bluuebunny/crossref_metadata_2025_split huggingface dataset:
EvoGrader: an online formative assessment tool for automatically evaluating written evolutionary explanations
Authors: Moharreri Kayhan , Ha Minsu , Nehm Ross H 
Published: July 2014

AbstractEvoGrader is a free, online, on-demand formative assessment service designed for use in undergraduate biology classrooms. EvoGrader’s web portal is powered by Amazon’s Elastic Cloud and run with LightSIDE Lab’s open-source machine-learning tools. The EvoGrader web portal allows biology instructors to upload a response file (.csv) containing unlimited numbers of evolutionary explanations written in response to 86 different ACORNS (Assessing COntextual Reasoning about Natural Selection) instrument items. The system automatically analyzes the responses and provides detailed information about the scientific and naive concepts contained within each student’s response, as well as overall student (and sample) reasoning model types. Graphs and visual models provided by EvoGrader summarize class-level responses; downloadable files of raw scores (in .csv format) are also provided for more detailed analyses. Although the computational machinery that EvoGrader employs is complex, using the system is easy. Users only need to know how to use spreadsheets to organize student responses, upload files to the web, and use a web browser. A series of experiments using new samples of 2,200 written evolutionary explanations demonstrate that EvoGrader scores are comparable to those of trained human raters, although EvoGrader scoring takes 99% less time and is free. EvoGrader will be of interest to biology instructors teaching large classes who seek to emphasize scientific practices such as generating scientific explanations, and to teach crosscutting ideas such as evolution and natural selection. The software architecture of EvoGrader is described as it may serve as a template for developing machine-learning portals for other core concepts within biology and across other disciplines.
DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML
Authors: Lund Kirstin , Cole John J , VanderKraats Nathan D , McBryan Tony , Pchelintsev Nikolay A , Clark William , Copland Mhairi , Edwards John R , Adams Peter D 
Published: July 2014

Abstract
Background
Myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are neoplastic disorders of hematopoietic stem cells. DNA methyltransferase inhibitors, 5-azacytidine and 5-aza-2′-deoxycytidine (decitabine), benefit some MDS/AML patients. However, the role of DNA methyltransferase inhibitor-induced DNA hypomethylation in regulation of gene expression in AML is unclear.

Results
We compared the effects of 5-azacytidine on DNA methylation and gene expression using whole-genome single-nucleotide bisulfite-sequencing and RNA-sequencing in OCI-AML3 cells. For data analysis, we used an approach recently developed for discovery of differential patterns of DNA methylation associated with changes in gene expression, that is tailored to single-nucleotide bisulfite-sequencing data (Washington University Interpolated Methylation Signatures). Using this approach, we find that a subset of genes upregulated by 5-azacytidine are characterized by 5-azacytidine-induced signature methylation loss flanking the transcription start site. Many of these genes show increased methylation and decreased expression in OCI-AML3 cells compared to normal hematopoietic stem and progenitor cells. Moreover, these genes are preferentially upregulated by decitabine in human primary AML blasts, and control cell proliferation, death, and development.

Conclusions
Our approach identifies a set of genes whose methylation and silencing in AML is reversed by DNA methyltransferase inhibitors. These genes are good candidates for direct regulation by DNA methyltransferase inhibitors, and their reactivation by DNA methyltransferase inhibitors may contribute to therapeutic activity.
The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas
Authors: Saraconi Giulia , Severi Francesco , Sala Cesare , Mattiuz Giorgio , Conticello Silvestro G 
Published: July 2014

Abstract
Background
The AID/APOBECs are deaminases that act on cytosines in a diverse set of pathways and some of them have been linked to the onset of genetic alterations in cancer. Among them, APOBEC1 is the only family member to physiologically target RNA, as the catalytic subunit in the Apolipoprotein B mRNA editing complex. APOBEC1 has been linked to cancer development in mice but its oncogenic mechanisms are not yet well understood.

Results
We analyze whether expression of APOBEC1 induces a mutator phenotype in vertebrate cells, likely through direct targeting of genomic DNA. We show its ability to increase the inactivation of a stably inserted reporter gene in a chicken cell line that lacks any other AID/APOBEC proteins, and to increase the number of imatinib-resistant clones in a human cellular model for chronic myeloid leukemia through induction of mutations in the BCR-ABL1 fusion gene. Moreover, we find the presence of an AID/APOBEC mutational signature in esophageal adenocarcinomas, a type of tumor where APOBEC1 is expressed, that mimics the one preferred by APOBEC1 in vitro.

