Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mayak Worker Dosimetry System (MWDS-2013): Implementation of the Dose Calculations

The calculation of internal doses for the Mayak Worker Dosimetry System (MWDS-2013) involved extensive computational resources due to the complexity and sheer number of calculations required. The required output consisted of a set of 1000 hyper-realizations: each hyper-realization consists of a set (1 for each worker) of probability distributions of organ doses. This report describes the hardware components and computational approaches required to make the calculation tractable. Together with the software, this system is referred to here as the 'PANDORA system'. It is based on a commercial SQL server database in a series of six work stations. A complete run of the entire Mayak worker cohort entailed a huge amount of calculations in PANDORA and due to the relatively slow speed of writing the data into the SQL server, each run took about 47 days. Quality control was monitored by comparing doses calculated in PANDORA with those in a specially modified version of the commercial software 'IMBA Professional Plus'. Suggestions are also made for increasing calculation and storage efficiency for future dosimetry calculations using PANDORA.
Tracking control of a convoy of autonomous robotic cars with a prescribed performance

This paper studies the tracking control of a convoy of multiple autonomous cars or car-like robots in the planar motion without any collision with a prescribed performance that has not been addressed sufficiently in the literature yet. Toward this end, a coordinate transformation is initially employed to transform the posture errors between each two successive cars in a group from the earth-fixed frame into their relative distance and angle errors that should satisfy some predefined transient and steady-state constraints. By employing the prescribed performance technique, a nonlinear transformation is used to transform the constrained relative distance and angle errors and to obtain an unconstrained kinematic error equation. Then, a novel kinematic controller is designed to satisfy the prescribed transient and steady-state performance specifications without any collision and any controller singularity. Next, the Dynamic Surface Control technique is effectively used to simplify the convoy controller design at the dynamic level by using a first-order filter. An adaptive neural network is used to maintain the control system robustness against modelling errors and external disturbances. The Lyapunov theory proves the stability of the convoy control system and, finally, simulation examples verify the controller performance for multiple autonomous cars in intelligent transportation applications.
What Just Happened? A Framework for Social Event Detection and Contextualisation

In course of a breaking news event, such as natural calamity, political uproar etc., a massive crowd sourced data is generated over social media which makes social media platforms an important source of information in such scenarios. The value of the information being propagated via social media is being increasingly realised by the news organisations and the journalists. Better tools and methodologies are needed to facilitate them in utilising this information for news production. A lot of analysis over social media, by the journalists, is performed via rigorous manual labour. However, the sheer volume of the data produced on social media is overwhelming and acts as a major obstacle for manual inspection of the streaming data for finding, aggregating and contextualising the emerging event in a short time span. This is a day-to-day challenge for journalists and media organisations. This paper addresses the above problem for journalist in handling the voluminous social media data, viewing it from an information retrieval perspective, by proposing an 'event detection and contextualisation' framework that processes an input stream of social media data into the clusters of likely events.
Characterising 3D-printed Soft Fin Ray Robotic Fingers with Layer Jamming Capability for Delicate Grasping

Motivated by the growing need within the agri-food industry to automate the handling of delicate produce, this paper presents soft robotic fingers utilising the Fin Ray® effect to passively and gently adapt to delicate targets. The proposed Soft Fin Ray fingers feature thin ribs and are entirely 3D printed from a flexible material (NinjaFlex) to enhance their shape adaptation, compared to the original Fin Ray fingers. To overcome their reduced force generation, the effects of the angle and spacing of the flexible ribs were experimentally characterised. The results showed that at large displacements, layer jamming between tilted flexible ribs can significantly enhance the force generation, while minimal contact forces can be still maintained at small displacements for delicate grasping.
On the calculation of a "reference change" for comparing two consecutive measurements.

We describe a statistical method for calculating a "reference change," defined as that difference between two consecutive test results in an individual that is statistically significant in a given proportion of all similar persons. By allowing for variation in within-person variances, this procedure computes a reference change that is more specific (i.e., less prone to false positives) than that obtained directly from the distribution of observed differences between measurements. Moreover, the method may easily be extended to a test for trend in three successive measurements. The method has been applied to semi-annual measurements of serum calcium and alkaline phosphatase in 698 men and women enrolled in a large health-maintenance program. We believe that these ideas may also be usefully applied to successive laboratory tests in carefully defined patient populations--but this introduces special problems, which are discussed briefly.
Labeling of prokaryotic mRNA in live cells using fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB)

