Miracle-dz/UniFAR-FTUs huggingface dataset:
Initiation and Characterization of Small Cell Lung Cancer Patient-Derived Xenografts from Ultrasound-Guided Transbronchial Needle Aspirates

Small cell lung cancer (SCLC) is a devastating disease with limited treatment options. Due to its early metastatic nature and rapid growth, surgical resection is rare. Standard of care treatment regimens remain largely unchanged since the 1980’s, and five-year survival lingers near 5%. Patient-derived xenograft (PDX) models have been established for other tumor types, amplifying material for research and serving as models for preclinical experimentation; however, limited availability of primary tissue has curtailed development of these models for SCLC. The objective of this study was to establish PDX models from commonly collected fine needle aspirate biopsies of primary SCLC tumors, and to assess their utility as research models of primary SCLC tumors. These transbronchial needle aspirates efficiently engrafted as xenografts, and tumor histomorphology was similar to primary tumors. Resulting tumors were further characterized by H&E and immunohistochemistry, cryopreserved, and used to propagate tumor-bearing mice for the evaluation of standard of care chemotherapy regimens, to assess their utility as models for tumors in SCLC patients. When treated with Cisplatin and Etoposide, tumor-bearing mice responded similarly to patients from whom the tumors originated. Here, we demonstrate that PDX tumor models can be efficiently established from primary SCLC transbronchial needle aspirates, even after overnight shipping, and that resulting xenograft tumors are similar to matched primary tumors in cancer patients by both histology and chemo-sensitivity. This method enables physicians at non-research institutions to collaboratively contribute to the rapid establishment of extensive PDX collections of SCLC, enabling experimentation with clinically relevant tissues and development of improved therapies for SCLC patients.
Protein Eight Secondary Structure Classes Prediction Using Artificial Neural Networks

Protein is considered the backbone of any human being. Protein is responsible for many functionalities in the human body, these functionalities differ according to the way protein amino acids (amino acids are the raw elements of protein) bond together. Then the protein forms its secondary,tertiary and quaternary structures from the amino acid structure (primary sequence) by forming hydrogen bonds. Many machine learning techniques have been used through the past decade to try to predict the protein secondary structure. The most commonly used paradigm was the Artificial Neural Networks. A lot of research was conducted in this field. This paper presents the usage of Artificial Neural Networks to predict the protein secondary structure. The difference this paper proposes is predicting the eight classes of secondary structure not only the three main classes named: alpha, beta and coil. The maximum accuracy reached is 71% which is better that other discussed methods.
breast cancer progression A developmentally regulated inducer of EMT , LBX 1 , contributes to Material Supplemental

Material Supplemental http://genesdev.cshlp. org/content/suppl/2009/08/03/23.15. 1737.DC1. html References http://genesdev.cshlp. org/content/23/15/1737.full. html#ref-list-1 This article cites 28 articles, 10 of which can be accessed free at: Open Access Open Access option. Genes & Development Freely available online through the Service Email Alerting click here. right corner of the article or Receive free email alerts when new articles cite this article sign up in the box at the top
MEASURING THE STELLAR MASSES OF z ∼ 7 GALAXIES WITH THE SPITZER ULTRAFAINT SURVEY PROGRAM (SURFS UP)

We present Spitzer/IRAC observations of nine z′-band dropouts highly magnified (2 ≲ μ ≲ 12) by the Bullet Cluster. We combine archival imaging with our Exploratory program (SURFS UP), which results in a total integration time of ∼30 hr per Infrared Array Camera (IRAC) band. We detect (≳ 3σ) in both IRAC bands the brightest of these high-redshift galaxies, with [3.6] = 23.80 ± 0.28 mag, [4.5] = 23.78 ± 0.25 mag, and (H − [3.6]) = 1.17 ± 0.32 mag. The remaining eight galaxies are undetected to [3.6] ∼ 26.4 mag and [4.5] ∼ 26.0 mag with stellar masses of ∼5 × 107 M☉. The detected galaxy has an estimated magnification of μ = 12 ± 4, which implies this galaxy has an ultraviolet luminosity of —the lowest-luminosity individual source detected in IRAC at z ≳ 7. By modeling the broadband photometry, we estimate the galaxy has an intrinsic star formation rate (SFR) of SFR ∼ 1.3 M☉ yr−1 and stellar mass of M ∼ 2.0 × 109 M☉, which gives a specific star formation rate of sSFR ∼ 0.7 Gyr−1. If this galaxy had sustained this SFR since z ∼ 20, it could have formed the observed stellar mass (to within a factor of ∼2). We also discuss alternate star formation histories and argue that the exponentially increasing model is unlikely. Finally, based on the intrinsic SFR, we estimate that this galaxy has a likely [C ii] flux of 〈f[C ii]〉 = 1.6 mJy.
Novel surfaces to improve oligonucleotide immobilisation and hybridisation for breast cancer assay development

