bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Copy Number Variation in Male Breast Cancer by aCGH
Authors: Tommasi Stefania , Mangia Anita , Iannelli Giuseppina , Chiarappa Patrizia , Rossi Elena , Ottini Laura , Mottolese Marcella , Zoli Wainer , Zuffardi Orsetta , Paradiso Angelo 
Published: January 2015

Background: Male breast cancer (MBC) is a rare disease and little is known about its etiopathogenesis. Array comparative genomic hybridization (aCGH) provides a method to quantitatively measure the changes of DNA copy number and to map them directly onto the complete linear genome sequences. The aim of this study was to investigate DNA imbalances by aCGH and compare them with a female breast cancer dataset.Methods: We used Agilent Human Genome CGH Microarray Kit 44B and 44K to compare genomic alterations in 25 male breast cancer tissues studied at NCC of Bari and 16 female breast cancer deposited with the Gene Expression Omnibus (GSE12659). Data analysis was performed with Nexus Copy Number 5.0 software.Results: All the 25 male and 16 female breast cancer samples displayed some chromosomal instability (110.93 alterations per patient in female, 69 in male). However, male samples presented a lower frequency of genetic alterations both in terms of loss and gains.Conclusion: aCGH is an effective tool for analysis of cytogenetic aberrations in MBC, which involves different biological processes than female. Male most significant altered regions contained genes involved in cell communication, cell division and immunological response, while female cell–cell junction maintenance, regulation of transcription and neuron development.
Multispectral Enhancement towards Digital Staining
Authors: Bautista Pinky A. , Yagi Yukako 
Published: January 2015

Background: Digital staining can be considered as a special form of image enhancement wherein the concern is not only to increase the contrast between the background objects and objects of interest, but to also impart the colors that mark the objects’ unique reactions to a specific stain. In this paper, we extended the previously proposed multispectral enhancement methods such that the colors of the background pixels can also be changed.Methods: In the previous multispectral enhancement methods a shifting factor is provided to the original spectrum. To implement digital staining, a spectral transformation process is introduced prior to spectral shifting.Results: The enhancement method is applied to multispectral images of H&E stained liver tissue. The resulting digitally stained images show good correlation with the serial-section images of the tissue which are physically stained with Masson's trichrome.Conclusion: We have presented a multispectral enhancement method that can be adjusted to produce digitally stained-images. The current experimental results show the viability of the method. However, to achieve robust enhancement performance issues that arise from variations in staining conditions has to be addressed as well. This would be part of our future work.
Absolute Quantification of Choline-Related Biomarkers in Breast Cancer Biopsies by Liquid Chromatography Electrospray Ionization Mass Spectrometry
Authors: Mimmi Maria Chiara , Finato Nicoletta , Pizzolato Gloria , Beltrami Carlo Alberto , Fogolari Federico , Corazza Alessandra , Esposito Gennaro 
Published: January 2015

It has been repeatedly demonstrated that choline metabolism is altered in a wide variety of cancers. In breast tumours, the choline metabolite profile is characterized by an elevation of phosphocholine and total choline-compounds. This pattern is increasingly being exploited as biomarker in cancer diagnosis.The majority of in vitro metabolomics studies, for biomarkers quantification in cell cultures or tissues, entail proton NMR spectroscopy. Although many “targeted” approaches have been proposed to quantify metabolites from standard one-dimensional (1D) NMR experiments, the task is often made difficult by the high degree of overlap characterizing 1H NMR spectra of biological samples.Here we present an optimized protocol for tissue extraction and absolute quantification of choline, phosphocholine and glycerophosphocholine by means of liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS). The selected chromatographic separation system with a HILIC (hydrophilic interaction chromatography) amide column effectively separates free choline and its phopshorylated derivatives, contrary to failure observed using standard reversed-phase chromatography. The metabolite absolute quantification is based on external calibration with commercial standards, and is validated by a parallel 1D proton NMR analysis.The LC-MS/NMR analysis is applied to three breast carcinoma specimens obtained by surgical excision, each one accompanied by a control tissue sample taken outside the tumor margin. The metabolite concentrations measured are in good agreement with previous results on metabolic profile changes of breast cancer. Each of the three cancerous biopsies, when compared with the control tissue, exhibit a highly increased levels phosphocholine, total choline and phosphocholine/glycerophosphocholine ratio.
Investigation of Climatological Onset and Withdrawal of the Rainy Season in Panama Based on a Daily Gridded Precipitation Dataset with a High Horizontal Resolution
Authors: Nakaegawa Tosiyuki , Arakawa Osamu , Kamiguchi Kenji 
Published: January 2015

