Miracle-dz/UniFAR-FTUs huggingface dataset:
Band selection for hyperspectral images based on self-tuning spectral clustering

Hyperspectral imaging (HSI) is an emerging technique,which allows to consistently capture images in the visible as well as infrared light range. Many materials can be easily discriminated by means of their spectra, rendering HSI an interesting method for the reliable classification of contents in a scene. As the number of features for each pixel in hyperspectral images is considerably high, further processing and classification is time consuming and stresses resources. Thus, efficient methods to select useful bands are required. We present a novel two-step scheme based on a clustering approach followed by representatives selection from each cluster. The classification results of real hyperspectral images demonstrate that the proposed method easily outperforms common as well as state-of-the-art methods.
Revisiting the Middle Molecule Hypothesis of Uremic Toxicity: A Systematic Review of Beta 2 Microglobulin Population Kinetics and Large Scale Modeling of Hemodialysis Trials In Silico

Background Beta-2 Microglobulin (β2M) is a prototypical “middle molecule” uremic toxin that has been associated with a higher risk of death in hemodialysis patients. A quantitative description of the relative importance of factors determining β2M concentrations among patients with impaired kidney function is currently lacking. Methods Herein we undertook a systematic review of existing studies reporting patient level data concerning generation, elimination and distribution of β2M in order to develop a population model of β2M kinetics. We used this model and previously determined relationships between predialysis β2M concentration and survival, to simulate the population distribution of predialysis β2M and the associated relative risk (RR) of death in patients receiving conventional thrice-weekly hemodialysis with low flux (LF) and high flux (HF) dialyzers, short (SD) and long daily (LD) HF hemodialysis sessions and on-line hemodiafiltration at different levels of residual renal function (RRF). Results We identified 9 studies of 106 individuals and 156 evaluations of or more compartmental kinetic parameters of β2M. These studies used a variety of experimental methods to determine β2M kinetics ranging from isotopic dilution to profiling of intra/inter dialytic concentration changes. Most of the patients (74/106) were on dialysis with minimal RRF, thus facilitating the estimation of non-renal elimination kinetics of β2M. In large scale (N = 10000) simulations of individuals drawn from the population of β2M kinetic parameters, we found that, higher dialytic removal materially affects β2M exposures only when RRF (renal clearance of β2M) was below 2 ml/min. In patients initiating conventional HF hemodialysis, total loss of RRF was predicted to be associated with a RR of death of more than 20%. Hemodiafiltration and daily dialysis may decrease the high risk of death of anuric patients by 10% relative to conventional, thrice weekly HF dialysis. Only daily long sessions of hemodialysis consistently reduced mortality risk between 7–19% across the range of β2M generation rate. Conclusions Preservation of RRF should be considered one of the therapeutic goals of hemodialysis practice. Randomized controlled trials of novel dialysis modalities may require large sample sizes to detect an effect on clinical outcomes even if they enroll anuric patients. The developed population model for β2M may allow personalization of hemodialysis prescription and/or facilitate the design of such studies by identifying patients with higher β2M generation rate.
Source apportionment of carbonaceous aerosol in southern Sweden

A one-year study was performed at the Vav- ihill background station in southern Sweden to estimate the anthropogenic contribution to the carbonaceous aerosol. Weekly samples of the particulate matter PM10 were col- lected on quartz filters, and the amounts of organic carbon, elemental carbon, radiocarbon ( 14 C) and levoglucosan were measured. This approach enabled source apportionment of the total carbon in the PM10 fraction using the concentra- tion ratios of the sources. The sources considered in this study were emissions from the combustion of fossil fuels and biomass, as well as biogenic sources. During the summer, the carbonaceous aerosol mass was dominated by compounds of biogenic origin (80 %), which are associated with biogenic primary and secondary organic aerosols. During the winter months, biomass combustion (32 %) and fossil fuel combus- tion (28 %) were the main contributors to the carbonaceous aerosol. Elemental carbon concentrations in winter were about twice as large as during summer, and can be attributed to biomass combustion, probably from domestic wood burn- ing. The contribution of fossil fuels to elemental carbon was stable throughout the year, although the fossil contribution to organic carbon increased during the winter. Thus, the organic aerosol originated mainly from natural sources during the summer and from anthropogenic sources during the winter. The result of this source apportionment was compared with results from the EMEP MSC-W chemical transport model. The model and measurements were generally consistent for total atmospheric organic carbon, however, the contribution of the sources varied substantially. E.g. the biomass burning contributions of OC were underestimated by the model by a factor of 2.2 compared to the measurements.
Squamous Cell Lung Cancer: From Tumor Genomics to Cancer Therapeutics

