Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Pulsed-FRAP and Conventional-FRAP for Determination of Protein Mobility in Prokaryotic Cells

Background Macromolecule mobility is often quantified with Fluorescence Recovery After Photobleaching (FRAP). Throughout literature a wide range of diffusion coefficients for GFP in the cytoplasm of Escherichia coli (3 to 14 µm2/s) is reported using FRAP-based approaches. In this study, we have evaluated two of these methods: pulsed-FRAP and “conventional”-FRAP. Principal Findings To address the question whether the apparent discrepancy in the diffusion data stems from methodological differences or biological variation, we have implemented and compared the two techniques on bacteria grown and handled in the same way. The GFP diffusion coefficients obtained under normal osmotic conditions and upon osmotic upshift were very similar for the different techniques. Conclusions Our analyses indicate that the wide range of values reported for the diffusion coefficient of GFP in live cells are due to experimental conditions and/or biological variation rather than methodological differences.
USP17 is required for clathrin mediated endocytosis of epidermal growth factor receptor

Previously we have shown that expression of the deubiquitinating enzyme USP17 is required for cell proliferation and motility. More recently we reported that USP17 deubiquitinates RCE1 isoform 2 and thus regulates the processing of ‘CaaX’ motif proteins. Here we now show that USP17 expression is induced by epidermal growth factor and that USP17 expression is required for clathrin mediated endocytosis of epidermal growth factor receptor. In addition, we show that USP17 is required for the endocytosis of transferrin, an archetypal substrate for clathrin mediated endocytosis, and that USP17 depletion impedes plasma membrane recruitment of the machinery required for clathrin mediated endocytosis. Thus, our data reveal that USP17 is necessary for epidermal growth factor receptor and transferrin endocytosis via clathrin coated pits, indicate this is mediated via the regulation of the recruitment of the components of the endocytosis machinery and suggest USP17 may play a general role in receptor endocytosis.
A Unifying Formalism for Shortest Path Problems with Expensive Edge Evaluations via Lazy Best-First Search over Paths with Edge Selectors

While the shortest path problem has myriad applications, the computational efficiency of suitable algorithms depends intimately on the underlying problem domain. In this paper, we focus on domains where evaluating the edge weight function dominates algorithm running time. Inspired by approaches in robotic motion planning, we define and investigate the Lazy Shortest Path class of algorithms which is differentiated by the choice of an edge selector function. We show that several algorithms in the literature are equivalent to this lazy algorithm for appropriate choice of this selector. Further, we propose various novel selectors inspired by sampling and statistical mechanics, and find that these selectors outperform existing algorithms on a set of example problems.
Development of Coronal Mass Ejections: Radio Shock Signatures

We present observational imaging evidence for the existence of metric radio bursts closely associated with the front edge of coronal mass ejections (CMEs). These radio bursts drift in frequency similarly to type II bursts. They are weak and usually go undetected on spectrograph data. We find the same measured projected velocity for the displacement of, respectively, the radio source (when observed at two or more frequencies) and the CME leading edge. The position of the emitting source coincides with the CME leading edge. Among the events analyzed, the fastest of them, with a velocity over 1400 km s-1, was associated with interplanetary type II bursts.
A Classification-Based Path Selection Scheme for Video Streaming over Multi-Hop Networks

A classification-based method is proposed to select an optimal path for video streaming over multi-hop mesh networks. Our main contribution is translating of path selection over multi-hop networks to a standard classification problem. The classification is based on minimizing average video packet distortion at the receiving nodes. We also consider long range dependence (LRD) characteristics of variable bit rate (VBR) video encoders by modeling the link as a fractional Brownian motion queue. In our method, a support vector machine is applied at each hop to optimally assign the next hop (partial path) for each video packet received at that hop. Wireless channel conditions (WCC) including packet loss probability of the channel and maximum achievable rate are used as class prototypes. Sample feature vectors include video content features (VCF) and video encoding parameters (VEP) extracted from video sequences. The classifiers are trained offline using a vast collection of video sequences and wireless channel conditions in order to yield optimal performance during real time path selection. Our method substantially reduces the complexity of conventional exhaustive optimization methods and results in high quality (low distortion). Simulations are conducted over an elementary multi-hop structure and cascades of such structure which not only proves the superiority of our method in terms of low complexity and high peak signal to noise ratio (PSNR) performance, but also provides important insights that can guide the design of network infrastructures and streaming protocols for video streaming.
Minimizing control overheads in adaptive load sharing

