Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of single-walled carbon nanotubes on the bioavailability of PCBs in field-contaminated sediments

Abstract Adsorption of hydrophobic organic contaminants (HOCs) to black carbon is a well-studied phenomenon. One emerging class of engineered black carbon materials are single-walled carbon nanotubes (SWNTs). Little research has investigated the potential of SWNT to adsorb and sequester HOCs in complex environmental systems. This study addressed the capacity of SWNT, amended to polychlorinated biphenyl (PCB)-contaminated New Bedford Harbor (NBH) sediment, to reduce the toxicity and bioaccumulation of these HOCs to benthic organisms. Overall, SWNT amendments increased the survival of two benthic estuarine invertebrates, Americamysis bahia and Ampelisca abdita, and reduced the accumulation of PCBs to the benthic polychaete, Nereis virens. Reduction in PCB bioaccumulation by SWNT was independent of Kow. Further, passive sampling-based estimates of interstitial water concentrations indicated that SWNT reduced PCB bioavailability. Results from this study suggest that SWNT are a good adsorbent for PCBs and might be useful for remediation in the future once SWNT manufacturing technology improves and costs decrease.
Performance-Portable Autotuning of OpenCL Kernels for Convolutional Layers of Deep Neural Networks

We present a portable and highly-optimized Deep Neural Network (DNN) algorithm and its implementation techniques. Our approach is a novel combination of existing HPC techniques that methodically applies autotuning as well as data layout and low-level optimizations that achieve performance matching and/or exceeding what is possible with either reverse engineering and manual assembly coding or proprietary vendor libraries. The former was done inside the maxDNN implementation and the latter is represented by cuDNN. Our work may be directly applied to the most time consuming part of DNN workflow, namely the training process which often needs a restart when it stagnates due to, for example, diminishing gradients and getting stuck in local minima. With the result of performance tests on a consumer-grade GPU with the latest High Bandwidth Memory (HBM) stack, our methodology can match a server grade hardware at a fraction of the price. Another tuning sweep on a new GPU architecture from a different vendor also attests to the portability of our approach and the quality of our implementation.
Differential Inhibition of Prion Propagation by Enantiomers of Quinacrine

Prion diseases are fatal neurologic disorders caused by accumulation of a pathogenic isoform (PrPSc) of the prion protein (PrP). The recent discovery of the inhibitory action of quinacrine on PrPSc formation in scrapie-infected neuroblastoma (ScN2a) cells raised the possibility of a treatment for patients with prion disease. To investigate the efficacy of quinacrine enantiomers, we measured the inhibitory effect of these isomers on PrPSc formation in ScN2a cells. (S)-quinacrine exhibited superior antiprion activity compared with (R)-quinacrine and two generic quinacrines that appear to be racemates. Treatment with these various forms of quinacrine did not induce adverse changes affecting cell survival and the expression of marker proteins over a range of potentially therapeutic concentrations. Thus, quinacrine enantiomers demonstrated stereoselectivity on prion elimination but not cytotoxicity in ScN2a cells. Our results raise the possibility that in vivo treatment using one enantiomer of quinacrine may be superior to a racemic mixture, which is the form that is generally used when quinacrine is employed to treat parasitic diseases.
An Improved Adaptive Genetic Algorithm for Image Segmentation and Vision Alignment Used in Microelectronic Bonding

In order to improve the precision and efficiency of microelectronic bonding, this paper presents an improved adaptive genetic algorithm (IAGA) for the image segmentation and vision alignment of the solder joints in the microelectronic chips. The maximum between-cluster variance (OTSU) threshold segmentation method was adopted for the image segmentation of microchips, and the IAGA was introduced to the threshold segmentation considering the features of the images. The performance of the image segmentation was investigated by computational and experimental tests. The results show that the IAGA has faster convergence and better global optimality compared with standard genetic algorithm (SGA), and the quality of the segmented images becomes better by using the OTSU threshold segmentation method based on IAGA. On the basis of moment invariant approach, the microvision alignment was realized. Experiments were carried out to implement the microvision alignment of the solder joints in the microelectronic chips, and the results indicate that there are no alignment failures using the OTSU threshold segmentation method based on IAGA, which is superior to the OTSU method based on SGA in improving the precision and speed of the vision alignments.
Online monitoring of collagen fibre alignment in tissue‐engineered tendon by PSOCT