This thesis mainly focuses on development of suitable films and imobilisation methods for bio conjugation of the biomolecules to solid supports with future application as biosensors for early breast cancer (BC) detection. Point-of-care (POC) device in biosensor format are recognised as a valuable tool in diagnostics field. However there are number of limitations such as non-specific binding, sensitivity, cost, and fabrication challenges. Hence, new formats of POC platforms are required to improve overall performance of the devices. The fabrication and evaluation of surfaces including carboxylic acid and amino deposition by both wet chemistry and Plasma Enhanced Chemical Vapour Depositions (PECVD) are discussed in detail in this thesis. The recipes and production methods as well as morphological, structural and functional characterisation of deposited films are investigated using a panel of different techniques. This thesis presents that through appropriate surface treatment, poly(methyl methacrylate) (PMMA) can be oxidised using simple methods to form a carboxylic acid surface to enable the covalent attachment of biomolecules for bioassay development. Although spin coating PMMA is a relatively well-known process, to date there has been no direct comparison of the different oxidation methods to activate the surface, nor has oxidised spin coated PMMA been used as a platform for DNA hybridisation or immunoassays. Here, a comparison of the stability, functionality and fabrication process of spin coating and surface activating a thin film of PMMA on a variety of underlying substrates is described. This research reports on the conditions under which amino-modified ssDNA immobilisation onto carboxylic acid surfaces using 1-ethyl-3-(3 dimethylaminopropyl) carbodiimide hydrochloride (EDC) linkers leads to binding at multiple anchoring sites, i.e. back bone (BB) binding; the effects of such binding on overall hybridisation efficiency are described. An alternative conjugation method, click chemistry (CC), is shown to improve the quantity and quality of target binding by enabling direct covalent attachment of probe oligonucleotides to the surface without BB binding. EDC and CC approaches are compared in terms of hybridisation efficiency in a direct and sandwich DNA hybridisation experiments. This thesis includes the investigation of the orientation of miR16 DNA probe upon hybridisation with miR16 DNA target and miR195 DNA target on various substrates
Risk factors related to persistent airflow obstruction in severe asthma in Chinese Han population.

OBJECTIVE To explore the significance of assessing persistent airway obstruction (PAO) in asthma patients by airway wall remodeling with bronchoscopy, high-resolution computed tomography (HRCT), and biological markers in the induced sputum and serum, exhaled nitric oxide (FENO), and lung function. METHODS The study was conducted in 119 patients with PAO and 125 patients with reversible airway obstruction (RAO). Endobronchial biopsy specimens were analyzed for airway smooth muscle (ASM) area, and reticular basement membrane (RBM) thickness. Airway thickness was also measured by HRCT scanning. Levels of matrix metalloproteases-9 (MMP-9), metalloproteinase 33 (ADAM33), and vascular endothelial growth factor (VEGF) were measured in the induced sputum and serum by enzyme linked immunosorbent assay. RESULT PAO was associated with longer disease duration, absence of atopy and rhinitis, and larger ASM area (SMA%) (15.83%±2.32% [n=9] vs. 8.0%±1.68% [n=7], P=0.02), thicker RBM (16.27±2.32 μm [n=9] vs. 8.71±2.41 μm [n=7], P=0.042); No differences in any of the biomarker molecules measured in airway thickness in HRCT, sputum and blood individually between groups were found. CONCLUSION Severe asthma patients with longer disease duration and the absence of atopy and rhinitis are more likely to develop PAO in Chines Han population. PAO patients have increased ASM area and RBM thickness appear to be valuable in the evaluation of airway remodeling in asthma patients in Chinese Han population.
Correlation of MRI T 2-star mapping and the expression of γ-glutamyl carboxylase in degenerative knee cartilage