Two algorithms are developed for minimizing control overheads in exchanging state information arising from the control messages used in determining the load levels at other servers. In the first algorithm, the load levels at other servers are guessed using a simple heuristic algorithm. Such a model is found to provide significant improvements compared to the no-load sharing case. The second algorithm improves upon the first one by replacing some unnecessary task transfers by a single probe. The simulation results obtained from these algorithms are presented and compared to an algorithm based on random selection of destinations for transfer tasks. It was concluded that a load sharing policy should try to maximize the success rate in finding good destinations for transfer tasks while minimizing the control overheads. <<ETX>>
Ursodeoxycholic acid in cholestasis: Potential mechanisms of action and therapeutic applications

ULRICH BEUERS,1 JAMES L. BOYER,2 AND GUSTAV PAUMGARTNER1 The dihydroxy bile acid, ursodeoxycholic acid (UDCA), is increasingly used for the treatment of chronic cholestatic liver diseases. First reports of a beneficial effect on serum liver tests in cholestatic disorders were published in the 1980s in the Western literature,1-3 but similar observations had been made previously in Japan.4,5 Today, the therapeutic efficacy of UDCA has been shown for only one cholestatic disorder, primary biliary cirrhosis (PBC). 6 The mechanism of action of UDCA in cholestasis has also not yet been clearly identified. Therefore, the aim of this article is to summarize clinical and experimental work that may help to clarify possible mechanisms of action of UDCA in cholestasis and provide a clearer rationale for the administration of UDCA in special cholestatic disorders.
Comparisons of Rabbit Bone Marrow Mesenchymal Stem Cell Isolation and Culture Methods In Vitro

Bone marrow mesenchymal stem cells (BMSCs) have great potential in tissue engineering and clinical therapy, and various methods for isolation and cultivation of BMSCs have been reported. However, the best techniques are still uncertain. Therefore, we sought the most suitable among the four most common methods for BMSC separation from rabbits. BMSCs were obtained from untreated whole bone marrow (BM) adherent cultures, 3 volumes of red blood cells (RBC) lysed with ammonium chloride, 6 volumes of RBC lysed with ammonium chloride, and Ficoll density gradient centrifugation. Then, isolated BMSCs were evaluated with respect to primary cell yield, number of CFU-F colonies, proliferative capacity, cell phenotype, and chondrogenic differentiation potential. Our data show that BMSCs were successfully isolated by all four methods, and each method was similar with regard to cell morphology, phenotype, and differentiation potential. However, BMSCs from untreated whole BM adherent cultures had greater primary cell yields, larger colonies, and the shortest primary culture time (P<0.05). Moreover, the 4th generation of cultured cells had the strongest proliferative activity, the fastest growth rate and the most numerous cells compared with other cell passage generations (P<0.05). In conclusion, untreated whole BM adherent cultures are best for rabbit BMSC isolation and the 4th generation of cells has the strongest proliferation capacity.
Combination of aspiration and non-aspiration fine needle biopsy for cytological diagnosis of thyroid nodules.

BACKGROUND Good cytological sample is very important for the cytological diagnosis of thyroid nodules. The aim of this study was to evaluate the adequacy of prepared samples by the combination of aspiration and non- aspiration fine needle biopsy. METHODS In this descriptive - analytical study, sampling was done simultaneously for each patient in fine needle aspiration and non-aspiration biopsy. The sufficiency of samples was studied using Mair Scoring System. Wilcoxon Signed Rank test was used for the data analysis. RESULTS Three hundred two cases (289 females, 13 males) with the mean age of 43.83±12.9 years were evaluated. Inadequate samples were 31 (10.3%) in fine needle aspiration, 40 (13.2%) in non-aspiration and 13 cases (4.3%) by using two methods together (p=0.0001). The average total score was 6.00±2.17 in fine needle aspiration and 5.76±2.26 in non-aspiration method (p=0.08), and 6.6±1.98 in the combination of the two methods (p<0001 comparing with one method alone). CONCLUSION The results show that using both methods simultaneously in each nodule considerably increases the efficiency of samples for cytological diagnosis.
Influence of institutional culture and policies on do-not-resuscitate decision making at the end of life.

