Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Glypican-3 as a Novel Tumor Marker for Melanoma

Purpose: We reported recently the novel tumor marker glypican-3 (GPC3) for hepatocellular carcinoma. In the present study, we investigated the expression of GPC3 in human melanoma cell lines and tissues and asked whether GPC3 could be a novel tumor marker for melanoma. Experimental Design: Expression of GPC3 mRNA and protein was investigated in human melanoma cell lines and tissues using reverse transcription-PCR and immunohistochemical analysis. Secreted GPC3 protein was quantified using ELISA in culture supernatants of melanoma cell lines and in sera from 91 patients with melanoma and 28 disease-free patients after surgical removal of primary melanoma. All of the subjects were Japanese nationals. Results: In >80% of melanoma and melanocytic nevus, there was evident expression of GPC3 mRNA and protein. Furthermore, GPC3 protein was evidenced in sera of 39.6% (36 of 91) of melanoma patients but not in sera from subjects with large congenital melanocytic nevus (0 of 5) and from healthy donors (0 of 60). Twenty-seven of 36 serum GPC3-positive patients were negative for both serum 5-S-cysteinyldopa and melanoma-inhibitory activity, well-known tumor markers for melanoma. The positive rate of serum GPC3 (39.6%) was significantly higher than that of 5-S-cysteinyldopa (26.7%) and of melanoma-inhibitory activity (20.9%). Surprisingly, we detected serum GPC3 even in patients with stage 0 in situ melanoma. The positive rate of serum GPC3 at stage 0, I, and II (44.4%, 40.0%, and 47.6%) was significantly higher than that of 5-S-cysteinyldopa (0.0%, 8.0%, and 10.0%). Also observed was the disappearance of GPC3 protein in sera from 11 patients after surgical removal of the melanoma. Conclusions: GPC3 is apparently a novel tumor marker useful for the diagnosis of melanoma, especially in early stages of the disorder.
Transient cochlear ischemia causes delayed cell death in the organ of Corti: An experimental study in gerbils

To elucidate whether ischemia–reperfusion can cause delayed cell death in the cochlea, the effects of transient cochlear ischemia on hearing and on neuronal structures in the cochlea were studied in Mongolian gerbils. Ischemia was induced by bilaterally occluding the vertebral arteries for 5 minutes in gerbils, which lack posterior cerebral communicating arteries. In gerbils, the labyrinthine arteries are fed solely by the vertebral arteries. Occlusion of the vertebral arteries caused a remarkable increase in the threshold of compound action potentials (CAPs), which recovered over the following day. However, 7 days after the onset of reperfusion, the threshold began to increase again. Morphologic changes in the hair cell stereocilia were revealed by electron microscopy. The number of nuclear collapses was counted in cells stained for DNA and F‐actin to evaluate the degree of cell death in the organ of Corti. Changes in spiral ganglion cell (SGC) neuron number were detected, whether or not progressive neuronal death occurred in the SGC. These studies showed that sporadic fusion of hair cells and the disappearance of hair cell stereocilia did not begin until 4 days after ischemia. On subsequent days, the loss of hair cells, especially inner hair cells (IHCs), and the degeneration of SGC neurons became apparent. Ten days after ischemia, the mean percentage cell loss of IHCs was 6.4% in the basal turn, 6.4% in the second turn, and 0.8% in the apical turn, respectively, and the number of SGC neurons had decreased to 89% of preischemic status. These results indicate that transient ischemia causes delayed hearing loss and cell death in the cochlea by day 7 after ischemia. J. Comp. Neurol. 456:105–111, 2003. © 2002 Wiley‐Liss, Inc.
Assessing vocabulary skills in Cantonese-speaking adolescents

Abstract Purpose: This study investigated the feasibility of a pilot version of Vocabulary Assessment for Cantonese-speaking Adolescents (VACA) in evaluating the vocabulary ability of Cantonese-speaking adolescents with and without language impairment (LI) in Hong Kong. Method: A list of 300 vocabularies was located from local textbooks, dictionaries, and multimedia resources. The list was reduced to 91 vocabularies according to secondary school teachers' judgment. Three receptive tasks, two expressive tasks, and a vocabulary-learning strategy task were devised to examine five domains: (1) academic words, (2) idioms, (3) slangs, (4) homophones, and (5) lexical inferencing strategies. Sixty Cantonese-speaking adolescents with normal language (NL) and 17 with LI (aged 12;01–17;06) were tested on VACA. Results: The composite scores increased significantly with grade level in the NL group. The LI group performed significantly weaker than their matched peers in the NL group in all five domains and the composite scores. Conclusion: The results of this study demonstrated a continual growth of semantic knowledge during adolescence and VACA can be a feasible assessment tool for evaluating the vocabulary knowledge of Cantonese-speaking adolescents in Hong Kong.
Soft Tissue and Epithelial Models

