Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures.
Modified extradural temporopolar approach with mini-peeling of dura propria for paraclinoid and/or parasellar tumors: Operative technique and nuances

Background: Modified extradural temporopolar approach (EDTPA) with mini-peeling of the dura propria can provide extensive exposure of the anterior clinoid process and early exposure, as well as complete mobilization and decompression of the optic nerve and internal carotid artery, which can prevent intraoperative neurovascular injury for paraclinoid and/or parasellar lesions. The present study investigated the usefulness of this modified technique and discusses the operative nuances. Methods: We retrospectively reviewed medical charts of 27 consecutive patients with neoplastic paraclinoid and/or parasellar lesions who underwent this modified approach between September 2009 and August 2016. Results: Preoperative visual acuity worsened in 2 patients (7.4%), and worsening of visual field function occurred in 2 patients (7.4%). Postoperative outcome was good recovery in 25 patients (92.6%) and moderate disability in 2 (7.4%). No operation-related mortality occurred in the series. Conclusions: The modified EDTPA is safe and recommended for surgical treatment of paraclinoid and/or parasellar tumors to reduce the risk of intraoperative optic neurovascular injury.
Using the Internet to Promote Health Behavior Change: A Systematic Review and Meta-analysis of the Impact of Theoretical Basis, Use of Behavior Change Techniques, and Mode of Delivery on Efficacy

Background The Internet is increasingly used as a medium for the delivery of interventions designed to promote health behavior change. However, reviews of these interventions to date have not systematically identified intervention characteristics and linked these to effectiveness. Objectives The present review sought to capitalize on recently published coding frames for assessing use of theory and behavior change techniques to investigate which characteristics of Internet-based interventions best promote health behavior change. In addition, we wanted to develop a novel coding scheme for assessing mode of delivery in Internet-based interventions and also to link different modes to effect sizes. Methods We conducted a computerized search of the databases indexed by ISI Web of Knowledge (including BIOSIS Previews and Medline) between 2000 and 2008. Studies were included if (1) the primary components of the intervention were delivered via the Internet, (2) participants were randomly assigned to conditions, and (3) a measure of behavior related to health was taken after the intervention. Results We found 85 studies that satisfied the inclusion criteria, providing a total sample size of 43,236 participants. On average, interventions had a statistically small but significant effect on health-related behavior (d+ = 0.16, 95% CI 0.09 to 0.23). More extensive use of theory was associated with increases in effect size (P = .049), and, in particular, interventions based on the theory of planned behavior tended to have substantial effects on behavior (d+ = 0.36, 95% CI 0.15 to 0.56). Interventions that incorporated more behavior change techniques also tended to have larger effects compared to interventions that incorporated fewer techniques (P < .001). Finally, the effectiveness of Internet-based interventions was enhanced by the use of additional methods of communicating with participants, especially the use of short message service (SMS), or text, messages. Conclusions The review provides a framework for the development of a science of Internet-based interventions, and our findings provide a rationale for investing in more intensive theory-based interventions that incorporate multiple behavior change techniques and modes of delivery.
Microfluidic wound model for studying the behaviors of Pseudomonas aeruginosa in polymicrobial biofilms

Pseudomonas aeruginosa is a particularly problematic opportunistic pathogen due to its capacity to form recalcitrant biofilm structures, while cohabiting with other harmful/pathogenic species and harboring the capability to release toxins that cause tissue necrosis. Although it is now recognized that the majority of biofilm infections are polymicrobial, little is known about the complex interactions that occur within polymicrobial communities and few tools exist for studying these interactions. In this study, we have designed a microfluidic model that mimics the relevant physiological properties of wound microenvironment, while incorporating materials present in the human extracellular matrix/wound environment. Using microfluidics combined with imaging techniques, we have validated the robustness of our model comparing traditional GFP‐tagging to new fluorescent staining techniques to visualize/resolve individual species within a polymicrobial habitat. We have also demonstrated that chemotactic stimuli may be incorporated into our model through specialized ports in our chamber. Our system is specifically designed for use with high resolution imaging techniques, allowing for data collection throughout the life of the biofilm and in real‐time. Ultimately, this model can be used to investigate the spatio‐temporal mechanobiological structures of the wound environment, and the response of the bacteria to the drug transport which will significantly contribute to our understanding of the development and progression of polymicrobial biofilm infections. Biotechnol. Bioeng. 2015;112: 2351–2359. © 2015 Wiley Periodicals, Inc.
The Frontier of Technology Development in Remaining Life Assessment for High Temperature Components