IMPORTANCE Controversy exists regarding whether the decision to pursue a do-not-resuscitate (DNR) order should be grounded in an ethic of patient autonomy or in the obligation to act in the patient's best interest (beneficence). OBJECTIVE To explore how physicians' approaches to DNR decision making at the end of life are shaped by institutional cultures and policies surrounding patient autonomy. DESIGN, SETTING, AND PARTICIPANTS We performed semistructured in-depth qualitative interviews of 58 internal medicine physicians from 4 academic medical centers (3 in the United States and 1 in the United Kingdom) by years of experience and medical subspecialty from March 7, 2013, through January 8, 2014. Hospitals were selected based on expected differences in hospital culture and variations in hospital policies regarding prioritization of autonomy vs best interest. MAIN OUTCOMES AND MEASURES This study identified the key influences of institutional culture and policies on physicians' attitudes toward patient autonomy in DNR decision making at the end of life. RESULTS A hospital's prioritization of autonomy vs best interest as reflected in institutional culture and policy appeared to influence the way that physician trainees conceptualized patient autonomy. This finding may have influenced the degree of choice and recommendations physician trainees were willing to offer regarding DNR decision making. Trainees at hospitals where policies and culture prioritized autonomy-focused approaches appeared to have an unreflective deference to autonomy and felt compelled to offer the choice of resuscitation neutrally in all situations regardless of whether they believed resuscitation to be clinically appropriate. In contrast, trainees at hospitals where policies and culture prioritized best-interest-focused approaches appeared to be more comfortable recommending against resuscitation in situations where survival was unlikely. Experienced physicians at all sites similarly did not exclusively allow their actions to be defined by policies and institutional culture and were willing to make recommendations against resuscitation if they believed it would be futile. CONCLUSIONS AND RELEVANCE Institutional cultures and policies might influence how physician trainees develop their professional attitudes toward autonomy and their willingness to make recommendations regarding the decision to implement a DNR order. A singular focus on autonomy might inadvertently undermine patient care by depriving patients and surrogates of the professional guidance needed to make critical end of life decisions.
How much does expertise matter?: a barrier walkthrough study with experts and non-experts

Manual accessibility evaluation plays an important role in validating the accessibility of Web pages. This role has become increasingly critical with the advent of the Web Content Accessibility Guidelines (WCAG) 2.0 and their reliance on user evaluation to validate certain conformance measures. However, the role of expertise, in such evaluations, is unknown and has not previously been studied. This paper sets out to investigate the interplay between expert and non-expert evaluation by conducting a Barrier Walkthrough (BW) study with 19 expert and 51 non-expert judges. The BW method provides an evaluation framework that can be used to manually assess the accessibility of Web pages for different user groups including motor impaired, hearing impaired, low vision, cognitive impaired, etc. We conclude that the level of expertise is an important factor in the quality of accessibility evaluation of Web pages. Expert judges spent significantly less time than non-experts; rated themselves as more productive and confident than non-experts; and ranked and rated pages differently against each type of disability. Finally, both effectiveness and reliability of the expert judges are significantly higher than non-expert judges.
Interannual variation patterns of total ozone and temperature in observations and model simulations