One of the major challenges in engineering a functional tendon is to be able to monitor the evolving arrangement of collagen fibres, which leads to the formation of a complex extracellular matrix. Polarization‐sensitive optical coherence tomography (PSOCT) is a non‐destructive imaging technique capable of examining the organization of tissues online. In this study, PSOCT was used for the first time to visualize the evolution of the collagen fibre alignment in tissue‐engineered tendons in response to varying growth environments. The tendon constructs consisted of rat tenocytes embedded in collagen hydrogels and cultured in Flexcell Tissue Train Culture plates. They were subjected to cyclical loading for 1 h at 1 Hz every day, using the Flexcell system. Different strain level and cell seeding densities were examined at different time points over a 14 day period. The birefringence, a characteristic of the growing tendon, was found to increase over culture time and with the increase of cell‐seeding densities. In addition, it was revealed that the effect of contraction of tenocytes on the fibre alignment was greater than the application of external forces during stretching. These results demonstrate that PSOCT can be a powerful tool for monitoring the change in collagen organization online and non‐destructively at different time points in growing engineered tendons. Copyright © 2008 John Wiley & Sons, Ltd.
Analysis of Pig Vomeronasal Receptor Type 1 (V1R) Promoter Region Reveals a Common Promoter Motif but Poor CpG Islands

ABSTRACT Promoters are, generally, located immediately upstream of a transcription start site (TSS) and have a variety of regulatory motifs, such as transcription factors (TFs) and CpG islands (CGIs), that participate in the regulation of gene expression. Here analysis of the promoter region for pig vomeronasal receptor type 1 (V1R) was described. In the analysis, TSSs for pig V1R genes was first identified and five motifs (MV1, MV2, MV3, MV4, and MV5) were found that are shared by at least 50% of the pig V1R promoter input sequences from both strands. Among the five motifs, MV2 was identified as a common promoter motif shared by all (100%) pig V1R promoters. For further analysis, to better characterize and get deeper biological insight associated with MV2, TOMTOM web application was used. MV2 was compared to the known motif databases (such as JASPAR) to see if they are similar to a known regulatory motif (transcription factor). Hence, it was revealed that MV2 serves as the binding site mainly for the BetaBetaAlpha-zinc finger (BTB-ZF) transcription factor gene family to regulate expression of pig V1R genes. Moreover, it was shown that pig V1R promoters are CpG poor, suggesting that their gene expression regulation pattern is in tissue specific manner.
The region encompassing the procyclic acidic repetitive protein (PARP) gene promoter plays a role in plasmid DNA replication in Trypanosoma brucei.

We have previously reported the construction and characterization of an autonomously replicating plasmid in Trypanosoma brucei. In this plasmid the procyclic acidic repetitive protein (PARP) gene promoter drives the transcription of a selectable marker. Deletion of this promoter incapacitates the plasmid, suggesting its utilization as a promoter-trap. Three independent libraries were created by inserting variously digested T.brucei genomic DNA into this promoterless construct. Transfection of these libraries into procyclic T.brucei and the subsequent isolation of episomes led only to the reisolation of the PARP promoter. Additionally, a ribosomal RNA promoter failed to keep the construct as an episome, although it can sustain mRNA transcription in T.brucei and was shown to be an efficient promoter in this construct. Finally, by using a transient replication assay involving the methylation-sensitive restriction endonuclease DpnI to distinguish between input and replicated DNA, we showed that the PARP promoter-bearing construct could replicate autonomously in procyclic T.brucei, but the corresponding construct with the rRNA promoter could not. The close association between elements that sustain transcription and DNA replication in T.brucei mirrors results observed in several higher eukaryotes and their viruses and suggests an ancient origin of this feature.
Subcortical input heterogeneity in the mouse inferior colliculus