* 正 会 員 名城大学理工学部機械システム工学科 〒468-8502 名古屋市天白区塩釜口,Dept. of Mech. Eng., Meijo Univ., Tempaku-ku, Nagoya, 468-8502 1 は じ め に EBSD (Electron BackScatter Diffraction) 法 1)は,材料 表面の結晶構造に関するデジタル情報をもとに,材料の 微視構造を明らかにすることができる手段として幅広く 利用されている. EBSDで得られる方位差情報は,材料 の転位分布と密接に関係していることから,ひずみや損 傷の指標になりうるものとして,まず室温における塑性 ひずみの評価と高サイクル疲労に関する研究が活発に行 われ,その後,高温におけるクリープやクリープ疲労に ついての研究が活発になってきている. その中で,2006 年には,日本材料学会高温強度部門委員会内に損傷評価 WGが発足し,まず EBSDによる損傷評価法に必要な試 験条件の明確化とラウンドロビン試験によるデータ比較 が行われた. 本活動の中で,EBSD法が損傷の実体の理 解に極めて有効な手段であり,また,EBSD観察から得 られる情報の物理的意味を明確にして評価を行うことが 必要であるという認識が得られた. 本稿では,EBSD法によるひずみ評価手段に関する研 究動向を概観した後,上記損傷評価WGでの情報交換な どにより得られた高温クリープやクリープ疲労に関する 「材料」 (Journal of the Society of Materials Science, Japan), Vol. 61, No. 11, pp. 919-924, Nov. 2012 講 座
The Impact of Global Warming and Anoxia on Marine Benthic Community Dynamics: an Example from the Toarcian (Early Jurassic)

The Pliensbachian-Toarcian (Early Jurassic) fossil record is an archive of natural data of benthic community response to global warming and marine long-term hypoxia and anoxia. In the early Toarcian mean temperatures increased by the same order of magnitude as that predicted for the near future; laminated, organic-rich, black shales were deposited in many shallow water epicontinental basins; and a biotic crisis occurred in the marine realm, with the extinction of approximately 5% of families and 26% of genera. High-resolution quantitative abundance data of benthic invertebrates were collected from the Cleveland Basin (North Yorkshire, UK), and analysed with multivariate statistical methods to detect how the fauna responded to environmental changes during the early Toarcian. Twelve biofacies were identified. Their changes through time closely resemble the pattern of faunal degradation and recovery observed in modern habitats affected by anoxia. All four successional stages of community structure recorded in modern studies are recognised in the fossil data (i.e. Stage III: climax; II: transitional; I: pioneer; 0: highly disturbed). Two main faunal turnover events occurred: (i) at the onset of anoxia, with the extinction of most benthic species and the survival of a few adapted to thrive in low-oxygen conditions (Stages I to 0) and (ii) in the recovery, when newly evolved species colonized the re-oxygenated soft sediments and the path of recovery did not retrace of pattern of ecological degradation (Stages I to II). The ordination of samples coupled with sedimentological and palaeotemperature proxy data indicate that the onset of anoxia and the extinction horizon coincide with both a rise in temperature and sea level. Our study of how faunal associations co-vary with long and short term sea level and temperature changes has implications for predicting the long-term effects of “dead zones” in modern oceans.
High Strength Aluminum Alloys Reinforced by Nanosize Quasicrystalline Particles for Elevated Temperature Application

Powders and rods from 6 alloys of the group ALMFexCryTizZr6.x. y.z were produced and investigated. Powders were produced by a water atomization process and after degassing consolidated to rods by severe plastic deformation at 350 °C 400 °C without sintering of the powders (by extrusion of powders in the preliminary evacuated and pressurized ampoules). Such a method of producing powders makes it possible to avoid liquation and other non-uniformities in chemical composition, to obtain the metastable quasicrystalline reinforcing particles in nanostructured aluminum matrix. The presence of the quasicrystalline icosahedral phase (the i-phase) in addition to α Al matrix in the produced powders and rods of alloys Al.MFexCryTizZr6-x. y-7, is confirmed by X-ray diffraction analysis and TEM / SEM investigation. The high strength at 300°C (up to 330 MPa) and sufficient plasticity at room temperature (5-8%) were obtained in investigated rods.
Non-invasive characterization of intracranial tumors by magnetic resonance elastography