We report results from a multiple linear regression analysis of long-term total ozone observations (1979 to 2002, by TOMS/SBUV), of temperature reanalyses (1958 to 2002, NCEP), and of two chemistry-climate model simulations (1960 to 1999, by ECHAM4.L39(DLR)/CHEM (=E39/C), and MAECHAM4-CHEM). The model runs are transient experiments, where observed sea surface temperatures, increasing source gas concentrations (CO2, CFCs, CH4, N2O, NOx), 11-year solar cycle, volcanic aerosols and the quasi-biennial oscillation (QBO) are all accounted for. MAECHAM4-CHEM covers the atmosphere from the surface up to 0.01 hPa (? 80 km). For a proper representation of middle atmosphere (MA) dynamics, it includes a parametrization for momentum deposition by dissipating gravity wave spectra. E39/C, on the other hand, has its top layer centered at 10 hPa (? 30 km). It is targeted on processes near the tropopause, and has more levels in this region. Both models reproduce the observed amplitudes and much of the observed low-latitude patterns of the various modes of interannual variability, MAECHAM4-CHEM somewhat better than E39/C. Total ozone and lower stratospheric temperature show similar patterns. Main contributions to the interannual variations of total ozone and lower stratospheric temperature at 50 hPa come from a linear trend (up to ? 30 Dobson Units (DU) per decade, or ? 1.5 K/decade), the QBO (up to 25 DU, or 2.5 K peak to peak), the intensity of the polar vortices (up to 50 DU, or 5 K peak to peak), and from tropospheric weather (up to 30 DU, or 3 K peak to peak). Smaller variations are related to the 11-year solar cycle (generally less than 25 DU, or 2.5 K), and to ENSO (up to 15 DU, or 1.5 K). Volcanic eruptions have resulted in sporadic changes (up to ? 40 DU, or +3 K). Most stratospheric variations are connected to the troposphere, both in observations and simulations. At low latitudes, patterns are zonally symmetric. At higher latitudes, however, strong, zonally non-symmetric signals are found close to the Aleutian Islands or south of Australia. Such asymmetric features appear in the model runs as well, but often at different longitudes than in the observations. The results point to a key role of the zonally asymmetric Aleutian (or Australian) stratospheric anti-cyclones for interannual variations at high- latitudes, and for coupling between polar vortex strength, QBO, 11-year solar cycle and ENSO.
Prenatal alcohol intake in a rural, caucasian clinic.

BACKGROUND AND OBJECTIVES This study examined prior use and psychosocial factors associated with alcohol and/or drug use in pregnant women from a predominantly Caucasian, rural clinic in northeastern Maine. METHODS We conducted archival record reviews of 217 pregnant women who delivered at the Family Practice Clinic of Eastern Maine Medical Center As part of the standard initial prenatal visit during thefirst trimester, a nurse practitioner interviewed and collected data from pregnant women concerning pre-pregnancy and current-pregnancy use of alcohol, tobacco, and other drugs. Data were available for 212 subjects. RESULTS The reported prevalence of pre-pregnancy alcohol abuse in this sample was 25%. Women in this cohort reported a significant decrease in tobacco and alcohol use following pregnancy awareness. However, pre-pregnancy alcohol intake levels and years of alcohol use were associated with alcohol intake during pregnancy. Other markers of maternal alcohol intake during pregnancy included tobacco use patterns and history of drug use. Family history of alcohol problems and drug use were associated with maternal substance use history and use by the father of the baby. Levels of maternal alcohol use during the current pregnancy were negatively associated with an alcohol problem in the father of the baby. CONCLUSIONS Alcohol and other substance use were relatively common in our sample of rural Caucasian women in Maine. Several risk factors can be identified, and awareness of these risk factors may assist physicians in the diagnosis of substance abuse among pregnant women.
Dissimilatory Arsenate and Sulfate Reduction in Sediments of Two Hypersaline, Arsenic-Rich Soda Lakes: Mono and Searles Lakes, California

