbiota (MAM) in healthy subjects. The present study aimed to clarify the characteristics of the gastrointestinal MAM from the oral cavity to the rectum in healthy Japanese subjects. Methods: Seventeen healthy subjects were enrolled. In this study, 5 mucosa samples from the upper gut (intraoral, mid-esophagus, gastric corpus, gastric antrum, and duodenum) and 7 from the lower gut (ileum, cecum, ascending colon, transverse colon, descending colon, sigmoid colon, and rectum) were collected with a brush under endoscopic examination. MAM profiles of each sample were analyzed by 16S-rRNA V3-V4 gene sequences. Results: Collecting mucosa samples by brushing provided sufficient material for MAM profiling without causing adverse effects. The upper and lower gut MAM profiles differed significantly (p < 0.0001). In the upper and lower gut, the intra- and inter-individual MAM profiles were significantly different (p = 0.0008 and p < 0.0001 respectively). Conclusions: The MAM profiles of the upper and lower gut were significantly different. The inter-individual differences in MAM were remarkable compared to the intra-individual differences.
PHYLOGENETIC ASSESSMENT OF GIANT CLAMS (TRIDACNIDAE) USING PARTIAL AMINO ACIDS SEQUENCES OF CYTOCHROME C OXIDASE I GENE
Authors: Nuryanto Agus , Nuryadi Dedi , Soedharma D. , D Blohm 
Published: February 2019

Phylogenetic assessment of the giant clams need to be improved using various genetic markers since their relaionships are plagued by inconsistency result of several studies. This is especially true for the species under sub-genus Chametrachea. Here we studied the phylogeny of the giant clams using amino acid sequence of the mitochondrial COI gene. This study is aimed to assess and better understand the relationships of the giant clams, especially for three species under subgenus Chametrachea. The result showed close proximity between T. crocea and T. squamosa and between T. maxima and T. gigas.Â However, amino acids sequences of cytochrome c oxidase I gene was not strong enough to discriminate between T. crocea and T. squamosa. The majority of mutations were hydrophobic to hydrophilic amino acids.
POPULATION STRUCTURE OF TOPSHELLS (TROCHUS NILOTICUS) IN SAPARUA ISLAND, CENTRAL MOLUCCAS-INDONESIA
Authors: Leimena Handy Erwin Pier , Subahar Tati S. , Adianto  
Published: February 2019

Lola snail (Trochus niloticus) is one of the largest sea snails that live in coral reefsat Indo Pacific region and Indonesia including Saparua Island, the province of Moluccas. In a few recent years, the exploitation of lola snails has been increasing, so that the population of lola snails in nature decreases.. The yield of lola snail in Saparua Island and in the archipelagos of Banda from 1979 until 1992 showed a decrease from around 4 tons of dry shells to only around 0.25 tons. Furthermore, this research was aimed to estimate the size structure, age structure, and the sex ratio of lola snails population in Saparua Island, the regency of Central Moluccas. The sampling of lola snails used transects strip method. Â Each transect was 100 m long and 2 m wide, which were divided into 10 segments of 10 m x 2 m. Transect was laid perpendicular to the coast line started from the lowest fall of the tides to the coast. The Bhattacharya method was applied for data analysis. The frequency distribution of shell diameter revealed that lola snails in Saparua Island consisted of nine size classes and two different age classes, which indicated that the population of lola snails in Saparua Island had two periods of spawning. Finally, from this research it could be concluded that the sex ratio of lola snail was 1:1.Â
CLONING OF A GENE ENCODING PROTEIN BELONGING TO ABC TRANSPORTER INVOLVED IN BACTERIAL MAGNETIC PARTICLE SYNTHESIS IN MAGNETOSPIRILLUM MAGNETICUM AMB-1
Authors: TRI WAHYUDI ARIS 
Published: February 2019

Magnetospirillum magneticum AMB-1 synthesizes intracellular magnetic particles, magnetite (Fe3O4), enveloped by membrane called magnetosome under micro-aerobic conditions. Initial study of random transposon-based mutagenesis generated 62 nonmagnetic mutants of AMB-1 in a mini-Tn5 library. In order to identify a gene involved in bacterial magnetic particle (BMP) synthesis in the magnetic bacterium M. magneticum AMB-1, a nonmagnetic mutant from the library designated as NMA38-4, was analyzed. h e amino acid sequence deduced from the gene directly interrupted by transposon, ORF4 (1482 bp), showed homology to ATP binding cassette (ABC) transporter of Mesorhizobium loti with 62 % identity and 74 % similarity. It was strongly indicated by the occurrence of putative consensus sequence of ATP-binding motifs (ATP-binding protein). h e ORF4 was subsequently cloned in pET-15b and the recombinant ORF4-Histag fusion protein was heterologously expressed in Escherichia coli BL21 (DE3) pLysS. A 55 kDa protein corresponding to the ORF4-Histag fusion protein was obtained after puriï¬ cation using Ni-NTA column. h is is the ï¬ rst report describing a gene cluster containing gene encoding protein belonging to ABC transporter organized in an operon which is involved in BMP synthesis. Key words: Magnetospirillum magneticum AMB-1, Bacterial Magnetic Particle (BMP), ATP Binding Cassette (ABC) Transporter, transposon mutagenesis.
EXOPOLYSACCHARIDE PRODUCTION AND ITS BIOACTIVITIES OF THE EDIBLE PLEUROTUS OSTREATUS IN SUBMERGED CULTURE
Authors: SASKIAWAN IWAN 
Published: February 2019