Conclusions
Our findings suggest that the ability of APOBEC1 to trigger genetic alterations represents a major layer in its oncogenic potential. Such APOBEC1-induced mutator phenotypes could play a role in the onset of esophageal adenocarcinomas. APOBEC1 could be involved in cancer promotion at the very early stages of carcinogenesis, as it is highly expressed in Barrett's esophagus, a condition often associated with esophageal adenocarcinoma.
MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes
Authors: Zheng Xiaoqi , Zhao Qian , Wu Hua-Jun , Li Wei , Wang Haiyun , Meyer Clifford A , Qin Qian Alvin , Xu Han , Zang Chongzhi , Jiang Peng , Li Fuqiang , Hou Yong , He Jianxing , Wang Jun , Wang Jun , Zhang Peng , Zhang Yong , Liu Xiaole Shirley 
Published: July 2014

AbstractWe propose a statistical algorithm MethylPurify that uses regions with bisulfite reads showing discordant methylation levels to infer tumor purity from tumor samples alone. MethylPurify can identify differentially methylated regions (DMRs) from individual tumor methylome samples, without genomic variation information or prior knowledge from other datasets. In simulations with mixed bisulfite reads from cancer and normal cell lines, MethylPurify correctly inferred tumor purity and identified over 96% of the DMRs. From patient data, MethylPurify gave satisfactory DMR calls from tumor methylome samples alone, and revealed potential missed DMRs by tumor to normal comparison due to tumor heterogeneity.
Experimental NMR and DFT Studies of Persistent Carbocations Derived from Hetero-Polycyclic Aromatic Hydrocarbons Containing Oxygen Atom: Dibenzo[b,d]furan, Benzo[b]naphtho[1,2-d]furan, Benzo[b]naphtho[2,3-d]furan, Benzo[b]naphtho[2,1-d]furan, and Dinaphtho[2,1-b:1′,2′-d]furan
Authors: Okazaki Takao , Nakagawa Madoka , Kitagawa Toshikazu , Laali Kenneth K 
Published: July 2014

Abstract
Persistent protonation carbocations generated from hetero-PAHs containing oxygen atoms in their aromatic rings, dibenzo[b,d]furan (5), benzo[b]naphtho[1,2-d]furan (6), benzo[b]naphtho[2,3-d]furan (7), benzo[b]naphtho[2,1-d]furan (8), and dinaphtho[2,1-b:1′,2′-d]furan (9), were directly observed by NMR measurements in superacid. Compound 5 was protonated mainly at C(2) in FSO3H–SbF5 (1:1) or (4:1)/SO2ClF, and 6, 8, and 9 were protonated exclusively at C(5) in CF3SO3H or FSO3H/SO2ClF, whereas 7 was protonated at C(6) and C(11) to give two species in FSO3H/SO2ClF. Surprisingly, compound 5 resists protonation in FSO3H/SO2ClF to show NMR spectra corresponding to that of the intact material. Positive charge delocalization mapping for carbocations based on experimental Δδ13C values indicates limited delocalization in these systems. The chemical shifts and charge delocalization modes derived by DFT calculations agreed with the experimental results.
Total Synthesis of 2,6-Dideoxy-3-O-methylpyranosylillustrol, a Seco-norpregnaneglycoside from Mandevilla illustris
Authors: Tamiya Minoru , Isaka Nobuhisa , Ishizawa Kazuya , Ikeda Mayu , Ishiguro Masaji 
Published: July 2014

Abstract
2,6-Dideoxy-3-O-methylpyranosylillustrol (3) was stereoselectively synthesized through the oxidative construction of a cage-like DEF ring moiety and stereoselective glycosylation of a 2,6-dideoxysaccharide derivative.
Synthesis of a Trinuclear Tropolone–Palladium(II) Macrocycle and Its C60 Inclusion Properties
Authors: Otani Hiroyuki , Sumi Chisaki , Shimizu Hideyuki , Hasegawa Masashi , Iyoda Masahiko 
Published: July 2014