Presurgical, non-invasive methods of differentiating brain tumors have remained unsatisfactory even for specialized academic hospitals. Despite major advances in clinical and neuroradiological diagnostic techniques, the majority of neurooncology patients still need to undergo a brain biopsy for diagnosis. Recent single cell experiments suggested that biomechanical cell properties might be very sensitive in detecting cellular malignancy. Accordingly, we investigated magnetic resonance elastography (MRE) as an investigative tool for the clinical routine diagnostic work-up of intracranial neoplasm. In order to obtain sufficient spatial resolution for the biomechanical characterization of intracranial tumors, we modified a recently introduced least-squares solution of the stationary wave equation, facilitating stable solutions of the magnitude |G*| and the phase angle φ of the complex shear modulus G*. MRE was added to a routine diagnostic or presurgical neuroradiological magnetic resonance imaging work-up in 16 prospective patients and it was well tolerated in all cases. Our preliminary tumor MRE data revealed alterations in viscoelastic constants, e.g. a loss of stiffness in malignancies compared to healthy reference tissue, or benign variants. Based on larger studies on selected tumor entities to establish threshold and reference values for future diagnostic purposes, MRE may thus provide a predictive marker for tumor malignancy and thereby contribute to an early non-invasive clinical assessment of suspicious cerebral lesions.
Neopterygian phylogeny: the merger assay

The phylogenetic relationships of the recently described genus †Ticinolepis from the Middle Triassic of the Monte San Giorgio are explored through cladistic analyses of the so far largest morphological dataset for fossil actinopterygians, including representatives of the crown-neopterygian clades Halecomorphi, Ginglymodi and Teleostei, and merging the characters from previously published systematic studies together with newly proposed characters. †Ticinolepis is retrieved as the most basal Ginglymodi and our results support the monophyly of Teleostei and Holostei, as well as Halecomorphi and Ginglymodi within the latter clade. The patterns of relationships within these clades mostly agree with those of previous studies, although a few important differences require future research. According to our results, ionoscopiforms are not monophyletic, caturids are not amiiforms and leptolepids and luisiellids form a monophyletic clade. Our phylogenetic hypothesis confirms the rapid radiation of the holostean clades Halecomorphi and Ginglymodi during the Early and Middle Triassic and the radiation of pholidophoriform teleosts during the Late Triassic. Crown-group Halecomorphi have an enormous ghost lineage throughout half of the Mesozoic, but ginglymodians and teleosts show a second radiation during the Early Jurassic. The crown-groups of Halecomorphi, Ginglymodi and Teleostei originated within parallel events of radiation during the Late Jurassic.
Adopted daughters and adopted daughters-in-law in Taiwan: a mortality analysis

Adoption is sometimes considered paradoxical from an evolutionary perspective because the costs spent supporting an adopted child would be better spent on rearing one's own. Kin selection theory is commonly used to solve this paradox, because the adoption of closely related kin contributes to the inclusive fitness of the adoptive parent. In this paper, we perform a novel test of kin selection theory in the context of adoption by asking whether adopted daughters-in-law, who contribute directly (i.e. genealogically) to the perpetuation of their adoptive families' lineages, experience lower mortality than daughters adopted for other purposes in historical Taiwan. We show that both classes of adopted daughter suffer lower mortality than biological daughters, but that the protective effect of adoption is stronger among daughters who were not adopted with the intention of perpetuating the family lineage. We speculate as to the possible benefits of such a pattern and emphasize the need to move beyond typological definitions of adoption to understand the specific costs and benefits involved in different forms of caring for others' children.
Towards elimination of visceral leishmaniasis in the Indian subcontinent—Translating research to practice to public health

Background The decade following the Regional Strategic Framework for Visceral Leishmaniasis (VL) elimination in 2005 has shown compelling progress in the reduction of VL burden in the Indian subcontinent. The Special Programme for Research and Training in Tropical Diseases (TDR), hosted by the World Health Organization (WHO) and other stakeholders, has coordinated and financed research for the development of new innovative tools and strategies to support the regional VL elimination initiative. This paper describes the process of the TDR’s engagement and contribution to this initiative. Methodology/principal findings Multiple databases were searched to identify 152 scientific papers and reports with WHO funding or authorship affiliation around the following 3 framework strategies: detection of new cases, morbidity reduction, and prevention of infection. TDR has played a critical role in the evaluation and subsequent use of the 39-aminoacid–recombinant kinesin antigen (rK39) rapid diagnostic test (RDT) as a confirmatory test for VL in the national program. TDR has supported the clinical research and development of miltefosine and single-dose liposomal amphotericin B as a first-line treatment against VL. TDR has engaged with in-country researchers, national programme managers, and partners to generate evidence-based interventions for early detection and treatment of VL patients. TDR evaluated the quality, community acceptance, and cost effectiveness of indoor residual spraying, insecticide-treated bed nets, insecticide-impregnated durable wall linings, insecticidal paint, and environmental management as tools for integrated vector management in reducing sandfly density. Conclusions/significance TDR’s engagement with country policy makers, scientists, and clinicians in the development of effective diagnosis, treatment, case detection, and vector control represents an important example of TDR’s stewardship toward the elimination of VL in the Indian subcontinent.
BOP2: Bayesian optimal design for phase II clinical trials with simple and complex endpoints