Squamous cell lung cancer (SCC) represents an area of unmet need in lung cancer research. For the past several years, therapeutic progress in SCC has lagged behind the now more common non–small cell lung cancer histologic subtype of adenocarcinoma. However, recent efforts to define the complex biology underlying SCC have begun to bear fruit in a multitude of ways, including characterization of previously unknown genomic and signaling pathways, delineation of new, potentially actionable molecular targets, and subsequent development of a large number of agents directed against unique SCC-associated molecular abnormalities. For the first time, SCC-specific prognostic gene signatures and predictive biomarkers of new therapeutic agents are emerging. In addition, recent and ongoing clinical trials, including the Lung-MAP master protocol, have been designed to facilitate approval of targeted therapy–biomarker combinations. In this comprehensive review, we describe the current status of SCC therapeutics, recent advances in the understanding of SCC biology and prognostic gene signatures, and the development of innovative new clinical trials, all of which offer new hope for patients with advanced SCC. Clin Cancer Res; 21(10); 2236–43. ©2015 AACR. See all articles in this CCR Focus section, “Progress in Lung Cancer. ”
Family background, parenting practices, and child outcomes: Chinese migrants’ offspring in Hong Kong

Using data from the 2011 population census and the Hong Kong Panel Study of Social Dynamics, this paper examines the academic performance and non-cognitive skills of the children of Chinese migrants in Hong Kong aged 14 and below. Our analyses show that the poorer academic performance of Chinese migrants’ children results mainly from disadvantageous family background and parenting practices. Children of cross-border and migrant families do not differ from children of natives in Chinese, mathematics, or English, once parental education and parent–child communication about school life are controlled for. Children from migrant families have significantly higher levels of non-cognitive ability than children of natives. Our analyses also show that parental education is positively associated with Chinese and English performances; parents talking with children about school life significantly improves children’s performance in Chinese, mathematics, and English; and parental migrant status and parenting practices have positive effects on non-cognitive skills.
Genetic and Clinical Analysis of ABCA4-Associated Disease in African American Patients

Autosomal recessive Stargardt disease (STGD1) is caused by hundreds of mutations in the ABCA4 gene, which are often specific to racial and ethnic groups. Here, we investigated the ABCA4 variation and their phenotypic expression in a cohort of 44 patients of African American descent, a previously under‐characterized racial group. Patients were screened for mutations in ABCA4 by next‐generation sequencing and array‐comparative genomic hybridization (aCGH), followed by analyses for pathogenicity by in silico programs. Thorough ophthalmic examination was performed on all patients. At least two (expected) disease‐causing alleles in the ABCA4 gene were identified in 27 (61.4%) patients, one allele in 11 (25%) patients, and no ABCA4 mutations were found in six (13.6%) patients. Altogether, 39 different disease‐causing ABCA4 variants, including seven new, were identified on 65 (74%) chromosomes, most of which were unique for this racial group. The most frequent ABCA4 mutation in this cohort was c.6320G>A (p.(R2107H)), representing 19.3% of all disease‐associated alleles. No large copy number variants were identified in any patient. Most patients reported later onset of symptoms. In summary, the ABCA4 mutation spectrum in patients of West African descent differs significantly from that in patients of European descent, resulting in a later onset and “milder” disease.
Bidirectional Interplay between Tracking and the Rider Simulator and Its Application to Snowboarding