Abstract
4,5-Dialkyl-1,2-bis(5-tropolonylethynyl)benzenes 5a and 5b were synthesized, and dioctyl derivative 5a was converted into the corresponding trinuclear palladium(II) macrocycle 1a by reacting it with Pd(OAc)2. Macrocyclic supramolecular coordination complex 1a has an inner cavity just large enough to include C60. Although trinuclear palladium complex 1a incompletely incorporated C60 in solution owing to weak interactions between the bis(tropolono)palladium(II) moieties and C60, it formed an inclusion complex with C60 in the solid state. The inclusion complex showed a moderate charge-transfer absorption in the UV–vis–NIR spectra.
Venous leg ulcer after acupuncture treatment
Authors: Gkogkolou P. , Lorenz M. B. , Goerge T. 
Published: July 2014

ZusammenfassungIn diesem Fallbericht beschreiben wir eine 64-jährige Patientin, die ein chronisches Ulcus am dorsomedialen rechten Unterschenkel nach Akupunktur-Behandlung für Ostero-arthritis des rechten Knies entwickelte. Die duplexsonographische Diagnostik zeigte eine beidseitige Insuffizienz der Venae saphena parva (VSP) sowie eine periulzeröse Seitenastvarikosis der rechten VSP. Da die Patientin eine operative Behandlung ablehnte, wurde eine Schaumsklerosierung der periulzerösen Varikosis durchgeführt. Darunter zeigte sich eine vollständige Abheilung der Ulzeration innerhalb von 12 Wochen.
Foam sclerotherapy of a large postoperative seroma after inguinal lymph node excision
Authors: Recke A. L. , Kahle B. , Trog L. 
Published: July 2014

ZusammenfassungDie Basistherapie eines Seroms besteht aus einer Drainage der Wundhöhle in Kombination mit einer konsequenten Kompression. Diese Therapie ist jedoch langwierig. Wir zeigen an einem Fallbericht die erfolgreiche Sklerosierung eines postoperativen Seroms mit einer verkürzten und vollständigen Abheilung.
Recurrent benign adrenal pheochromocytomas associated with hemihypertrophy
Authors: Pikilidou Maria , Yavropoulou Maria , Katsounaros Marios 
Published: July 2014

SummaryWe report a case of a female with hemihypertrophy, who developed five recurrences of pheochromocytomas until the age of 35. Timely follow-up of the patient's blood pressure assisted in early diagnosis and treatment of recurrent tumors.Learning pointsRecurrent benign pheochromocytomas should raise suspicion of a genetic syndrome.A pheochromocytoma at a young age has a high propensity to recur and strict follow-up is mandatory.
Cellular Automata Simulations of Thermal Transport Properties of Thin-Film Polymer/CNTs Nano-Composites for Improved Design
Authors: Kalakonda P. , Casey A. , Iannacchione G. S. , Georgiev G. Y. , Cabrera Y. , Judith R. , Cebe P. 
Published: July 2014

ABSTRACTA computational algorithm has been developed to simulate the transport properties of oriented and un-oriented thin film nanocomposites of isotactic Polypropylene (iPP) and carbon nanotubes (CNT) with increasing CNT concentration. Our goal is to be able to design materials with optimal properties using these simulations. We use a cellular automata approach in a Matlab 3-D array environment. The percolation threshold is reproduced in the simulations, matching experimental data. Upon percolation, the thermal transport in the films increases sharply, due to the large difference in the thermal conductivities of the CNTs and the polymer. To verify the simulation, the thin-film samples were sheared in the melt at 200C at 1 Hz in a Linkan microscope shearing hot stage. The thermal conductivity measurements were performed on the same cell arrangement with the transport perpendicular to the thin-film plane using a DC method. The thermal conductivity is higher for the un-sheared as compared to the sheared samples. Our cellular automata simulations provide information about the microstructuremacroscopic property relation in the thin film nanocomposites and can be extended to simulations of other important materials.
Mathematical modeling of the fluid flow in a mixing device for melting/dissolving solid particles in a liquid alloy
Authors: Delgado-Álvarez J. A. , Perea-Zurita J. G. , Antonio-Morales A. , González-Rivera C. , Ramírez-Argáez M. A. 
Published: July 2014