ABSTRACT A radioisotope method was devised to study bacterial respiratory reduction of arsenate in sediments. The following two arsenic-rich soda lakes in California were chosen for comparison on the basis of their different salinities: Mono Lake (∼90 g/liter) and Searles Lake (∼340 g/liter). Profiles of arsenate reduction and sulfate reduction were constructed for both lakes. Reduction of [73As]arsenate occurred at all depth intervals in the cores from Mono Lake (rate constant [k] = 0.103 to 0.04 h−1) and Searles Lake (k = 0.012 to 0.002 h−1), and the highest activities occurred in the top sections of each core. In contrast, [35S]sulfate reduction was measurable in Mono Lake (k = 7.6 ×104 to 3.2 × 10−6 h−1) but not in Searles Lake. Sediment DNA was extracted, PCR amplified, and separated by denaturing gradient gel electrophoresis (DGGE) to obtain phylogenetic markers (i.e., 16S rRNA genes) and a partial functional gene for dissimilatory arsenate reduction (arrA). The amplified arrA gene product showed a similar trend in both lakes; the signal was strongest in surface sediments and decreased to undetectable levels deeper in the sediments. More arrA gene signal was observed in Mono Lake and was detectable at a greater depth, despite the higher arsenate reduction activity observed in Searles Lake. A partial sequence (about 900 bp) was obtained for a clone (SLAS-3) that matched the dominant DGGE band found in deeper parts of the Searles Lake sample (below 3 cm), and this clone was found to be closely related to SLAS-1, a novel extremophilic arsenate respirer previously cultivated from Searles Lake.
Reading comprehension, word decoding and spelling in girls with autism spectrum disorders (ASD) or attention-deficit/hyperactivity disorder (AD/HD): performance and predictors.

BACKGROUND Difficulties with aspects of literacy are often seen in children with autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (AD/HD). The bases of the connections between these disorders and literacy difficulties are poorly understood. Furthermore, it is not clear if existing research is representative for girls. AIMS There were three aims: (1) to compare performance in reading comprehension, word decoding, and spelling in girls with ASD (n = 20), AD/ HD (n = 36), and community girls with typical developing (girls; n = 54); (2) to assess rates of reading and writing disorders within groups; and (3) to examine the predictive value of measures of autistic and AD/HD symptomatology to reading comprehension in the whole girl sample. METHODS & PROCEDURES Participants were aged between 8 and 17 years, and had a full scale IQ>70. Standardized tests of literacy, oral vocabulary, and non-verbal ability were administered. Parent ratings of degree of autistic symptomatology and both parent and teacher ratings of AD/HD symptomatology were collected for all girls. OUTCOMES & RESULTS Girls with diagnosed ASD could not be separated significantly from typically developing girls or girls with AD/HD on average performance on any literacy test. However, among girls with ASD, 40% had at least one reading and writing disorder. Girls with AD/HD performed lower than typically developing girls in reading comprehension, word decoding, and spelling, and 56% had at least one reading and writing disorder. In regression analysis, using the total sample, both degrees of autistic and AD/HD symptomatology negatively contributed to the variance in reading comprehension after controlling for oral vocabulary, word decoding, and non-verbal ability. Whereas AD/HD contributed to the variance in reading comprehension once autistic symptomatology was controlled for, the opposite was not true. However, a large bivariate correlation between autistic and AD/HD symptomatology somewhat complicates the interpretation of that result. CONCLUSIONS & IMPLICATIONS The findings highlight the importance of monitoring and supporting the literacy development in girls with ASD or AD/HD. Results from regression analyses suggested that word decoding and/or oral vocabulary training may not be sufficient for the girls fully to overcome difficulties in the important skill of reading comprehension.
Contextual Bidirectional Long Short-Term Memory Recurrent Neural Network Language Models: A Generative Approach to Sentiment Analysis

Traditional learning-based approaches to sentiment analysis of written text use the concept of bag-of-words or bag-of-n-grams, where a document is viewed as a set of terms or short combinations of terms disregarding grammar rules or word order. Novel approaches de-emphasize this concept and view the problem as a sequence classification problem. In this context, recurrent neural networks (RNNs) have achieved significant success. The idea is to use RNNs as discriminative binary classifiers to predict a positive or negative sentiment label at every word position then perform a type of pooling to get a sentence-level polarity. Here, we investigate a novel generative approach in which a separate probability distribution is estimated for every sentiment using language models (LMs) based on long short-term memory (LSTM) RNNs. We introduce a novel type of LM using a modified version of bidirectional LSTM (BLSTM) called contextual BLSTM (cBLSTM), where the probability of a word is estimated based on its full left and right contexts. Our approach is compared with a BLSTM binary classifier. Significant improvements are observed in classifying the IMDB movie review dataset. Further improvements are achieved via model combination.