Non‐technical summary Sensory information appears to be represented in a well‐organized manner in the central nervous system, but it is unclear whether this still holds true at the level of individual neurons. Here we found that the responses to sound of two neurons in the auditory midbrain that were lying right next to each other were not more similar than neurons that were far apart. Our results suggest a high local specialization of neuronal responses to sound stimulation in the dorsal cortex of the mouse inferior colliculus.
Combining Hydrophobicity with PSSM for Improving Prediction Accuracy of alpha-Helix Using BP Neural Network

A two-stage neural network has been used to predict protein secondary structure based on the method of combining hydrophobicity of amino acid residues with PSSM. We employed CB513 as the dataset. After excluding the protein chains containing X-. B and which with sequence length shorter than 30 amino acids , there were 492 protein chains in this dataset totally. The network has been trained and tested by 4-fold cross- validation. The result indicated that alpha-helix has been predicted with an averaged accuracy of nearly 79%, sensitivity of 79% and specificity of 91%. The total prediction accuracy of secondary structure reached 75.96%, which is higher than that of only using PSSM as input.
Learning from those who were successful: an exploration into the lived experiences of community college entrants who as adult learners completed their baccalaureate online.

The purpose of this study was to explore the lived experiences of online, adult learners who navigated transitions and overcame challenges to succeed in earning a baccalaureate online via a community college starting point. Through studying these students who were actually successful, by examining their pathways, and by finding out how they succeeded, information was gained that can help higher education professionals better understand, engage, educate, and support community college entrants who seek to complete a four-year degree. A phenomenological approach was implemented. The study site for this research was a large, urban, private university in the northeastern United States. Specifically, the study site was one of the colleges within that university which enrolls a high number of online, adult baccalaureate-seekers who began their studies at the community college level. The research participants were adult learners who completed their baccalaureate online and who began their studies at the community college level as campus-based students. Participants were students who reached their four-year degree goal in 2016. Specifically, five undergraduate degree completers from an April 2016 degree conferral were chosen. A number of common findings emerged from the research. Specifically, inner drive or selfmotivation, influence of family and friends as motivators, overall institutional support, a specific person or event, and success paving the way for more success were found to be important to student success and persistence. Discussion of the findings and implications for institutions as well as future researchers, were discussed.
An Empirical Examination of the Relation between the Option-Implied Volatility Smile and Heterogeneous Beliefs

An option contract is a zero-sum game, so two identical risk-averse investors would never take opposite sides of it. While they will agree on the correct option price, they would never trade with each other. Heterogeneity is essential for options trading to exist, and aggregating diverse expectations into a single market clearing price is an important function of any derivatives market. In this article, the authors look at the impact of heterogeneous beliefs about earnings, as reflected in the dispersion of analysts’ forecasts in the IBES database. The effect on the market is measured by the slopes of the volatility smile for out-of-the-money (OTM) minus at-the-money (ATM) puts (left side of the smile) and OTM minus ATM calls (right side). Smiles for individual stocks are higher and more smile-shaped than for the SPX index and show significant and interesting effects from the explanatory variables, including firm size, liquidity, market volatility, and book-to-market. But controlling for those effects, dispersion in earnings forecasts raises OTM IVs relative to ATM IVs, both in regressions and in portfolio sorts. Interesting differences appear between systematic and idiosyncratic components of the smile slope, with systematic effects especially important for OTM puts, while OTM calls are more influenced by the idiosyncratic component.
Atimia and Outlawry in Archaic and Classical Greece

This article challenges the commonly held belief that atimia in its earliest Greek usage meant exile, arguing instead that atimia and outlawry were always two entirely distinct, though not mutually exclusive, concepts. It is often claimed that atimia originated as a penalty of death or exile, but that over time its harshness became modified so that those who suffered under its restrictions could not be killed or assaulted with impunity. A careful study of the evidence will show that atimia never meant outlawry, and moreover, its archaic cognates do not imply that in early times to lose time was the same as losing membership in a political community. Rather, atimazesthai entailed the loss of social honour and status which was an all-encompassing value in the aristocratic societies of archaic Greece. Atimia in the Classical period is similarly a loss of rights ( timai ), and because penalties and conditions such as exile and outlawry can be easily described, in Greek, as involving the loss of prerogatives ( timai ), they are conceptually forms of atimia . However, in the legal language of democratic Athens atimia is and always was something distinct from exile, and this legal distinction went back to the very earliest times.
RISK FACTORS ASSESSMENT OF DIABETIC FOOT ULCER USING THE SIXTY SECONDS SCREENING TOOL: A HOSPITAL BASED CROSS-SECTIONAL STUDY AT TIKUR ANBESSA SPECIALIZED HOSPITAL.