Submerged cultures were used to study the influence ofÂ various carbon sources on the mycelial biomass and exopolysaccharide production ofÂ PleurotusÂ ostreatus. The antimicrobial and antioxidant activity ofÂ Â the exopolysaccharide were also determined.Â Â The yield ofÂ mycelial biomass ofÂ 7.06 g/l, 5.12 g/l, 4.66 g/l, and 2.96 g/l was obtained by utilization ofÂ maltose, glucose,Â lactoseÂ andÂ starchÂ asÂ aÂ carbonÂ source,Â respectively.Â Furthermore,Â inÂ the medium containing maltose, lactose, glucose, and starch produce 100.05 mg/l, 97.73 mg/l, 78.63 mg/l, and 70.45 mg/l ofÂ exopolysaccharide, respectively.Â The assay ofÂ antimicrobial and antioxidant activity showed that the exopolysaccharide is more active to inhibit the growth ofÂ B. subtilis ratherÂ thanÂ thoseÂ ofÂ E.Â coliÂ andÂ S.Â cerevisiae. Furthermore,Â theÂ exopolysaccharide wasÂ also indicatedÂ to have antioxidant activity.Key words: Pleurotus ostreatus, exopolysaccharide, antimicrobial activity, antioxidant activityÂ
ISOLATION AND CHARACTERIZATION OF PARTIAL CDNA OF SUCROSE SYNTHASE PUTATIVE GENE IN PALMYRA PALM (BORASSUS FLABELLIFER)
Authors: INABUY FAINMARINAT , Pancoro Adi 
Published: February 2019

Intensification of biofuel resources is urgently needed considering the decrease in availability of worldâ€™s fossil fuel. Palmyra palm (Borassus flabellifer) is highly potential to be developed as bioethanol source regarding the high sucrose content in its nira. It was observed that nira produced in dry season is sweeter than that in rainy season, which presumed to be influenced by a difference in expression level of sucrose-related genes during the two seasons. Studies on Â Â Sucrose Synthase (SUS) gene of palmyra are therefore required prior to study the gene expression. Palmyra SUS gene sequence is currently unavailable in GenBank, thereby pair of primers was designed from highly conserved region of SUS proteins among monocots. A 1866 bp partial cDNA fragment of SUS putative gene has been succesfully isolated from RNA of the young leaves of B. flabellifer. BLASTn and BLASTp aligments showed that either BfSUS cDNA or BfSUS polypeptide has high similarity with SUS cDNA and proteins from diverse plant species, with the highest similarity shown by Tulipa gesneriana. The phylogenetic tree showed that SUS protein sequences of monocot species were distinctively grouped and splitted from those of dicot species. The BfSUS was clustered in monocot group, although not specifically grouped with particular monocot species. Nevertheless, B. flabellifer showed nearest genetic distance with Tulipa gesneriana and Oncidium cv.â€™Goldianaâ€™. Characterization of BfSUS polypeptide using Geneious 4.6.2 indicated the presence of sucrose synthase (SUS) and glycosyl transferase (GT) domains, four putative UDP-glucose binding pockets within the GT domain, and a calcium-dependent Ser/Thr protein kinase binding site within the SUS domain. These domains and motifs are highly conserved in SUS proteins across plant species, hence confirming that the cDNA fragment obtained in this study is the putative gene of sucrose synthase of B. flabellifer.
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Keywords: Borassus flabellifer, nira, sucrose, sucrose synthase, SUS domain, GT domain,
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SACCHARIFICATION OF CORNCOB USING CELLULOLYTIC BACTERIA FOR BIOETHANOL PRODUCTION
Authors: SUNARTI TITI CANDRA , MERYANDINI ANJA , SOFIYANTO M. EDY , RICHANA NUR 
Published: February 2019