The applicability of a biomaterial for the manufacturing of oral implants is determined by its physicochemical and geometric surface properties. Research, therefore, is concerned with the cellular reactions that occur when an implant material comes into contact with body tissues. For permucosal oral implants, this involves both the reaction of bone and gingival cells. In vitro cell culturing-including the use of various analytical techniques like light microscopy, scanning and transmission electron microscopy, confocal laser scanning microscopy, and digital image analysis-is a good tool whereby investigators can obtain more insight into the relevant components of implant-tissue adhesion. In the current overview, the role of cell models in oral implant research is discussed, specifically with reference to responses of epithelial cells and fibroblasts.
Diff-Def: Diffusion-Generated Deformation Fields for Conditional Atlases

Anatomical atlases are widely used for population analysis. Conditional atlases target a particular sub-population defined via certain conditions (e.g. demographics or pathologies) and allow for the investigation of fine-grained anatomical differences - such as morphological changes correlated with age. Existing approaches use either registration-based methods that are unable to handle large anatomical variations or generative models, which can suffer from training instabilities and hallucinations. To overcome these limitations, we use latent diffusion models to generate deformation fields, which transform a general population atlas into one representing a specific sub-population. By generating a deformation field and registering the conditional atlas to a neighbourhood of images, we ensure structural plausibility and avoid hallucinations, which can occur during direct image synthesis. We compare our method to several state-of-the-art atlas generation methods in experiments using 5000 brain as well as whole-body MR images from UK Biobank. Our method generates highly realistic atlases with smooth transformations and high anatomical fidelity, outperforming the baselines.
Prospective Study of Alcohol Consumption and Risk of Oral Premalignant Lesions in Men

Recent case-control studies indicate that alcohol increases the risk of oral premalignant lesions (OPL) among tobacco users, but the independent association between alcohol and OPL remains unclear. We prospectively evaluated the association between alcohol consumption and the incidence of OPL. Participants were 41,458 men in the Health Professionals Follow-up Study. Alcohol consumption was assessed every 4 years using validated food frequency questionnaires. We confirmed clinically or histopathologically diagnosed OPL events occurring between 1986 and 2002 by medical record review (193 cases). Multivariate-adjusted relative risks of OPL were calculated from Cox proportional hazards models. With detailed control for tobacco and other variables, multivariate relative risks (95% confidence intervals) were 1.7 (0.9-3.2) for drinkers of 0.1 to 14.9 g/d, 2.9 (1.5-5.6) for 15 to 29.9 g/d, and 2.5 (1.3-5.1) for ≥30 g/d, compared with nondrinkers. Approximately one additional drink per day (12.5 g) was associated with a 22% increase in risk (P < 0.001). The associations did not vary by beverage type, frequency, or consumption with meals. Results were similar when restricted to cases of oral epithelial dysplasia. Alcohol increased OPL risk in never-users of tobacco as well as in past or current users. An interaction between alcohol and tobacco was apparent by their more-than-additive joint effects. Alcohol is an independent risk factor for OPL, regardless of beverage type or drinking pattern. Recommendations to reduce alcohol intake have the potential to reduce incidence of OPL in nonsmokers and smokers alike. (Cancer Epidemiol Biomarkers Prev 2006;15(4):774–81)
Clinical and prognostic value of advanced glycation end-products in chronic heart failure.