Abstract
The present study investigated the onset and withdrawal dates of the rainy season in Panama by using newly developed, gridded, daily precipitation datasets with a high horizontal resolution of 0.05° based on ground precipitation observations. The onset and withdrawal dates showed very complicated geographical features, although the country of Panama is oriented parallel to latitude lines, and the geographical patterns of the onset and withdrawal dates could simply reflect the latitudinal migration of the intertropical convergence zone, as seen in other regions and countries. An absolute threshold value of 3 mm day−1 (pentad mean precipitation) was used to determine the onset and withdrawal dates. The onset and withdrawal dates obtained from the gridded daily precipitation dataset clearly depicted the migration of the rainy season. The rainy season starts suddenly in pentad 21 (11–15 April) in most of eastern Panama and in pentad 22 (16–20 April) in most of western Panama. The termination of the rainy season begins in Los Santos Province during pentad 67 (27 November–1 December) and expands to both the eastern and western surrounding areas. There is no dry season in the western part of the Caribbean coastal zone. Water vapor fluxes and topography suggest dynamical causes, such as a topographically induced upward mass flux accompanied by high humidity, for the complicated geographical features of the onset and withdrawal dates. An assessment was made of uncertainties in the timing of the onset and withdrawal associated with the definition of these terms.
A Hybrid Particle–Ensemble Kalman Filter for Lagrangian Data Assimilation
Authors: Slivinski Laura , Spiller Elaine , Apte Amit , Sandstede Björn 
Published: January 2015

Abstract
Lagrangian measurements from passive ocean instruments provide a useful source of data for estimating and forecasting the ocean’s state (velocity field, salinity field, etc.). However, trajectories from these instruments are often highly nonlinear, leading to difficulties with widely used data assimilation algorithms such as the ensemble Kalman filter (EnKF). Additionally, the velocity field is often modeled as a high-dimensional variable, which precludes the use of more accurate methods such as the particle filter (PF). Here, a hybrid particle–ensemble Kalman filter is developed that applies the EnKF update to the potentially high-dimensional velocity variables, and the PF update to the relatively low-dimensional, highly nonlinear drifter position variable. This algorithm is tested with twin experiments on the linear shallow water equations. In experiments with infrequent observations, the hybrid filter consistently outperformed the EnKF, both by better capturing the Bayesian posterior and by better tracking the truth.
Tobacco Use and Exposure among Children in Migrant and Non-Migrant Households in Java, Indonesia
Authors: Sukamdi  , Wattie Anna Marie 
Published: January 2015

This research note aims to understand the impact of parental migration on the children who stay behind by examining the issue of smoking. It asks whether tobacco use and exposure are higher among children in migrant households compared with those in non-migrant households in Java, Indonesia. Data were collected in 2008 in two provinces, West Java and East Java, as part of the Child Health and Migrant Parents in South-East Asia (CHAMPSEA) Project. The analytical sample used here relates to children aged 9, 10 and 11 living in both non-migrant and transnational households (N=451). The findings show that the incidence of ever having smoked among these primary school-aged children is relatively low at less than 10 percent, but that boys are much more likely to have used tobacco than girls. Findings from multivariate logistic models predicting smoking behavior show no difference between the children of migrants and non-migrants; nor does household wealth appear to influence whether or not a child has tried to-bacco. Gender, child stunting (low height-for-age), carer's education, family functioning and tobacco use by friends are the four main factors found to be significantly associated with child smoking.
Comparison of volume perfusion computed tomography and contrast-enhanced ultrasound for assessment of therapeutic effect of transarterial chemoembolization in patients with hepatocellular carcinoma: a preliminary report
Authors: Kaufmann Sascha , Schulze Maximilian , Spira Daniel , Horger Marius 
Published: January 2015