ABSTRACTA study of the fluid flow in a mixing device proposed to dissolve alloying elements in iron baths is performed through a mathematical model in order to predict the best operating conditions for a proper melting/dissolution of solid alloying particles. The mathematical model consists in the mass and momentum conservation equations (continuity and Turbulent Navier-Stokes equations), and the standard two k-epsilon turbulence model. The model is numerically solved in transient regime with the Volume of Fluid algorithm (VOF) to calculate the vortex shape. VOF is built-in the CFD (Computational Fluid Dynamics) software ANSYS FLUENT 14. A flow of metal enters tangentially in the mixing chamber of the proposed mixing device (taken from an open patent) to generate a vortex. The shape and height of the vortex reached in this chamber depends on several design variables, but in this work only the presence or absence of a barrier in the device is analyzed. Results are obtained on the vortex sizes and shapes, liquid flow patterns, turbulent structure, residence times of the particles of alloying elements added to the melt and mixing times (Residence time distribution curves) of two devices: one with a barrier and the other without this barrier. It is found that the presence of the barrier in the device increases turbulence, destroys the vortex, decreases the residence time of the particles, and decreases the volume of fluid in the device. Most of the features of the barrier are detrimental for mixing and inhibits melting/dissolution of the alloying elements. Then, it is suggested a device without the presence of barrier for better performance.
Adhesion and Tensile Properties of a Novel Fiber-Metal Laminate Based on Polypropylene Reinforced with Aramid Fibers.
Authors: González-Canché Nancy G. , Carrillo J.G. , Gamboa R.A. 
Published: July 2014

ABSTRACTThe aim of the present study is to analyze interfacial adhesion and characterize the tensile properties of a FML elaborated from thin layers of an aluminum alloy and layers of maleic anhydride modified polypropylene (MAHPP) reinforced with an aramid woven fabric. For the analysis of interfacial adhesion, a microbond test is carried out on the MAHPP-aramid fiber system and a single lap joint test is performed on FML constituent materials, as well as the tensile characterization of the FML and its constituents is conducted accordingly. Microbond testing revealed an improvement in interfacial shear strength for the MAHPP-aramid fiber system in comparison with that of polypropylene-aramid fiber systems reported in the literature. The apparent shear strength between the FML constituent materials is comparable to that for bonding of aluminum with MAHPP. Tensile characterization of the FML and its constituents showed that the FML presented greater tensile strength than the aluminum alloy; and a more ductile behavior in comparison with its individual components due to the degree of adhesion between the constituents which allows the material to deform in unison.
Scale‐dependent thresholds in the dominant controls of wildfire size in semi‐arid southwest Australia
Authors: O'Donnell A. J. , Boer M. M. , McCaw W. L. , Grierson P. F. 
Published: July 2014

We aimed to characterize the size distribution of naturally occurring wildfires and to determine how fuel characteristics influence wildfire size in a vegetation mosaic of shrublands and woodlands in semi‐arid southwest Australia. The shape of frequency‐size distributions of fires can be used to elucidate shifts in the dominant drivers or constraints of fire size. We modeled the cumulative frequency‐size distribution of wildfires in southwest Australia using a segmented linear model with two break points. Three fire size categories were defined by the break points of the segmented model: “small” (<2,286 ha), “medium” (2,286–41,020 ha), and “large” fires (>41,020 ha). Break points were interpreted as thresholds in fire size that may represent shifts in the dominant controls of fire spread.We tested whether the influence of fuel characteristics on fire spread varied among fire size categories by comparing the composition of vegetation types and fuel ages among burnt and adjacent unburnt areas using selection ratios (ωx).Small and medium fires burnt shrub‐dominated vegetation types in proportion to their availability (ωx ≈ 1), but tended to burn smaller proportions of sparsely‐vegetated woodlands (ωx < 0.62). In contrast, large fires tended to burn woodlands in proportion to their availability (ωx ≈ 1). Young fuels (<20 years) were under‐represented in burnt areas regardless of fire size (ωx < 0.62), while older fuels (>30 years) burnt in proportion to their availability (ωx ≈ 1).Fire size in semi‐arid southwest Australia is generally limited by fuel mass in recently burnt areas and by fuel continuity in sparsely vegetated woodlands. However, following unusually wet years and subsequent growth of ephemeral plants, fuels in woodland vegetation likely become spatially continuous and capable of supporting the spread of large fires.
Silicon solar cells with Al2O3 antireflection coating
Authors: Dobrzański Leszek , Szindler Marek , Drygała Aleksandra , Szindler Magdalena 
Published: July 2014