AIMS Advanced glycation end-products (AGEs) have been proposed as a novel factor involved in the development and progression of chronic heart failure (CHF). We aimed to determine whether plasma levels of N(epsilon)-(carboxymethyl)lysine (CML) and N(epsilon)-(carboxyethyl)lysine (CEL), two well-known AGEs, are related to the severity and prognosis of CHF. METHODS AND RESULTS A total of 102 CHF patients, aged 58 +/- 12 years, with an average left ventricular ejection fraction of 28 +/- 9% were followed for 1.7 (1.2-1.9) years. NYHA functional class and NT-pro-BNP were used as estimates of the severity of CHF. CML and CEL were determined by LC-MS/MS. CML levels were associated with NYHA functional class (P < 0.001) and NT-pro-BNP levels (P < 0.001). Survival analysis for the combined end-point of death, heart transplantation, ischaemic cardiovascular event, and hospitalization for heart failure revealed that CML levels predicted outcome, even after adjustment for age, gender, aetiology of CHF, identified risk modifiers, and several known predictors of outcome in CHF. The predictive value of CML subsided after correction for renal function. CEL was not associated with the severity or prognosis of CHF. CONCLUSION Plasma AGEs, in particular CML levels, are related to the severity and prognosis of CHF. The fact that the relation between CML and prognosis subsided after correction for renal function may suggest that AGE accumulation in renal failure explains part of the prognostic value of renal function in CHF. However, further investigation is warranted to exclude the possibility that CML is just an innocent marker of renal function.
Slower CCN growth kinetics of anthropogenic aerosol compared to biogenic aerosol observed at a rural site

Abstract. Growth rates of water droplets were measured with a static diffusion cloud condensation chamber in May–June 2007 at a rural field site in Southern Ontario, Canada, 70 km north of Toronto. The observations include periods when the winds were from the south and the site was impacted by anthropogenic air from the U.S. and Southern Ontario as well as during a 5-day period of northerly wind flow when the aerosol was dominated by biogenic sources. The growth of droplets on anthropogenic size-selected particles centred at 0.1 μm diameter and composed of approximately 40% organic and 60% ammonium sulphate (AS) by mass, was delayed by on the order of 1 s compared to a pure AS aerosol. Simulations of the growth rate on monodisperse particles indicate that a lowering of the water mass accommodation coefficient from αc=1 to an average of αc=0.04 is needed (assuming an insoluble organic with hygroscopicity parameter, κorg, of zero). Simulations of the initial growth rate on polydisperse anthropogenic particles agree best with observations for αc=0.07. In contrast, the growth rate of droplets on size-selected aerosol of biogenic character, consisting of >80% organic, was similar to that of pure AS. Simulations of the predominantly biogenic polydisperse aerosol show agreement between the observations and simulations when κorg=0.2 (with upper and lower limits of 0.5 and 0.07, respectively) and αc=1. Inhibition of water uptake by the anthropogenic organic applied to an adiabatic cloud parcel model in the form of a constant low αc increases the number of droplets in a cloud compared to pure AS. If the αc is assumed to increase with increasing liquid water on the droplets, then the number of droplets decreases which could diminish the indirect climate forcing effect. The slightly lower κorg in the biogenic case decreases the number of droplets in a cloud compared to pure AS.
Skeletal development and abnormalities of the vertebral column and of the fins in hatchery-reared turbot Scophthalmus maximus.

To describe the skeletal development and abnormalities in turbot Scophthalmus maximus, samples were collected every day from hatching to 60 days after hatching (DAH). A whole-mount cartilage and bone-staining technique was used. Vertebral ontogeny started with the formation of anterior haemal arches at 5·1 mm standard length (L(S) ) c. 11 DAH, and was completed by the full attainment of parapophyses at 16·9 mm L(S) c. 31 DAH. Vertebral centra started to develop at 6·3 mm L(S) c. 16 DAH and ossification in all centra was visible at 11·0 mm L(S) c. 25 DAH. The caudal fin appeared at 5·1 mm L(S) c. 11 DAH and ossification was visible at 20·6 mm L(S) c. 37 DAH. The onset of dorsal and anal fin elements appeared at 5·8 mm L(S) c. 15 DAH and 6·3 mm L(S) c. 16 DAH, respectively. Ossifications of both dorsal fin and anal fin were visible at 20·6 mm L(S) c. 37 DAH. The pectorals were the only fins present before first feeding, their ossifications were completed at 23·5 mm L(S) c. 48 DAH. Pelvic fins began forming at 7·2 mm L(S) c. 19 DAH and calcification of the whole structure was visible at 19·8 mm L(S) c. 36 DAH. In the present study, 24 types of skeletal abnormalities were observed. About 51% of individuals presented skeletal abnormalities, and the highest occurrence was found in the haemal region of the vertebral column. As for each developmental stage, the most common abnormalities were in the dorsal fin during early metamorphic period (stage 2), vertebral fusion during climax metamorphosis (stage 3) and caudal fin abnormality during both late-metamorphic period (stage 4) and post-metamorphic period (stage 5). Such research will be useful for early detection of skeletal malformations during different growth periods of reared S. maximus.
How does very prolonged practice improve decision speed