High-throughput sequencing and cellular imaging have expanded our knowledge of microbial diversity and expression of cellular activity. However, it remains challenging to characterize low-abundance, slow-growing microorganisms that play key roles in biogeochemical cycling. With the goal of isolating transcriptionally active cells of these microorganisms from environmental samples, we developed fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB) to label living prokaryotic cells. FISH-TAMB utilizes polyarginine cell-penetrating peptides to deliver molecular beacons across cell walls and membranes. Target cells are fluorescently labeled via hybridization between molecular beacons and messenger RNA of targeted functional genes. FISH-TAMB’s target specificity and deliverance into both bacterial and archaeal cells were demonstrated by labeling intracellular methyl-coenzyme M reductase A (mcrA) transcripts expressed by Escherichia coli mcrA+, Methanosarcina barkeri, and a methanogenic enrichment of deep continental fracture fluid. Growth curve analysis supported sustained cellular viability following FISH-TAMB treatment. Flow cytometry and confocal microscopy detected labeled single cells and single cells in aggregates with unlabeled cells. As FISH-TAMB is amenable to target any functional gene of interest, when coupled with cell sorting, imaging, and sequencing techniques, FISH-TAMB will enable characterization of key uncharacterized rare biosphere microorganisms and of the syntrophically activated metabolic pathways between physically associated microorganisms.
Influenza reverse genetics: dissecting immunity and pathogenesis

Reverse genetics systems allow artificial generation of non-segmented and segmented negative-sense RNA viruses, like influenza viruses, entirely from cloned cDNA. Since the introduction of reverse genetics systems over a decade ago, the ability to generate ‘designer’ influenza viruses in the laboratory has advanced both basic and applied research, providing a powerful tool to investigate and characterise host–pathogen interactions and advance the development of novel therapeutic strategies. The list of applications for reverse genetics has expanded vastly in recent years. In this review, we discuss the development and implications of this technique, including the recent controversy surrounding the generation of a transmissible H5N1 influenza virus. We will focus on research involving the identification of viral protein function, development of live-attenuated influenza virus vaccines, host–pathogen interactions, immunity and the generation of recombinant influenza virus vaccine vectors for the prevention and treatment of infectious diseases and cancer.
A Subband Energy Modification Method for Elevation Control in Median Plane

Elevation perception is crucial for binaural reproduction. A recent study proposed an elevation control method by modifying the energy of HRTFs in each auditory scale subband, such as the ERB and Mel subband. However, this subband division is designed based on auditory excitation patterns and may not be consistent with the elevation localization cues. To this end, this study proposes a novel subband division strategy which emphasizes the physiological information involved in elevation localization based on a statistical analysis of the HRTF. Then, the elevation controlled HRTFs are constructed by modifying the energy of the HRTF magnitudes in each subband. Results of the listening test demonstrate that our method with the proposed subband division strategy outperforms the method with ERB scale subdivision in terms of the accuracy for controlling the perceived elevation of sound image.
Cortical thinning and flattening in schizophrenia and their unaffected parents

Background: Schizophrenia is a neurodevelopmental disorder with high heritability. Widespread cortical thinning has been identified in schizophrenia, suggesting that it is a result of cortical development deficit. However, the findings of other cortical morphological indexes of patients are inconsistent, and the research on their relationship with genetic risk factors for schizophrenia is rare. Methods: In order to investigate cortical morphology deficits and their disease-related genetic liability in schizophrenia, we analyzed a sample of 33 patients with schizophrenia, 60 biological parents of the patients, as well as 30 young controls for patients and 28 elderly controls for parents with age, sex and education level being well-matched. We calculated vertex-wise measurements of cortical thickness, surface area, local gyrification index, sulcal depth, and their correlation with the clinical and cognitive characteristics. Results: Widespread cortical thinning of the fronto-temporo-parietal region, sulcal flattening of the insula and gyrification reduction of the frontal cortex were observed in schizophrenia patients. Conjunction analysis revealed that patients with schizophrenia and their parents shared significant cortical thinning of bilateral prefrontal and insula, left lateral occipital and fusiform regions (Monte Carlo correction, P<0.05), as well as a trend-level sulcal depth reduction mainly in bilateral insula and occipital cortex. We observed comprehensive cognitive deficits in patients and similar impairment in the speed of processing of their unaffected parents. Significant associations between lower processing speed and thinning of the frontal cortex and flattening of the parahippocampal gyrus were found in patients and their parents, respectively. However, no significant correlation between abnormal measurements of cortical morphology and clinical characteristics was found. Conclusion: The results suggest that cortical morphology may be susceptible to a genetic risk of schizophrenia and could underlie the cognitive dysfunction in patients and their unaffected relatives. The abnormalities shared with unaffected parents allow us to better understand the disease-specific genetic effect on cortical development.
On Profile Likelihood

Abstract We show that semiparametric profile likelihoods, where the nuisance parameter has been profiled out, behave like ordinary likelihoods in that they have a quadratic expansion. In this expansion the score function and the Fisher information are replaced by the efficient score function and efficient Fisher information. The expansion may be used, among others, to prove the asymptotic normality of the maximum likelihood estimator, to derive the asymptotic chi-squared distribution of the log-likelihood ratio statistic, and to prove the consistency of the observed information as an estimator of the inverse of the asymptotic variance.
The ultrastructure of Leishmania donovani.