Background Evaluation of transarterial chemoembolization (TACE) by using contrast-enhanced ultrasound (CEUS) and volume perfusion computed tomography (VPCT) as methods that display tumor vascularization. Purpose To assess early results of TACE in patients with hepatocellular carcinoma (HCC) using CEUS and VPCT. Material and Methods Twenty patients with HCC underwent CEUS and VPCT in the pre- and post-TACE setting (1 day). Hepatic perfusion index (HPI), arterial liver perfusion (ALP), blood flow (BF), and blood volume (BV) were measured with VPCT. Peak intensity (PI), time-to-peak (TTP), and regional blood flow (RBF) were measured with CEUS. Sensitivity, specificity, negative and positive predictive values, and cutoff values for these parameters were calculated. Immediate tumor response after TACE was classified as responder or non-responder. Results were compared with those at follow-up after 2 and 4 months (FU2mo/FU4mo) following modified RECIST. Results CEUS and VPCT showed comparable immediate post-TACE results in 20/20 cases. Complete response was confirmed in 10/20 patients at FU2mo and in 9/20 at FU4mo. For responders, reduction in HPI, ALP, BV, and BF at day 1 post TACE proved significant ( P < 0.001). For non-responders, the course of all VPCT parameters proved non-significant. A cutoff of 40% reduction in HPI and a reduction in ALP of >29.6%, in BV of >41.4%, or in BF of >53.1% was indicative of response according to FU2mo. For responders only, changes in PI ( P < 0.001), TTP ( P < 0.01), and BF ( P < 0.01) proved significant whereas for non-responders, all CEUS parameters proved non-significant. Conclusion CEUS performs equally to VPCT for assessment of early response to TACE in HCC by a lesion-by-lesion assessment and showed prognostic value at mid-term.
Tocotrienol preserves ovarian function in cyclophosphamide therapy
Authors: Saleh HS , Omar E , Froemming GRA , Said RM 
Published: January 2015

Introduction: Cyclophosphamide (CPA) chemotherapy leads to ovarian failure and infertility. Tocotrienol (T3) is an antioxidant and anti-inflammatory agent. The role of T3 in ovarian protection throughout chemotherapy remains unclear. Aim: To investigate the role of T3 in the preservation of female fertility in CPA treatment. Method: Sixty female mice were divided into five treatment groups, namely, normal saline, corn oil only, T3 only, CPA and CPA + T3. The treatment was given for 30 days, followed by administration of gonadotrophin to induce ovulation. After killing, both ovaries were collected and examined histologically. Results: There was significant reduction in ovarian size in the CPA group compared with the normal group (CPA versus normal, mean area ± SD; 0.118 ± 0.018 vs. 0.423 ± 0.024 cm2; p ≤ 0.005), whilst concurrent administration of T3 with CPA leads to conservation of ovarian size (CPA + T3 vs. CPA, mean area ± SD; 0.285 ± 0.032 vs. 0.118 ± 0.018 cm2; p ≤ 0.005). Ovaries in CPA group showed abnormal folliculogenesis with accompanied reduced ovulation rate, follicular oedema, increased vascularity and inflammatory cell infiltration. These changes were reversed by concurrent T3 administration. Conclusion: Co-administration of T3 with CPA confers protection of ovarian morphology and function in vivo. These findings contribute to the further elucidation of CPA effect on ovary and suggest the potential of T3 use in preserving fertility in chemotherapy.
Carbon dioxide fluxes from contrasting ecosystems in the Sudanian Savanna in West Africa
Authors: Quansah Emmanuel , Mauder Matthias , Balogun Ahmed A , Amekudzi Leonard K , Hingerl Luitpold , Bliefernicht Jan , Kunstmann Harald 
Published: January 2015

Abstract

Background
The terrestrial land surface in West Africa is made up of several types of savanna ecosystems differing in land use changes which modulate gas exchanges between their vegetation and the overlying atmosphere. This study compares diurnal and seasonal estimates of CO2 fluxes from three contrasting ecosystems, a grassland, a mixture of fallow and cropland, and nature reserve in the Sudanian Savanna and relate them to water availability and land use characteristics.