Physical interactive games are recently hogging the limelight in the international game market, as they adopt a new concept of input devices that allows the players to interact and play with the games using their own bodies instead of hand-operated input devices. Since the concept is still tethered to a screen-based output, its feedback part is not as fluid and natural as its input part. This paper proposes a novel concept for a new gaming experience based on a bidirectional user interface wherein a user's body motion as a control input and physical/visual feedback from output devices interact with each other. The physical feedback is a means of providing a physical response to a player, and can be the output of game contents and/or responses or effects from the control input. To provide physical feedback, the proposed interface uses a rider simulator as the output device. Then a user-device control loop between the control input and output devices is created, which may result in a divergent feedback and eventually, dangerous circumstances that can lead to serious injury. Therefore, the proposed interface introduces an energy bounding algorithm to guarantee stable and safe game play, even if the game players stand on the simulator to play the game and take the feedback. A pilot user study was performed to analyze the performance of this algorithm and to verify how easily and effectively users enjoy the system, and the study showed that the proposed interface can provide an exciting experience for players on the basis of a new type of interface whereby they play with physical interactive games on the rider simulator.
Mathematical equation retrieval using plain words as a query

This paper proposes how to effectively retrieve the mathematical equations when the plain words are given as a query. The proposed system requires no complicated mathematical symbols, no particular input tool and no constraint of query. Users can enter a query with plain words like the traditional Information Retrieval. For this, we extract features from the plain texts that are converted from the real math equations. Experimental results show an outstanding performance, a MRR of 0.6585.
BayesDB : querying the probable implications of tabular data

BayesDB, a Bayesian database table, lets users query the probable implications of their tabular data as easily as an SQL database lets them query the data itself. Using the built-in Bayesian Query Language (BQL), users with little statistics knowledge can solve basic data science problems, such as detecting predictive relationships between variables, inferring missing values, simulating probable observations, and identifying statistically similar database entries. BayesDB is suitable for analyzing complex, heterogeneous data tables with no preprocessing or parameter adjustment required. This generality rests on the model independence provided by BQL, analogous to the physical data independence provided by the relational model. SQL enables data filtering and aggregation tasks to be described independently of the physical layout of data in memory and on disk. Non-experts rely on generic indexing strategies for good-enough performance, while experts customize schemas and indices for performance-sensitive applications. Analogously, BQL enables analysis tasks to be described independently of the models used to solve them. Non-statisticians can rely on a general-purpose modeling method called CrossCat to build models that are good enough for a broad class of applications, while experts can customize the schemas and models when needed. This thesis defines BQL, describes an implementation of BayesDB, quantitatively characterizes its scalability and performance, and illustrates its efficacy on real-world data analysis problems in the areas of healthcare economics, statistical survey data analysis, web analytics, and predictive policing. Thesis Supervisor: Vikash Mansinghka Title: Research Scientist
Structural changes at synapses after delayed perfusion fixation in different regions of the mouse brain

We recently showed by electron microscopy that the postsynaptic density (PSD) from hippocampal cultures undergoes rapid structural changes after ischemia‐like conditions. Here we report that similar structural changes occur after delay in transcardial perfusion fixation of the mouse brain. Delay in perfusion fixation, a condition that mimics ischemic stress, resulted in 70%, 90%, and 23% increases in the thickness of PSDs from the hippocampus (CA1), cerebral cortex (layer III), and cerebellar cortex (Purkinje spines), respectively. In step with PSD thickening, the amount of PSD‐associated α‐calcium calmodulin‐dependent protein kinase II (α‐ CaMKII) label increased more in cerebral cortical spines than in Purkinje spines. Although the Purkinje PSDs thickened only slightly after delayed fixation, they became highly curved, and many formed sub‐PSD spheres ∼80 nm in diameter that labeled for CaMKII. Delayed perfusion fixation also produced more cytoplamic CaMKII clusters (∼110 nm in diameter) in the somas of pyramidal cells (from hippocampus and cerebral cortex) than in Purkinje cells. Thus a short delay in perfusion fixation produces cell‐specific structural changes at PSDs and neuronal somas. Purkinje cells respond somewhat differently to delayed perfusion fixation, perhaps owing to their lower levels of CaMKII, and CaMKII binding proteins at PSDs. We present here a catalogue of structural changes that signal a perfusion fixation delay, thereby providing criteria by which to assess perfusion fixation quality in experimental structural studies of brain and to shed light on the subtle changes that occur in intact brain following metabolic stress. J. Comp. Neurol. 501:731–740, 2007. © 2007 Wiley‐Liss, Inc.
The Long-Run Behavior of Commodity Prices: Small Trends and Big Variability