Objective: The study objective was to investigate the correlation of MRI T2-star mapping and the expression of γ-glutamyl carboxylase (GGCX) in degenerative knee cartilage. Methods: In this study, 20 female patients with mild, moderate, or severe osteoarthritis (OA) were selected as the study subjects, and 20 healthy women were used as the control group. Using a GE 3.0T magnetic resonances canner, a conventional scan of the knee was first performed (sagittal, coronal T1WI and T2WI, axial T2WI), followed by T2-star mapping and diffusion-weighted imaging. The cartilage specimens in the NMR region of interest were obtained, and the expression level of GGCX in the cartilage was detected by immunohistochemistry and Western blot assays. Results: The averages of the T2-star values of different segments of the articular cartilage with mild, moderate, and severe knee OA were significantly higher than those in the control group, with statistically significant differences (P<0.05), and they were negatively correlated with the GGCX content in the cartilage. Conclusions: MRI T2-star mapping and the expression of GGCX in degenerative knee cartilage were found to be closely related. This correlation allows for early diagnoses prior to morphological changes in the knee cartilage as well as early intervention measures to improve treatment outcomes.
From Wintrobe to the XXI century. A Story of Inspiration and Effort

In 2014 we are celebrating the 80th anniversary of the Maxwell Myer Wintrobes pioneer works, one of the most important contribu- tions in Clinical Laboratory and Medicine. Red cell indices continue to provide an essential support to the diagnosis and classification of anemia. The erythrocyte indices mean cell volume, mean cell hemoglobin concentration, mean cell hemoglobin are called the Wintrobe indices. Hematology automation has progressed steadily since Wallace Coulter first applied electrical impedance technology to counting red cells and white cells. Technological advances being incorporated into hematology analyzers since then are now allowing the access to more cellular information than was ever available before through a "simple routine CBC". Current research is beginning to demonstrate that this information also has great potential to identify cellular changes that typically occur in several important medical conditions—bringing us all one step closer to using hematology analyzers as more than simple cell counters, but instead as powerful tools for the management of any medical condition that impacts the biology of blood cells. There are increasing amounts of data provided, which require specialist knowledge to interpret as well as understand the limitations in the measurement of the parameter. Both laboratory scientists and clinicians need to keep up to date with new parameters and methods in hematology, implying a stronger collaboration between them to improve clinical decision making.
A Conversation Based Approach for Modeling REST APIs

Conversations are a well-known concept in service design to describe complex interactions between a client and one or multiple services. The REST architectural style constrains the characteristics of clients, servers and their interactions in REST architectures which consequently has an impact on conversations in such systems. The relation between conversations and REST architectures and how such Restful conversations can be characterized has not been studied in detail yet. In this paper we discuss the characteristics of conversations in REST architectures and introduce an initial set of commonly used conversation types. Based on this, we propose to use conversations as a modeling tool for the design of REST APIs at a higher level of abstraction. We also introduce a corresponding interaction centric metamodel for REST APIs. The characterization of Restful conversations enables a new interaction centric viewpoint on REST architectures which can be also applied for modeling REST APIs on an abstraction level that enables users to focus on the essential functionality of their REST API.
Functional integrity of Colossoma macropomum (Cuvier, 1816) sperm cryopreserved with enriched extender solutions

Cryoprotectant solutions are used to protect the sperm from alterations caused by the low temperature in the cryopreservation process. We evaluated the quality of Colossoma macropomum semen after freezing, using dimethyl sulfoxide (DMSO) as a cryoprotectant, combined with two extender solutions (T1 - Solution 1: Glucose 90.0 g/L, Sodium Citrate 6.0 g/L, EDTA 1.5 g/L, Sodium Bicarbonate 1.5 g/L, Potassium Chloride 0.8 g/L, Gentamycin Sulphate 0.2 g/L, and T2 - Solution 2: Glucose 90.0 g/L, ACP(r)-104 10.0 g/L). Motility rate and motility time did not differ between T1 and T2 and were lower than fresh semen. The number of normal sperm was significantly different in treatments T1 (15.1%) and T2 (21.9%), and both showed a reduction in the percentage of normal sperm compared to fresh semen (57.4%). The values found for the rates of fertilization and hatching, mitochondrial functionality and sperm DNA, did not differ between the treatments (T1 and T2). Regarding membrane integrity, there was a higher percentage of spermatozoa with intact membranes in T1 (53.4%) than T2 (43.7%). The extender solutions, combined with 10% DMSO, maintained the sperm DNA intact in almost all the C. macropomum sperm cells, however there was a loss in their functionality.
Introducing and evaluating ukWaC , a very large web-derived corpus of English