Results
Over the study period, and for the three study sites, low soil moisture availability, high vapour pressure deficit and low ecosystem respiration were prevalent during the dry season (November to March), but the contrary occurred during the rainy season (May to October). Carbon uptake predominantly took place in the rainy season, while net carbon efflux occurred in the dry season as well as the dry to wet and wet to dry transition periods (AM and ND) respectively. Carbon uptake decreased in the order of the nature reserve, a mixture of fallow and cropland, and grassland. Only the nature reserve ecosystem at the Nazinga Park served as a net sink of CO2, mostly by virtue of a several times larger carbon uptake and ecosystem water use efficiency during the rainy season than at the other sites. These differences were influenced by albedo, LAI, EWUE, PPFD and climatology during the period of study.

Conclusion
These results suggest that land use characteristics affect plant physiological processes that lead to flux exchanges over the Sudanian Savanna ecosystems. It affects the diurnal, seasonal and annual changes in NEE and its composite signals, GPP and RE. GPP and NEE were generally related as NEE scaled with photosynthesis with higher CO2 assimilation leading to higher GPP. However, CO2 effluxes over the study period suggest that besides biomass regrowth, other processes, most likely from the soil might have also contributed to the enhancement of ecosystem respiration.
ALLMAPS: robust scaffold ordering based on multiple maps
Authors: Tang Haibao , Zhang Xingtan , Miao Chenyong , Zhang Jisen , Ming Ray , Schnable James C , Schnable Patrick S , Lyons Eric , Lu Jianguo 
Published: January 2015

AbstractThe ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.
Potential utilization of bagasse as feed material for earthworm Eisenia fetida and production of vermicompost
Authors: Bhat Sartaj Ahmad , Singh Jaswinder , Vig Adarsh Pal 
Published: January 2015

AbstractIn the present work bagasse (B) i.e waste of the sugar industry, was fed toEisenia fetidawith cattle dung (CD) support as feed material at various ratios (waste: CD) of 0:100 (B0), 25:75 (B25), 50:50 (B50), 75:25 (B75) and 100:0 (B100) on dry weight basis. Co-composting with cattle dung helped to improve their acceptability forE. fetidaand also improved physico-chemical characteristics. Best appropriate ratio for survival, maximum growth and population buildup ofE. fetidawas determined by observing population buildup, growth rate, biomass, mortality and cocoon formation. Minimum mortality and highest population size of worms was observed in 50:50 (B50) ratio. Increasing concentrations of wastes significantly affected the growth and reproduction of worms. Nutrients like nitrogen, phosphorus and sodium increased from pre-vermicompost to post-vermicompost, while organic carbon, and C:N ratio decreased in all the end products of post-vermicomposting. Heavy metals decreased significantly from initial except zinc, iron and manganese which increased significantly. Scanning electron microscopy (SEM) was used to recognize the changes in texture in the pre and post-vermicomposted samples. The post-vermicomposted ratios in the presence of earthworms validate more surface changes that prove to be good manure. The results observed from the present study indicated that the earthwormE. fetidawas able to change bagasse waste into nutrient-rich manure and thus play a major role in industrial waste management.
miRNA-221 is elevated in cystic fibrosis airway epithelial cells and regulates expression of ATF6
Authors: Oglesby Irene K , Agrawal Raman , Mall Marcus A , McElvaney Noel G , Greene Catherine M 
Published: January 2015

Abstract

Background
MicroRNA (miRNA) and messenger RNA (mRNA) expression differs in cystic fibrosis (CF) versus non-CF bronchial epithelium. Here, the role of miRNA in basal regulation of the transcription factor ATF6 was investigated in bronchial epithelial cells in vitro and in vivo.

Methods
Using in silico analysis, miRNAs predicted to target the 3′untranslated region (3′UTR) of the human ATF6 mRNA were identified.

Results
Three of these miRNAs, miR-145, miR-221 and miR-494, were upregulated in F508del-CFTR homozygous CFBE41o- versus non-CF 16HBE14o- bronchial epithelial cells and also in F508del-CFTR homozygous or heterozygous CF (n = 8) versus non-CF (n = 9) bronchial brushings. ATF6 was experimentally validated as a molecular target of these miRNAs through the use of a luciferase reporter vector containing the full-length 3′UTR of ATF6. Expression of ATF6 was observed to be decreased in CF both in vivo and in vitro. miR-221 was also predicted to regulate murine ATF6, and its expression was significantly increased in native airway tissues of 6-week-old βENaC-overexpressing transgenic mice with CF-like lung disease versus wild-type littermates.