Using the longest dataset publicly available (The Economist's index of industrial commodity prices), we analyze the behavior of real commodity prices over the period 1862-1999 and have two main findings. First, while there has been a downward trend in real commodity prices of about 1 percent per year over the last 140 years, little support is found for a break in the long-run trend decline in commodity prices. Second, there is evidence of a ratcheting up in the variability of price movements. The amplitude of price movements increased in the early 1900s, while the frequency of large price movements increased after the collapse of the Bretton Woods regime of fixed exchange rates in the early 1970s. Although there is a down-ward trend in real commodity prices, this is of little practical policy relevance, since it is small and completely dominated by the variability of prices.
CHADS2 versus CHA2DS2-VASc score in assessing the stroke and thromboembolism risk stratification in patients with atrial fibrillation: a systematic review and meta-analysis

Objective To perform a systematic review and meta-analysis of the predictive abilities of CHADS2 and CHA2DS2-VASc in stroke and thromboembolism risk stratification of atrial fibrillation (AF) patients. Methods We searched PubMed and EMBASE for English-language literature on comparisons of the diagnostic performance between CHADS2 and CHA2DS2-VASc in predicting stroke, or systemic embolism, in AF. We then assessed the quality of the included studies and pooled the C-statistics and 95% confidence intervals (95% CI). Results Eight studies were included. It was unsuitable to perform a direct meta-analysis because of high heterogeneity. When analyzed as a continuous variable, the C-statistic ranged from 0.60 to 0.80 (median 0.683) for CHADS2 and 0.64–0.79 (median 0.673) for CHA2DS2-VASc. When analyzed as a continuous variable in anticoagulation patients, the subgroup analysis showed that the pooled C-statistic (95% CI) was 0.660 (0.655–0.665) for CHADS2 and 0.667 (0.651–0.683) for CHA2DS2-VASc (no significant difference). For non-anticoagulation patients, the pooled C-statistic (95% CI) was 0.685 (0.666–0.705) for CHADS2 and 0.675 (0.656–0.694) for CHA2DS2-VASc (no significant difference). The average ratio of endpoint events in the low-risk group of CHA2DS2-VASc was less than CHADS2 (0.41% vs. 0.94%, P < 0.05). The average proportion of the moderate-risk group of CHA2DS2-VASc was lower than CHADS2 (11.12% vs. 30.75%, P < 0.05). Conclusions The C-statistic suggests a similar clinical utility of the CHADS2 and CHA2DS2-VASc scores in predicting stroke and thromboembolism, but CHA2DS2- VASc has the important advantage of identifying extremely low-risk patients with atrial fibrillation, as well as classifying a lower proportion of patients as moderate risk.
Generation from Computerized Clinical Guidelines

A framework has been developed that automatically generates context-specifi c query, and determines its query type, from computerized clinical practice guidelines (CPGs). The generated query can be submitted to PubMed using web services to retrieve and link relevant medical literature pertaining to the computerized CPGs content. This framework makes use of contexts, semantics, statistical information and meta-information of the medical phrases in the Extended-Knowledge Components of the computerized CPG content. The medical literature retrieved and linked, by our framework, is found to be relevant to the knowledge of the computerized CPG.
Fog Deposition Measurements with the Eddy Covariance Method