We propose a flexible Bayesian optimal phase II (BOP2) design that is capable of handling simple (e.g., binary) and complicated (e.g., ordinal, nested, and co‐primary) endpoints under a unified framework. We use a Dirichlet‐multinomial model to accommodate different types of endpoints. At each interim, the go/no‐go decision is made by evaluating a set of posterior probabilities of the events of interest, which is optimized to maximize power or minimize the number of patients under the null hypothesis. Unlike other existing Bayesian designs, the BOP2 design explicitly controls the type I error rate, thereby bridging the gap between Bayesian designs and frequentist designs. In addition, the stopping boundary of the BOP2 design can be enumerated prior to the onset of the trial. These features make the BOP2 design accessible to a wide range of users and regulatory agencies and particularly easy to implement in practice. Simulation studies show that the BOP2 design has favorable operating characteristics with higher power and lower risk of incorrectly terminating the trial than some existing Bayesian phase II designs. The software to implement the BOP2 design is freely available at www.trialdesign. org. Copyright © 2017 John Wiley & Sons, Ltd.
Solving Large Jigsaw Puzzles

This project attempts to reproduce the genetic algorithm in a paper entitled ”A Genetic Algorithm-Based Solver for Very Large Puzzles” by D. Sholomon, O. David, and N. Netanyahu. [3] There are two main challenges in solving jigsaw puzzles. The first is finding the right fitness function to judge the compatibility of two pieces. This has thoroughly been studied and as a result, there are many fitness functions available. This paper explores the second part that is crucial to solving jigsaw puzzles: finding an efficient and accurate way to place the pieces. The genetic algorithm attempts to do just that. The crucial part of the algorithm is in generating a new ordering of pieces called ’child’ from two possible orderings of pieces, called ’parents’. Each generation learns from good traits in the parents. After going through a hundred generations, the ordering will reflect the original image to a high accuracy. This paper also makes use of CNN to start with reasonable orderings of ’parents’. This cuts down on the number of generations required to reach the correct ordering of the pieces.
Analyses of surface deformation with SBAR InSAR method and its relationship with aquifer occurrence in Surabaya City, East Java, Indonesia

Rapid development of Surabaya City requires space for industry and settlement. The city development is followed by increasing of water demand for various purposes. Large amount of groundwater extraction may cause ground subsidence. According to groundwater extraction, we tried to delineate the possibility of aquifer potential based on ground surface deformation using Interferometric Synthetic Aperture Radar (InSAR) and Electrical Resistivity methods. The InSAR is a method to estimate surface deformation in millimeter scale based on different phase of SAR data between acquisition times. In this paper, surface deformation combined with ground resistivity was used to analyse the potential of aquifer related to subsidence at Surabaya City, East Java, Indonesia. The Small Based Subset (SBAS) method was used to reduce phase delayed in the interferogram due to atmospheric condition. Based on the SBAS InSAR the deformation was detected at Surabaya City in January 2007 to February 2008. The largest and lowest deformation about 40 mm/year and about 0-10 mm/year were located in North to Southeastern and Western part of the city, respectively. The geodetic Global Positioning System (GPS) campaign in Surabaya confirmed that the detected deformation correlated with the ground subsidence with correlation coefficient about 0.96. To obtain the subsurface structures at subsidence zones, the Electrical Resistivity survey with Schlumberger configuration was performed in Surabaya city. According to the SBAS InSAR and subsurface resistivity, the subsidence around Pabeancantikan, Kenjeran, Simokerto and Tenggilismejoyo sub-districts agreed to high resistivity about 7-18 Ωm. The Sandstone of Kabuh and Pucangan formations in this area served as ground water aquifer which used by more than 200 wells. Ground water extraction probably triggered the subsidence at ground surface. The high resistivity at subsidence zones originated from high porosity of rocks served as aquifer with high groundwater extraction.
Application of nanoparticles to reverse multi-drug resistance in cancer

Abstract Multi-drug resistance (MDR) poses a large obstacle to various human malignancies. For a long period, combination of multiple therapeutic agents has been the conventional method used to reverse MDR in cancer. However, it is still not an effective method as rather than cancer its serious side effects causes patient’s death. Nanoparticles (NPs) are emerging as a class of therapeutics for cancer, including overcoming MDR. In the present review, we focus on the application of NPs to reverse MDR in cancer. Several kinds of NPs developed for the reversal of MDR are summarized. In addition, investigations in vitro and in vivo are also shown to highlight the advancement in the application of NPs to reverse MDR.