Les modeles recents d'estimation des effets de la pratique affirment l'interchangeabilite de la vitesse et des erreurs comme indices de performance valides, sans tenir compte des «echanges» entre ces variables ni de leurs distributions. Test de ces affirmations et de l'effet d'une tres longue pratique sur le lien vitesse-erreur
Exploring the Recent Trend in Esophageal Adenocarcinoma Incidence and Mortality Using Comparative Simulation Modeling

Background: The incidence of esophageal adenocarcinoma (EAC) has increased five-fold in the United States since 1975. The aim of our study was to estimate future U.S. EAC incidence and mortality and to shed light on the potential drivers in the disease process that are conduits for the dramatic increase in EAC incidence. Methods: A consortium of three research groups calibrated independent mathematical models to clinical and epidemiologic data including EAC incidence from the Surveillance, Epidemiology, and End Results (SEER 9) registry from 1975 to 2010. We then used a comparative modeling approach to project EAC incidence and mortality to year 2030. Results: Importantly, all three models identified birth cohort trends affecting cancer progression as a major driver of the observed increases in EAC incidence and mortality. All models predict that incidence and mortality rates will continue to increase until 2030 but with a plateauing trend for recent male cohorts. The predicted ranges of incidence and mortality rates (cases per 100,000 person years) in 2030 are 8.4 to 10.1 and 5.4 to 7.4, respectively, for males, and 1.3 to 1.8 and 0.9 to 1.2 for females. Estimates of cumulative cause-specific EAC deaths between both sexes for years 2011 to 2030 range between 142,300 and 186,298, almost double the number of deaths in the past 20 years. Conclusions: Through comparative modeling, the projected increases in EAC cases and deaths represent a critical public health concern that warrants attention from cancer control planners to prepare potential interventions. Impact: Quantifying this burden of disease will aid health policy makers to plan appropriate cancer control measures. Cancer Epidemiol Biomarkers Prev; 23(6); 997–1006. ©2014 AACR.
A Systematic Review of Definitions and Classification Systems of Adjacent Segment Pathology

Study Design. Systematic review. Objective. To undertake a systematic review to determine how “adjacent segment degeneration,” “adjacent segment disease,” or clinical pathological processes that serve as surrogates for adjacent segment pathology are classified and defined in the peer-reviewed literature. Summary of Background Data. Adjacent segment degeneration and adjacent segment disease are terms referring to degenerative changes known to occur after reconstructive spine surgery, most commonly at an immediately adjacent functional spinal unit. These can include disc degeneration, instability, spinal stenosis, facet degeneration, and deformity. The true incidence and clinical impact of degenerative changes at the adjacent segment is unclear because there is lack of a universally accepted classification system that rigorously addresses clinical and radiological issues. Methods. A systematic review of the English language literature was undertaken and articles were classified using the Grades of Recommendation Assessment, Development, and Evaluation criteria. Results. Seven classification systems of spinal degeneration, including degeneration at the adjacent segment, were identified. None have been evaluated for reliability or validity specific to patients with degeneration at the adjacent segment. The ways in which terms related to adjacent segment “degeneration” or “disease” are defined in the peer-reviewed literature are highly variable. Conclusion. On the basis of the systematic review presented in this article, no formal classification system for either cervical or thoracolumbar adjacent segment disorders currently exists. Consensus Statement No recommendations regarding the use of current classification of degeneration at any segments can be made based on the available literature. A new comprehensive definition for adjacent segment pathology (ASP, the now preferred terminology) has been proposed in this Focus Issue, which reflects the diverse pathology observed at functional spinal units adjacent to previous spinal reconstruction and balances detailed stratification with clinical utility. A comprehensive classification system is being developed through expert opinion and will require validation as well as peer review. Strength of Statement: Strong
RetroFab: A Design Tool for Retrofitting Physical Interfaces using Actuators, Sensors and 3D Printing