The eddy covariance method is considered the only direct flux measurement method. Its application for fog deposition measurements is relatively new and has a high potential to allow the accurate determination of nutrient and trace element deposition due to fog droplet interception by vegetation canopies. Based on experiences gained at an agricultural site on the Swiss Plateau and a mountainous coniferous forest site in Germany we assessed the quality of our data. The accuracy of turbulent liquid water flux measured over a 30 minute period was found to be±0.63 mg m−2 s−1. The accuracy of average liquid water content was found to be 0.14 mg m−3. However, the high statistical noise level reduces the reliability of single short-term measurements and the measured variances of liquid water content. Nevertheless, the quality of the eddy covariance measurements can be considered sufficient for obtaining reliable data on fog interception or occult deposition.
Cardiovascular Molecular Imaging with Contrast Ultrasound: Principles and Applications

Methods for imaging the molecular or cellular profile of tissue are being developed for all forms of non-invasive cardiovascular imaging. It is thought that these technologies will potentially improve patient outcomes by allowing diagnosis of disease at an early-stage, monitoring disease progression, providing important information on patient risk, and for tailoring therapy to the molecular basis of disease. Molecular imaging is also already assuming an important role in science by providing a better understanding of the molecular basis of cardiovascular pathology, for assessing response to new therapies, and for rapidly optimizing new or established therapies. Ultrasound-based molecular imaging is one of these new approaches. Contrast-enhanced ultrasound molecular imaging relies on the detection of novel site-targeted microbubbles (MB) or other acoustically active particles which are administered by intravenous injection, circulate throughout the vascular compartment, and are then retained and imaged within regions of disease by ligand-directed binding. The technique is thought to be advantageous in practical terms of cost, time, and ease of use. The aim of this review is to discuss the molecular participants of cardiovascular disease that have been targeted for ultrasound imaging, general features of site-targeted MB, imaging protocols, and potential roles of ultrasound molecular imaging in cardiovascular research and clinical medicine.
Epigenetic Control of Gonadal Aromatase (cyp19a1) in Temperature-Dependent Sex Determination of Red-Eared Slider Turtles

In the red-eared slider turtle (Trachemys scripta), a species with temperature-dependent sex determination (TSD), the expression of the aromatase gene during gonad development is strictly limited to the female-producing temperature. The underlying mechanism remains unknown. In this study, we identified the upstream 5′-flanking region of the aromatase gene, gonad-specific promoter, and the temperature-dependent DNA methylation signatures during gonad development in the red-eared slider turtle. The 5′-flanking region of the slider aromatase exhibited sequence similarities to the aromatase genes of the American alligator, chicken, quail, and zebra finch. A putative TATA box was located 31 bp upstream of the gonad-specific transcription start site. DNA methylation at the CpG sites between the putative binding sites of the fork head domain factor (FOX) and vertebrate steroidogenic factor 1 (SF1) and adjacent TATA box in the promoter region were significantly lower in embryonic gonads at the female-producing temperature compared the male-producing temperature. A shift from male- to female-, but not from female- to male-, producing temperature changed the level of DNA methylation in gonads. Taken together these results indicate that the temperature, particularly female-producing temperature, allows demethylation at the specific CpG sites of the promoter region which leads the temperature-specific expression of aromatase during gonad development.
Design and development of a DC-DC boost converter with constant output voltage

The main purpose of this paper is to introduce a design and development method of a dc-dc boost converter with constant output voltage. From a fluctuating or a variable input voltage, boost converter is able to step up the input voltage to a higher constant dc output voltage using voltage feedback technique. By this technique, the output of the converter is measured and compared with a reference voltage. The differential of the compared value will be used to produce a pulse width modulation signal to control switch in the boost converter. Simulation results describe the performance of the proposed design. Experimental work was carried out with a circuit operated in continuous conduction mode with 24V output voltage, 100W output power and 20 kHz switching frequency. The test results showed that the proposed design able to produce a 24V constant voltage.