In this paper we introduce ukWaC, a large corpus of English constructed by crawling the . uk Internet domain. The corpus contains more than 2 billion tokens and is one of the largest freely available linguistic resources for English. The paper describes the tools and methodology used in the construction of the corpus and provides a qualitative evaluation of its contents, carried out through a vocabulary-based comparison with the BNC. We conclude by giving practical information about availability and format of the corpus.
Wave energy park interactions in short-crested waves

Highlights q A semi-analytical multiple scattering method has been extended to include multidirectional waves. q The method has been used to study the performance of an array of point-absorber wave energy converters in multidirectional and unidirectional waves. q The shadowing effect is less pronounced in multidirectional waves, and the performance is also affected by the wave spreading parameter and number of incident wave directions.
REVIEW: SINTESIS TITANIUM DIOKASIDA NANOPARTIKEL

Titanium dioksida (TiO 2 ) merupakan suatu material yang memiliki berbagai keunggulan baik dari segi sifat fisika maupun sifat kimia. Keunggulan sifat yang dimiliki TiO 2 ini menjadikannya memiliki aplikasi yang sangat luas dalam berbagai bidang. Performa TiO 2 tergantung pada metode sintesis yang berpengaruh terhadap ukuran partikel, kristalinitas, kemurnian, dan komposisi fasa (anatase, brookite, dan rutile). Sehingga perlu pendekatan lebih lanjut untuk mengetahui efektifitas berbagai metode yang digunakan para peneliti dalam melakukan sintesis TiO 2 nanopartikel. Namun, tidak semua rangkuman jurnal yang ada menunjukan informasi yang detail dan menyeluruh baik dari segi penjabaran metode maupun aplikasi materialnya. Dalam paper ini akan dikaji beberapa metode yang dapat digunakan dalam proses sintesis TiO 2 ­ nanopartikel, diantaranya: metode sol gel, metode hidrotermal, metode hidrolisis, metode supercritical-drying , metode pemrosesan dengan larutan basa , stagnation swirl flame (SSF), teknik Solvothermal, metode biomassa bakteri, dan teknik termolisis. Selain itu, akan dijabarkan juga informasi terkait aplikasi TiO 2 nanopartikel dalam berbagai bidang seperti: dye sensitized solar cell (DSSC), fotodegradasi zat warna, antibakterial, komposit logam, komposit polimer, dan degradasi senyawa organik.
Optimal Processing of Flax and Hemp Fibre Nonwovens

Processing was studied for air-laid nonwovens from natural hemp and flax fibres using SPIKE® air-laying technology (Formfiber Denmark ApS Company). The process of web-formation and the properties of the fibre-webs before needle-punching and reinforced fibre-mats were evaluated. The settings of the air-laying machine were found to influence the web-formation process and nonwoven properties. In order to monitor web-formation processes and evaluate the fibre-web or fibre-mat quality, several machine settings were defined that enhanced the productivity of the machine or favoured fabrication of nonwovens with high density or great tensile properties.
ชวบูลย์ เดชสุขุม , พจนพร ไกรดิษฐ์ , อรุณพร อิฐรัตน์ ภูมิหลัง : สาร dioscorealide B เป็นสารออกฤทธิ์ที ่แยกได้จาก rhizome ของ Dioscorea membranacea หรือหัวข้าวเย็น ซึ่งเป็นสมุนไพรไทยที่นํามาใช้ในตํารับยารักษามะเร็งของหมอพื้นบ้าน วัตถุประสงค์ : เพื่อศึกษาฤทธิ์และกลไกการต้านมะเร็งเต้านมของสาร dioscoreal

S277 Correspondence to: Itharat A, Department of Applied Thai Traditional Medicine, Faculty of Medicine , Thammasat University (Rangsit campus), Klong Luang Pathumthani , 12120 Thailand, Phone: 02-926-9749 & Fax: 02-926-9705 E-mail: iarunporn@yahoo.com J Med Assoc Thai 2010; 93 (Suppl. 7) : S277-S282 Full text. e-Journal: http://www.mat. or.th/journal Cytotoxic Effect and Its Mechanism of Dioscorealide B from Dioscorea membranacea against Breast Cancer Cells
RISQ! Renowned Individuals Semantic Quiz: a Jeopardy like quiz game for ranking facts