The use of cellulose degrading enzyme (cellulases) for hydrolysis of lignocellulosic material is a part of bioethanol production process.Â In this experiment, Â delignified corncob,Â its cellulose fraction and alpha cellulose were used as substrates to produce fermentable sugar by using three local isolates of celluloytic bacteria (C5-1, C4-4, C11-1 and Cmix ; mixed cultures of three isolates), and Saccharomyces cereviseae to produce ethanol. The results showed that all isolates of cellulolytic bacteria can grow on cellulose fraction better than on Â delignified corncob, and alpha cellulose.Â The highest hydrolytic activity produced from cellulose fraction was by isolate C4-4, which liberated 3.50 g/l of total sugar.Â Ethanol can be produced by mixed culture of bacteria and yeast, but because of competitive growth, the fermentation only produced 0.39-0.47 g/l of ethanol.
Keywords:Â Celluloses, delignified corncob
ECOLOGICAL STUDY IN TWO QUARRIED LIMESTONE KARST HILLS IN BOGOR WEST JAVA: VEGETATION STRUCTURE AND FLORISTIC COMPOSITION
Authors: SATYANTI ANNISA , CANDRA KUSUMA YAYAN WAHYU 
Published: February 2019

Many species extinctions have probably gone unnoticed on limestone that was destroyed before they could be sampled. Unless biodiversity surveys are intensified, the true magnitude of extinctions will never be ascertained. The objectives of this study were to determine tree species composition of limestone hills in Nyungcung and Ciampea; to determine quantitatively the dominant and less dominant species and to quantify floristic structure of the two limestone hills. Value of richness (Menhinick) and evenness in Nyungcung were 3.28 and 0.826 whilst in Ciampea were 3.29 and 0.823, respectively. In term of diversity (Shannon Wiener), Nyungcung seems to be more diverse than Ciampea as indicated by the higher value of diversity index. Nyungcung has 3.225 of diversity (Shannon Wiener) index while Ciampea has 2.859. The floristic composition of two sites was significantly different and Â mostly comprisedÂ Moraceae, Rubiaceae, and Euphorbiaceae. However, the highest presence of species were Antidesma montanum (Euphorbiaceae) and Chrysophyllum lanceolatum (Sapotaceae), and Pandanus sp. (Pandanaceae) in Nyungcung, whereas in Ciampea, Harpullia arborea (Sapindaceae), Ophiorhhiza canescens (Rubiaceae), and Allophyllus cobbe (Sapindaceae). Macaranga rhizinoides, O. canescens, A. montanum, and Turpinia montana , respectively , gained the highest importance values.
Key words: limestone, flora, composition, quarries
THE NATURAL HABITAT OF BEGONIA ON THE ISLAND OF BALI: MICROCLIMATE PREFERENCE IN TWO FOREST SITES IN BEDUGUL
Authors: Satyanti Annisa 
Published: February 2019

A study on Begoniaâ€™s ecology was conducted in two forest sites, a nature reserve and reboisation forest, respectively, in Bedugul Bali. The objective of the study was to describe Begonia species found in respective forest sites, to gather information on abiotic factors and to find the influences of these abiotic factors to the abundance of Begonia species. Three species were identified as B. multangula, B. baliensis and B. longifolia. There were two form of B. longifolia, white and red. The multivariate analysis (PCA) showed that abiotic factors measured were relatively similar among plots. In addition, no particular abiotic factor, from multivariate analysis, showed specific influence on Begonia species frequency.Â Interestingly, the multivariate analysis also implied that B. latifolia has different microclimate preference between forms (white and red).Â The abundance, refers to the frequency, of all of species in two forests was similar (t-test, p=0.061). Pooling the data from the fourty plots (two forest sites) and white and red forms of B. longifolia together, B. multangula and B. longifolia found were similarly abundant between species (t- test, p=0.460).
VEGETATION OF LOWLAND TROPICAL FOREST (WEST PAPUA), HUMAN PRESSURE, FOOD AVAILABILITY AND WALLABY (Dorcopsis muelleri) PRESENCE
Authors: Sykora KarlÃ¨ 
Published: February 2019

The presence of Dorcopsis muelleri in different habitats and related vegetation types has been studied in lowland tropical vegetation in the northern Part of Manokwari, West Papua. Four habitat types comprising 6 plant communities could be distinguished: Â 1. Grassland, Imperata cylindrica - Ipomea aquatica community; 2. Open forest: a. open forest transitional to grassland, Ficus robusta - Dendrochide sp. community, b. open forest after logging, Musa paradisiaca â€“ Callamus longipina community, c. open forest regenerated after logging,Â Diospyros hebecarpa-Lepinopsis ternatensisÂ community, d. open forest on rocky soil, regenerated after logging, Smilax malacensis-Pandanus tectorius community; 3. Undisturbed (â€œprimary) closed forest, Sommeria leuchophyllaâ€“Paraltropis glabra community. Â The forest wallaby has especially been noted in grassland, in open forest with only little logging activity and in undisturbed closed forest. It was however not registered from the forests with clear logging influence. D. muelleri appears to be very sensitive to human disturbance. Our results indicate that vegetation structure, food plant availability and possibly also vegetation composition is less important than human disturbance. There is a strong negative relation between on one hand presence of the forest wallaby and on the other hand logging, distance to villages and hunting.