BACKGROUND Diabetic foot ulcer is one of the most feared and common complications of diabetes. It is a major cause of disability, morbidity and mortality among diabetic patients and about 15% develop foot ulcers in their lifetime. Annual foot exam in diabetic patients and education on foot care is a cost effective way of preventing foot ulcers and amputations. METHODS A hospital based cross-sectional study was conducted at Tikur Anbessa Specialized Hospital Diabetes Center on 200 participants using the 60 seconds diabetic foot ulcer screening tool from April to August 2014. RESULTS A total of 200 patients were included in the study. The male to female ratio was 1 to 2.64 (55 to 145). The median age was 50 years (IQR, 39-59 years) and median duration of diabetes mellitus was 11 years (IQR, 6-11 years). Among the 200 patients, 169 (84.5%) had type 2 diabetes mellitus, whereas; 31(15.5%) had type 1 diabetes mellitus. Among the participants, only 9 (4.5%) had foot examination in the last 5 years. Thirty one (15.5%) participants had history of previous ulcer, 1 (0.5%) had history of amputation, 11 (5.5%) had deformity of shape and structure of the foot. Among the participants, 71 (35.5%) had at least one risk factor for the development of diabetic foot ulcer. CONCLUSION Diabetic foot problems are common among the diabetic patients examined at Tikur Anbessa Specialized Hospital Diabetic Center. Screening for diabetic foot ulcer is a very easy practice which will take maximum of 60 seconds per patient. Despite this fact it is barely practiced for outpatients visiting the diabetic clinics. We stress the need for a clinical diagnosis of diabetic foot ulcers using the 60 seconds screening tool.
PROFILE OF A LONE WOLF TERRORIST: A CRISIS MANAGEMENT PERSPECTIVE

This paper focuses on terrorist attacks carried out by so-called ‘lone wolves’ or ‘lone actors’. It provides an analytical evaluation of the basic characteristics of these attackers and discusses possible access to their identification in society. To create the profile of a ‘typical’ lone wolf, we collected information from a database of lone wolves who committed their terrorist attacks in the United States, Canada, the European Union, Switzerland, Norway and Australia from 1998 to 2016. Based on these data, it was demonstrated that lone wolves are not homogenous group, therefore, there is no one ‘typical’ lone wolf. Instead, three main groups of lone wolves were identified: 1) lone wolves with a criminal past, 2) lone wolves with a mental illness and 3) young lone wolves coming from minority groups in the country. These characteristics could be used as an auxiliary tool by state security forces during identification of potential lone wolf terrorists.
Association between melatonin secretion and daytime sleep complaints in night nurses.

STUDY OBJECTIVES To test the hypothesis that nightworkers' diurnal sleep complaints are associated with the timing of melatonin secretion. DESIGN After a minimum of three consecutive night shifts, the subjects were admitted to the laboratory for 24 hours during which they were allowed to eat and sleep ad lib. Urine was collected every two hours under dim illumination (<25 lux). Concentration of urinary 6-sulphatoxymelatonin (UaMT6s) was determined by radioimmunoassay. Sleep quality was assessed by questionnaires. SETTING NA PARTICIPANTS: Two groups of 15 night nurses with mild and severe daytime sleep complaints. INTERVENTIONS NA RESULTS: The proportion of the episode of UaMT6s excretion happening during the day (between 08:00 and 00:00 hours) was smaller in the group of nightworkers with severe daytime sleep complaints, and was negatively correlated with the severity of the complaints over the 30 subjects. A longer duration of melatonin secretion was associated with a lower severity of daytime sleep complaints. However, in most of the subjects with good daytime sleep quality, melatonin secretion remained essentially nocturnal, and the overlap with the time of their sleep episode was small or even absent. CONCLUSIONS Timing and duration of melatonin secretion were associated with better daytime sleep quality when the subjects had an increased proportion of melatonin secreted during the day. When there was an indication of circadian phase shift, the direction of the shift was not of primary importance for daytime sleep quality. A longer duration of melatonin secretion may increase the tolerance to an abnormal circadian phase.
Nonlinear and Adaptive Observers for Perspective Dynamic Systems