We present RetroFab, an end-to-end design and fabrication environment that allows non-experts to retrofit physical interfaces. Our approach allows for changing the layout and behavior of physical interfaces. Unlike customizing software interfaces, physical interfaces are often challenging to adapt because of their rigidity. With RetroFab, a new physical interface is designed that serves as a proxy interface for the legacy controls that are now operated by actuators. RetroFab makes this concept of retrofitting devices available to non-experts by automatically generating an enclosure structure from an annotated 3D scan. This enclosure structure holds together actuators, sensors as well as components for the redesigned interface. To allow retrofitting a wide variety of legacy devices, the RetroFab design tool comes with a toolkit of 12 components. We demonstrate the versatility and novel opportunities of our approach by retrofitting five domestic objects and exploring their use cases. Preliminary user feedback reports on the experience of retrofitting devices with RetroFab.
The Human T-cell Leukemia Virus-1 Transcriptional Activator Tax Enhances cAMP-responsive Element-binding Protein (CREB) Binding Activity through Interactions with the DNA Minor Groove*

Tax-1, the transcriptional activation protein of human T-cell leukemia virus-1, increases transcription from the human T-cell leukemia virus-1 long terminal repeat and specific cellular promoters through interactions with cellular DNA-binding proteins. The Tax response elements (TxREs) of the long terminal repeat resemble cAMP response elements (CREs), the target of cAMP-responsive element-binding protein (CREB). CREB binds the TxRE with reduced affinity; however, the interaction is specifically enhanced by Tax. Using a fluorescence quenching method, we determined that CREB dimerizes in the absence of DNA, and that Tax does not enhance dimerization. DNA footprinting of the TxRE with 1,10-phenanthroline-copper complex demonstrates that Tax contacts DNA and extends the footprint of CREB to GC-rich sequences flanking the core CRE-like element. The minor groove-binding drug chromomycin A3, but not distamycin A, disrupted Tax-enhanced CREB binding to the TxRE. Substitution of the guanine-rich sequences flanking the core of the TxRE with inosine residues also blocked the Tax effect. Finally, the IC-substituted TxRE binds CREB with increased affinity, suggesting flanking DNA influences the binding of CREB to the core CRE-like element. These data indicate that Tax does not regulate DNA binding of CREB by altering dimerization, but rather enhances DNA binding by additionally interacting with the minor groove of flanking DNA sequences.
When Color Names Are Used Metaphorically: The Role of Linguistic and Chromatic Information

Four experiments investigated the integration of chromatic with linguistic and conceptual information in the interpretation of narratives where color names were used metaphorically. The texts were visually presented with 5 shades of the color metaphorically used in the narratives. Participants were asked to choose the shade expressively most appropriate to the story content (Experiment 1) or to rank the appropriateness of each shade (Experiment 2). We then employed a completion task where participants were asked to complete the texts with the color name they felt more appropriate without any chromatic information provided to them (Experiment 3). In the final experiment, we reversed the direction of the mapping and asked participants to choose the narratives that fit best with a given color shade (Experiment 4). Overall, the results showed that participants indeed used chromatic information in their choices, as suggested by perceptually based theories.
A new effcient algorithm for solving the simple temporal problem

In this paper we propose a new efficient algorithm, the STP-solver, for computing the minimal network of the Simple Temporal Problem (STP). This algorithm achieves high performance by exploiting a topological property of the constraint graph (i.e., triangulation) and a semantic property of the constraints (i.e., convexity) in light of the results reported by Bliek and Sam-Haroud [1], which were presented for general CSPs and have not yet been applied to temporal networks. Importantly, we design the constraint propagation in STP-solver to operate on triangles instead of operating on edges and implicitly guarantee the decomposition of the constraint graph according to its articulation points. We also provide extensive empirical evaluations of all known algorithms for solving the STP on sets of randomly generated problems. Our experiments demonstrate significant improvements of STPsolver, in terms of number of constraint checks and CPU time, over previously reported algorithms such as the Floyd-Warshall algorithm (F-W) [5; 8], Directed-Path Consistency (DPC) [8], and Partial Path-Consistency (PPC) [1].