Conclusions
These results implicate miR-145, miR-221 and miR-494 in the regulation of ATF6 in CF bronchial epithelium, with miR-221 demonstrating structural and functional conservation between humans and mice. The altered miRNA expression evident in CF bronchial epithelial cells can affect expression of transcriptional regulators such as ATF6.
Tahap-tahap pendidikan karakter dalam pemikiran Ki Ageng Suryomentaram dan relevansinya dengan pendidikan akhlak Islam
Authors: Sumedi Dr. 
Published: January 2015

Morality shows people’s life quality and how the moral education could influence them.The religious people have assumption that religion always teaches the followers to do goodness and forbid them from doing badness. Islam, in the context of Indonesia, is of course influenced by the real condition of the society. In relation to this, there is Javanese philosopher, Ki Ageng Suryomemtaram, who thought the character building that is still relevant. He thought, “feeling is the center of everyone’s personality”. Based on his idea and feeling, he divides them into four dimensions of life. Moralitas menunjukkan kualitas kehidupan masyarakat dan bagaimana pendidikan moral bisa mempengaruhi mereka. Orang-orang beragama memiliki asumsi bahwa agama selalu mengajarkan pengikutnya untuk berbuat baik dan melarangnya melakukan kesalahan. Islam, dalam konteks Indonesia, tentu saja dipengaruhi oleh kondisi riil masyarakatnya. Sehubungan dengan ini, ada filsuf Jawa, Ki Ageng Suryomemtaram, yang memikirkan pembangunan karakter yang masih dianggap relevan. Baginya, “perasaan adalah pusat dari kepribadian setiap orang”.Berdasarkan pemikirannya pada perasaan, dia membaginya menjadi empat dimensi kehidupan.
Filsafat Tarbiyah berbasis kecerdasan makrifat
Authors: Mulkhan Abdul Munir 
Published: January 2015

Philosophy is the source of science and technology. The practice of Islamic Education works without being guided by Tarbiyah (Islamic Education) Philosophy, but by the seculer thinking, It develops without orientation and it is hard to compete with others. It’s time the Islamic education pratice to guiding by the Tarbiyah Philosophy, Tarbiyah Theories and Tarbiyah Technology which is structurally and functionally built from Islamic philosophy. As of the basic idea of Islamic philosophy, the essential of Tarbiyah Philosophy is Ma’rifat Quotient wich means the activity for understand and realize the presence of God in whole life, activities of man; that also means the knowledge about God and intimate relationship with Him. The practical of Tarbiyah Philosophy based on Ma’rifat Quotient it both a creative solution for all kind of education problems andalternatif educational model. Based on Ma’rifat Quotient, it can be used to develop boarding school in more effcient way to accelerate qualities learning only 8 years for elementary to senior high school before join to university.Filsafat merupakan sumber ilmu dan teknologi. Sementara praktik PendidikanIslam bergerak tanpa panduan Filsafat Pendidikan Islam (Tarbiyah), tapi dipandu pemikiran sekuler sehingga tumbuh tanpa arah dan sulit bersaing. Karena itu sudah waktunya praktik pendidikan Islam dipandu Filsafat Tarbiyah, Teori Tarbiyah dan Teknologi Tarbiyah yang secara struktural dan fungsional dibangun dari Filsafat Islam. Sesuai gagasan dasar Filsafat Islam, inti-isi Filsafat Tarbiyah ialah kecerdasan makrifat sebagai kemampuan memahami dan menyadari kehadiran Tuhan dalam segala kegiatan hidup manusia sekaligus pengetahuan tentang Tuhan dan kedekatan hubungan dengan-Nya. Praktik tarbiyah berbasis kecerdasan makrifat merupakan solusi kreatif berbagai problem pendidikan Islam sekaligus menawarkan model pendidikan alternatif. Dari sini boarding school dikembangkan bebas dari pemborosan tidak produktif, melainkan model percepatan bermutu, sehingga cukup 8 tahun menyelesaikan pendidikan dasar (SD 4 Th) dan menengah (SLTPSLTA 4 Th) sebelum memasuki jenjang pendidikan tinggi.