Estimation of 3D structure and motion from 2D images in computer vision systems can be performed using a dynamic system, often referred to as a perspective dynamic system. This paper presents a novel parametrization of the nonlinear perspective dynamic system, from which different estimators for rigid body structure as well as motion can be derived in a straightforward manner. The parametrization allows a structure estimator to be formulated as a nonlinear observer which estimates 3D position, assuming knowledge of angular and linear velocities. The observer performance is demonstrated using simulation examples, where it is also shown how a time scaling parameter can be used to tune the transient response. The parametrization also allows a motion estimator to be formulated as an adaptive observer, estimating angular velocity and 3D position assuming knowledge of the linear velocity. This is demonstrated by deriving an estimator and illustrating its performance in a simulation example. The presented investigations and simulations indicate that the parametrization has a potential for future development of estimators for structure as well as motion in perspective dynamic systems, and for the investigation of similarities and differences in comparison to discrete, projective geometry based, methods.
Concentrations of Progesterone in the Plasma of Mothers and Infants at Time of Birth

Extract: A higly sensitive method utilizing competitive protein binding was used to study concentrations of progesterone in the plasma of mothers, in umbilical cord plasma, and in the plasma of full-term and premature infants in the immediate postpartum period.Blood samples were obtained from 20 mothers during labor and from the cords of their infants at delivery. Most of these infants were also studied at 2 or 3 days of age. For purposes of comparison, a second series of samples was obtained from control subjects using needle aspiration to obtain samples from the umbilicus; 14 samples were studied.In the mothers, concentrations of progesterone in plasma ranged from 46 to 387 ng/ml (mean: 129 ± 78 SD); in cord blood, progesterone levels ranges from 440 to 2,000 ng/ml (mean: 1,030 ± 412 SD); and in blood from the umbilical vein, concentrations of progesterone ranges from 310 to 720 ng/ml (mean: 562 ± 140 SD). A total of 27 full-term newborns was studied at 24, 48, and 72 h of life. In four cases, blood was obtained from the same infant at 12,24, and 72 h of life. The highest concentrations of progesterone were noted during the first 24 h of life, with levels ranging from 13 to 32 ng/ml (mean: 19 ng/ml) at 12 h, and from 2 to 32 ng/ml (mean: 16 ng/ml) at 24 h. By day 2, levels of progesterone had decreased to 3-20 ng/ml (mean: 10 ng/ml) and by day 3 were reduced to 0-16 ng/ml (mean: 8 ng/ml). Thirty-two premature infants, with birth weights of from 1,317 to 2,465 g, and ranging in gestational age from 30 to 40 weeks, were also studied. In several cases serial blood samples were obtained by the same methods used with the full-term infants. Two sets of twins were included. In premature infants, decreasing rapidly to 2-6 ng/ml (mean: 3 ng/ml) by 24 h of life. These low concentrations poersisted throughout days 2 and 3.There was no singnificant difference between concentrations of progesterone in plasma in full-term and premature infants at 2-3 days of age. It appeated that premature infants were as able to clear progesterone from the plasma as were the full-term infants.Speculation: The data obtained in this study support the concept that large amounts of progesterone are delivered from the placenta to the fetus. This compound may be a precursor of C-21 steroids such as cortisol, synthesized by the fetal adrenal. Preogesterone has also been shown to effect respiration in animals and man [7, 8, 14, 15] and an effect on neonatal respiratory mechanisms and diease may occur, although this has not been demonstrated.Maternal blood has a relatively large concentration of pgrogesterone which dimis\shes rapidly following delivery of the placenta. Presumably the compound exerts some effect in the maintenance of pregnancy. Its exact role has not been established.