Abstract
The paper presents the possibility of using Al2O3 antireflection coatings deposited by atomic layer deposition ALD. The ALD method is based on alternate pulsing of the precursor gases and vapors onto the substrate surface and then chemisorption or surface reaction of the precursors. The reactor is purged with an inert gas between the precursor pulses. The Al2O3 thin film in structure of the finished solar cells can play the role of both antireflection and passivation layer which will simplify the process. For this research 50×50 mm monocrystalline silicon solar cells with one bus bar have been used. The metallic contacts were prepared by screen printing method and Al2O3 antireflection coating by ALD method. Results and their analysis allow to conclude that the Al2O3 antireflection coating deposited by ALD has a significant impact on the optoelectronic properties of the silicon solar cell. For about 80 nm of Al2O3 the best results were obtained in the wavelength range of 400 to 800 nm reducing the reflection to less than 1%. The difference in the solar cells efficiency between with and without antireflection coating was 5.28%. The LBIC scan measurements may indicate a positive influence of the thin film Al2O3 on the bulk passivation of the silicon.
Sertoli-Leydig tumor and male pseudohermaphroditism discovered during inguinal hernia surgery
Authors: Pallisera Anna , Jorba Rosa , Zárate Luis , Català Jordi , Moysset Irene , Jimeno Myreia 
Published: July 2014

Abstract
The diagnosis of inguinal hernia is usually clinical and it is performed with high sensitivity and specificity. Very occasionally, it may be confused with other diseases (lymphadenopathy, testicular pathology,etc). We report a rare case of a 80-year-old woman with a clinical diagnosis of hernia, which was underwent surgery and a tumor from the hernia orifice was found. After histological analysis we discovered that the misdiagnosed hernia was actually a tumor on a rudimentary testis. After radiological, gynecological and cytogenetic assessment we obtained an unexpected diagnosis: Male psheudohermaphroditism and Sertoli-Leydigtumor (SLCT) development on the testis. Diagnostic guidance for disorders of sexual development is based almost entirely on pediatric experience and very few guidelines are available for adults. Male pseudohermaphroditism is an intersex condition in which the carriers show a phenotype that includes external female genitalia, but a male genetic and gonadal sex. SLCT are sex-cord stromal tumors which develop in ovary and very rarely in the testis, representing 0.1–0.5% of ovarian tumors and less than 0.2% of testicular tumors. Thus far 24 case have been reported in the literature in which SLCT tumor has developed on testis.
Systemic Targeted Alpha Radiotherapy for Cancer - A Review
Authors: Allen Barry J 
Published: July 2014

The fundamental principles of internal targeted alpha therapy for cancer were established many decades ago. The high linear energy transfer (LET) of alpha radiation to the targeted cancer cells causes double strand breaks in DNA. At the same time, the short range of alpha- radiation spares adjacent normal tissues. This targeted approach complements conventional external beam radiotherapy and chemotherapy. Such therapies fail on several fronts, such as lack of control of some primary cancers (eg glioblastoma multiforme) and inhibition of the development of lethal metastatic cancer after successful treatment of the primary cancer. This review charts the developing role of systemic high LET in internal radiation therapy. Targeted alpha therapy is a rapidly advancing experimental therapy that holds promise to deliver high cytotoxicity to targeted cancer cells. Initially thought to be indicated for leukaemia and micrometastases, there is now evidence that solid tumours can also be regressed. Alpha therapy may be molecular or physiological in its targeting. Alpha emitting radioisotopes such as Bi-212, Bi-213, At-211 and Ac-225 are used to label monoclonal antibodies or proteins that target specific cancer cells. Alternatively, radium-233 is used for palliative therapy of breast and prostate cancers because of its bone seeking properties. In this review, preclinical studies and clinical trials of alpha therapy are discussed for leukaemia, lymphoma, melanoma, glioblastoma multiforme, bone metastases, ovarian cancer, pancreatic cancer and other cancers. DOI: http://dx.doi.org/10.3329/bjmp.v6i1.19755 Bangladesh Journal of Medical Physics Vol.6 No.1 2013 21-38