The structure of the intracellular form of Leishmania donovani as seen by the light microscope consists of a nucleus and usually a rod-like kinetoplast (Wenyon, 1926) within a homogeneous mass of cytoplasm, while the extracellular or culture form has, in addition to these structures, an anterior flagellum. The intracellular form is usually round or ovoid measuring 2-4 microns; the extracellular form measures about 14-20 microns in length and from 1.5-3.5 microns in breadth. Because of the small dimensions of the protozoan parasite and the limited resolution of the light microscope, relatively little information is available on its fundamental organization. With the great resolving power of the electron microscope, several workers have attempted to study its ultrastructure with this instrument. The studies of Emmel, Jakob and Golz (1942), Sen Gupta et al. (1951), Das Gupta et al. (1954) of this species, and Lofgren (1950) of Leishmania tropica using electron microscopy of the culture forms have failed to yield new information on the fine internal morphology because the parasites were examined as whole specimens. The thickness of the specimens does not allow for adequate electron beam penetration, and the parasites appear as dense masses. In this study however, this problem is eliminated by the use of thin sectioning. Fine structural detail is observed in these preparations in both the extraand intracellular forms. The accumulation of structural knowledge may enable us to understand the relationship of host cells and leishmania; i.e., the biology of this intracellular parasitism. This paper presents only a few observations of this host-parasite relationship and further work is necessary to make a thorough study of this problem.
Withaferin A suppresses the expression of vascular endothelial growth factor in Ehrlich ascites tumor cells via Sp1 transcription factor

In the ayurvedic system of medicine, the medicinal plant, Withania somnifera Dunal (Solanaceae) finds application for numerous ailments including cancer. This herbal plant yields a host of steroidal lactones called withanolides, some of which have shown growth inhibition of human tumor cell lines. Withaferin A amongst these withanolides reportedly is very active in impairing antitumor activity. However; the underlying molecular mechanisms of this activity remains still unclear. In the present study, we have shown that withaferin A inhibited vascular endothelial cell growth factor (VEGF) -induced tube formation by human umbilical vein endothelial cells (HUVECs) and angiogenesis in chick chorioallantoic membrane (CAM) assay. In Ehrlich ascites tumor (EAT) model, the animals treated with withaferin A suppressed in vivo, the peritoneal angiogenesis and microvessel density. When compared to the untreated animals, the withaferin A treated tumor bearing mice showed a decrease in the volume of ascites and tumor cell number. Quantitation of VEGF levels in ascites from withaferin A untreated or treated tumor bearing mice indicated decreased secretion of VEGF in ascites from treated mice, as measured by ELISA. Studies at molecular level revealed that withaferin A inhibits binding of Sp1 transcription factor to VEGF-gene promoter, in order to exert its antiangiogenic activity. These results clearly indicate the antiangiogenic potential of withaferin A in modulating antitumor activity.
L1-Norm-Based Common Spatial Patterns

Common spatial patterns (CSP) is a commonly used method of spatial filtering for multichannel electroencephalogram (EEG) signals. The formulation of the CSP criterion is based on variance using L2-norm, which implies that CSP is sensitive to outliers. In this paper, we propose a robust version of CSP, called CSP-L1, by maximizing the ratio of filtered dispersion of one class to the other class, both of which are formulated by using L1-norm rather than L2-norm. The spatial filters of CSP-L1 are obtained by introducing an iterative algorithm, which is easy to implement and is theoretically justified. CSP-L1 is robust to outliers. Experiment results on a toy example and datasets of BCI competitions demonstrate the efficacy of the proposed method.
Complete chloroplast genome sequence of Parnassia palustris (Celastraceae)

Abstract The complete chloroplast genome (cp) of Parnassia palustris was reported in this study. The cp genome was 148,700 bp in length including two inverted repeats (IRs) of 25,892 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 82,175 and 14,741 bp, respectively. The GC content was 37%. The genome encoded 124 functional genes, including 78 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Using the whole chloroplast genome sequences alignment of 8 species from Celastraceae, Oxalidaceae, and Malpighiaceae, the phylogenetic relationship was built. The phylogenetic position of P. palustris was consistent with APG IV. The plastid genome of P. palustris will be useful for developing markers for further studies on resolving the relationship within the genus.
JVirGel: calculation of virtual two-dimensional protein gels