In 2011 the IBM Computer Watson was beating its human opponents in the American TV quiz show Jeopardy! However, the questions for the quiz have been developed by a team of human authors. Authoring questions is a difficult task, because in a Jeopardy! game the questions should be neither too easy nor too hard and should fit the general scope of knowledge of the audience and players. Linked Open Data (LOD) provides huge amounts of information that is growing daily. Yet, there is no ranking that determines the importance of LOD facts, as e. g. by querying LOD for movies starring a distinct actor provides numerous answers, whereas it cannot be answered, which of the movies was the most important for this actor. To rank search results for semantic search various heuristics have been developed to cope with the problem of missing rank in the semantic web. This paper proposes a Jeopardy! like quiz game with questions automatically generated from LOD facts to gather ranking information for persons to provide a basis for the evaluation of semantic ranking heuristics.
DDAG K-TIPCAC: an ensemble method for protein subcellular localization

Protein subcellular location prediction is one of the most difficult multiclass prediction problems in modern computational biology. Many methods have been proposed in the literature to solve this problem, but all the existing approaches are affected by some limitations. In this contribution we propose a novel method for protein subcellular location prediction that performs multiclass classification by combining kernel classifiers through DDAG. Each base classifier, called K-TIPCAC, projects the points on a Fisher subspace estimated on the training data by means of a novel technique. Experimental results clearly indicated that DDAG K-TIPCAC performs equally, if not better, than state-of-the-art ensemble methods for protein subcellular location.
Quantitative evaluation of the mineralization level of dental tissues by Raman spectroscopy

Current routine clinical methodologies to diagnose diseases that affect the hard tissues of teeth present a certain lack of specificity and sensitivity, especially for incipient demineralization processes where early diagnosis is essential. The aim of this study was to investigate the reliability of Raman spectroscopy as a direct quantitative diagnostic tool for the determination of specific molecular changes in mineralized tissues and the establishment of a pattern of normality. Human healthy and caries-affected dental pieces were evaluated by Raman spectroscopy using an FT-Raman Bruker RFS100 coupled to a 1064 nm-Nd:YAG laser with an incident laser radiation up to 1500 mW. Data from the spectra were treated with OPUS™ software. The influence of Raman spectrometer parameters on the spectra dependence and repeatability was first studied, showing a linear relationship between the incident laser power and the intensity/area of the Raman bands. Two quantitative Raman mineralization indices for dental tissue diagnoses were then proposed. For them, the mineral part ( PO 4 − 3 ? > (bend) at 430 cm−1 and PO 4 − 3 ? > (stret) at 960 cm−1 for hydroxyapatite) was related to the organic part (C-Hx of lipids/proteins at 2941 cm−1) by calculating the ratio between these band areas as follows: MIb (Mineralization Index bending): 430 cm−1/2941 cm−1 and MIs (Mineralization Index stretching): 960 cm−1/2941 cm−1. A pattern of normality (healthy mineralization) was established with values in the range 1.35–1.75 for MIb and 4.01–5.19 for MIs. This methodology was successfully applied to two case studies where caries which could not be identified by conventional methodologies, such as radiography, were clearly diagnosed by the proposed quantitative Raman spectroscopy. Thus, its reliability as a routine clinical tool for quantitative diagnosis of dental demineralization by external inspection was demonstrated.
Pentosidine: Can Be Related To The Etiology Of Chronic Kidney Disease?

Objectives: Advanced glycation end products (AGEs) and their receptors are prominent contributors to diabetic kidney disease. Clinical importance of AGEs toxicity in kidney disease etiologies had been rarely reported. We measured serum AGEs, sRAGE and Pentosidine levels in diabetic patients with and without nephropathy and examined whether these biomarkers are related to the etiolo- gies of chronic kidney disease (CKD). Design and methods: We included 30 healthy control subjects and 116 diabetic patients who were further divided into 2 subgroups: one with 30 patients without CKD, the other with 86 CKD patients. AGEs, sRAGE and pentosidine were measured in serum by ELISA. Results: Serum levels of AGEs, sRAGE and pentosidine were significantly increased in diabetic patients without CKD compared to controls (579.78 ± 113.28 vs. 508.83 ± 119.68 pg/mL; 169.17 ± 30.41 vs. 148.72 ± 32.73 pg/mL; 247.84 ± 21.42 vs. 214.03 ± 55.05 pg/mL, P<0.001, P<0.01, P<0.05 respectively). In diabetic patients with CKD, serum AGEs, sRAGE and pentosidine levels were significantly higher than diabetic patients without CKD (P<0.001, P<0.01, P<0.001 respectively). Serum Pentosidine levels were in- creased in CKD patients with tubulointerstitial nephrophathy than other etiologies (P<0.001). Conclusions: Serum AGEs, sRAGE, and pentosidine levels are related with diabetic patients with and without CKD and pentosidine levels were increased in tubulointerstitial nephrophathy.