We developed JVirGel, a collection of tools for the simulation and analysis of proteomics data. The software creates and visualizes virtual two-dimensional (2D) protein gels based on the migration behaviour of proteins in dependence of their theoretical molecular weights in combination with their calculated isoelectric points. The utilization of all proteins of an organism of interest deduced from genes of the corresponding genome project in combination with the elimination of obvious membrane proteins permits the creation of an optimized calculated proteome map. The electrophoretic separation behaviour of single proteins is accessible interactively in a Java(TM) applet (small application in a web browser) by selecting a pI/MW range and an electrophoretic timescale of interest. The calculated pattern of protein spots helps to identify unknown proteins and to localize known proteins during experimental proteomics approaches. Differences between the experimentally observed and the calculated migration behaviour of certain proteins provide first indications for potential protein modification events. When possible, the protein spots are directly linked via a mouse click to the public databases SWISS-PROT and PRODORIC. Additionally, we provide tools for the serial calculation and visualization of specific protein properties like pH dependent charge curves and hydrophobicity profiles. These values are helpful for the rational establishment of protein purification procedures. The proteomics tools are available on the World Wide Web at http://prodoric.tu-bs.de/proteomics.php.
25th Anniversary Article: Organic Photovoltaic Modules and Biopolymer Supercapacitors for Supply of Renewable Electricity: A Perspective from Africa

The role of materials in civilization is well demonstrated over the centuries and millennia, as materials have come to serve as the classifier of stages of civilization. With the advent of materials science, this relation has become even more pronounced. The pivotal role of advanced materials in industrial economies has not yet been matched by the influence of advanced materials during the transition from agricultural to modern societies. The role of advanced materials in poverty eradication can be very large, in particular if new trajectories of social and economic development become possible. This is the topic of this essay, different in format from the traditional scientific review, as we try to encompass not only two infant technologies of solar energy conversion and storage by means of organic materials, but also the social conditions for introduction of the technologies. The development of organic‐based photovoltaic energy conversion has been rapid, and promises to deliver new alternatives to well‐established silicon photovoltaics. Our recent development of organic biopolymer composite electrodes opens avenues towards the use of renewable materials in the construction of wooden batteries or supercapacitors for charge storage. Combining these new elements may give different conditions for introduction of energy technology in areas now lacking electrical grids, but having sufficient solar energy inputs. These areas are found close to the equator, and include some of the poorest regions on earth.
Evidence for interstate transmission and increase in prevalence of bovine group B rotavirus strains with a novel VP7 genotype among diarrhoeic calves in Eastern and Northern states of India

SUMMARY During a surveillance study (2003–2005) in a cattle market in Kolkata city, state of West Bengal, Eastern India, 34 (13·0%) of 260 calves with diarrhoea were positive for group B rotaviruses (GBR) by RNA electrophoresis in polyacrylamide gels. Analysis of the partial VP7 gene sequence of 28 of the 34 GBR strains revealed maximum identities (97·7–99·5% at nucleotide level and 97·8–100% at amino-acid level) with the novel bovine GBR ‘Kolkata strains’ reported in an earlier surveillance study (1·5%, n=192, 2001–2002) from the same cattle market, and shared low identities of 73·7–78·9% and 80·8–89·6%; 62·6–66·2% and 59·8–65·4%; 58·9–62·2% and 48·6–54·9% at nucleotide and amino-acid level with other bovine, human, and murine GBR. The GBR-infected calves were traced to districts in neighbouring states of West Bengal. Therefore, the present study reports a rapid increase in prevalence (13·0% in 2003–2005 against 1·5% in 2001–2002) of novel GBR strains among calves with diarrhoea, and provides evidence for interstate transmission of GBR.
Comparison of the effects of Buteyko and pranayama breathing techniques on quality of life in patients with asthma – a randomized controlled trial

Objective: To compare two breathing exercises (Buteyko and pranayama) with a control group in patients with asthma. Design: Randomized controlled trial. Subjects: One hundred and twenty subjects were randomized to three groups through block randomization. Subjects with an Asthma Quality of Life Questionnaire score <5.5 participated in the study. Setting: Outpatient pulmonary medicine department. Interventions: Subjects in the Buteyko and pranayama groups were trained for 3–5 days and instructed to practise the exercises for 15 minutes twice daily, and for three months duration. The control group underwent routine pharmacological management during the study period. Outcome measures: Asthma Quality of Life Questionnaire, Asthma Control Questionnaire and pulmonary function test. Results: The baseline characteristics were similar in all three groups. Post intervention, the Buteyko group showed better trends of improvement (mean (95% confidence interval), P-value) in total Asthma Quality of Life Questionnaire score than the pranayama (0.47 (–0.008–0.95), P = 0.056) and control groups (0.97 (0.48–1.46), P = 0.0001). In comparison between the pranayama and control groups, pranayama showed significant improvement (0.50 (0.01–0.98), P = 0.042) in total Asthma Quality of Life Questionnaire score. Conclusion: The Buteyko group showed better trends of improvement in quality of life and asthma control than the group performing the pranayama breathing exercise.