Miracle-dz/UniFAR-FTUs huggingface dataset:
Information thermodynamics for interacting stochastic systems without bipartite structure

Fluctuations in biochemical networks, e.g. in a living cell, have a complex origin that precludes a description of such systems in terms of bipartite or multipartite processes, as is usually done in the framework of stochastic and/or information thermodynamics. This means that fluctuations in each subsystem are not independent: subsystems jump simultaneously if the dynamics is modeled as a Markov jump process, or noises are correlated for diffusion processes. In this paper, we consider information and thermodynamic exchanges between a pair of coupled systems that do not satisfy the bipartite property. The generalization of information-theoretic measures, such as learning rates and transfer entropy (TE) rates, to this situation is non-trivial and also involves introducing several additional rates. We describe how this can be achieved in the framework of general continuous-time Markov processes, without restricting the study to the steady-state regime. We illustrate our general formalism on the case of diffusion processes and derive an extension of the second law of information thermodynamics in which the difference of TE rates in the forward and backward time directions replaces the learning rate. As a side result, we also generalize an important relation linking information theory and estimation theory. To further obtain analytical expressions we treat in detail the case of Ornstein–Uhlenbeck processes, and discuss the ability of the various information measures to detect a directional coupling in the presence of correlated noises. Finally, we apply our formalism to the analysis of the directional influence between cellular processes in a concrete example, which also requires considering the case of a non-bipartite and non-Markovian process.
Pointing task on smart glasses: Comparison of four interaction techniques

Mobile devices such as smartphones, smartwatches or smart glasses have revolutionized how we interact. We are interested in smart glasses because they have the advantage of providing a simultaneous view of both physical and digital worlds. Despite this potential, pointing task on smart glasses is not really widespread. In this paper, we compared four interaction techniques for selecting targets : (a) the Absolute Head Movement and (b) the Relative Head Movement, where head movement controls the cursor on smart glasses in absolute or relative way, (c) the Absolute Free Hand interaction, where the forefinger control the cursor and (d) the Tactile Surface interaction, where the user controls the cursor via a small touchpad connected to smart glasses. We conducted an experiment with 18 participants. The Tactile Surface and Absolute Head Movement were the most efficient. The Relative Head Movement and Absolute Free Hand interactions were promising and require more exploration for other tasks.
The theory of scanning quantum dot microscopy

Electrostatic forces are among the most common interactions in nature and omnipresent at the nanoscale. Scanning probe methods represent a formidable approach to study these interactions locally. The lateral resolution of such images is, however, often limited as they are based on measuring the force (gradient) due to the entire tip interacting with the entire surface. Recently, we developed scanning quantum dot microscopy (SQDM), a new technique for the imaging and quantification of surface potentials which is based on the gating of a nanometer-size tip-attached quantum dot by the local surface potential and the detection of charge state changes via non-contact atomic force microscopy. Here, we present a rigorous formalism in the framework of which SQDM can be understood and interpreted quantitatively. In particular, we present a general theory of SQDM based on the classical boundary value problem of electrostatics, which is applicable to the full range of sample properties (conductive versus insulating, nanostructured versus homogeneously covered). We elaborate the general theory into a formalism suited for the quantitative analysis of images of nanostructured but predominantly flat and conductive samples.
Radicals and Ions Formed in Plasma-Treated Organic Solvents: A Mechanistic Investigation to Rationalize the Enhancement of Electrospinnability of Polycaprolactone

This paper reports and discusses the beneficial effects on the quality of electrospun polycaprolactone nanofibers brought about by pretreatment of the solvent with non-thermal plasma. Chloroform/dimethylformamide 9:1 (CHCl3:DMF 9:1) and pure chloroform were pretreated by a few minute exposure to the plasma generated by an atmospheric pressure plasma jet (APPJ). Interestingly, when pure chloroform was used, the advantages of plasma pretreatment of the solvent were way less pronounced than found with the CHCl3:DMF 9:1 mixture. The chemical modifications induced by the plasma in the solvents were investigated by means of complementary analytical techniques. GC-MS revealed the formation of solvent-derived volatile products, notably tetrachloroethylene (C2Cl4), 1,1,2,2-tetrachloroethane (C2H2Cl4), pentachloroethane (C2HCl5), hexachloroethane (C2Cl6) and, in the case of the mixed solvent, also N-methylformamide (C2H5NO). The chlorinated volatile products are attributed to reactions of ·Cl and Cl-containing methyl radicals and carbenes formed in the plasma-treated solvents. ·Cl and ·CCl3 radicals were detected and identified by EPR spectroscopy analyses. Ion chromatography revealed the presence of Cl−, NO3-, and HCOO− (the latter only in the presence of DMF) in the plasma-treated solvents, thus accounting for the observed increased conductivity and acidification of the solvent after plasma treatment. Mechanisms for the formation of these solvent derived products induced by plasma are proposed and discussed. The major role of radicals and ions in the plasma chemistry of chloroform and of the chloroform/dimethylformamide mixture is highlighted. The results provide insight into the interaction of plasma with organic solvents, a field so far little explored but holding promise for interesting applications.
Optimization of Exercise Countermeasures for Human Space Flight: Operational Considerations for Concurrent Strength and Aerobic Training

The physiological challenges presented by space flight and in microgravity (μG) environments are well documented. μG environments can result in declines muscle mass, contractile strength, and functional capabilities. Previous work has focused on exercise countermeasures designed to attenuate the negative effects of μG on skeletal muscle structure, function, and contractile strength and aerobic fitness parameters. Exposure to μG environments influences both strength and aerobic type physical qualities. As such, the current exercise recommendations for those experiencing μG involve a combination of strength and aerobic training or “concurrent training. ” Concurrent training strategies can result in development and maintenance of both strength and aerobic capabilities. However, terrestrial research has indicated that if concurrent training strategies are implemented inappropriately, strength development can be inhibited. Previous work has also demonstrated that the aforementioned inhibition of strength development is dependent on the frequency of aerobic training, modality of aerobic training, the relief period between strength and aerobic training, and the intra-session sequencing of strength and aerobic training. While time constraints and feasibility are important considerations for exercise strategies in μG, certain considerations could be made when prescribing concurrent strength and aerobic training to those experiencing human space flight. If strength and aerobic exercise must be performed in close proximity, strength should precede aerobic stimulus. Eccentric strength training methods should be considered to increase mechanical load and reduce metabolic cost. For aerobic capacity, maintenance cycle and/or rowing-based high-intensity intermittent training (HIIT) should be considered and cycle ergometry and/or rowing may be preferable to treadmill running.
Confirmation of the early prognostic value of bone scanning and pinhole imaging of the hip in Legg-Calvé-Perthes disease.

UNLABELLED In about half of all patients with Legg-Calvé-Perthes disease (LCP), severe hip disorders that could be prevented by early surgery will develop. A prognostic test for this complication is also needed as part of routine care to help the surgeon manage LCD. The purpose of this study was to confirm the prognostic value of the bone scanning and pinhole imaging of the hip in LCP that Conway's group proposed in 1997 and to define accurate prognostic scintigraphic patterns. METHODS Fifty-eight patients with LCP were recruited at initial presentation and followed for 1 y. Each patient underwent bone scanning initially and after 5, 8, and 12 mo of disease. The severity of the disease was assessed by radiography (the Catterall classification), MRI, and arthrography. Retrospectively, initial scintigraphic findings were correlated with severity. RESULTS Among the 60 hips studied (2 patients had bilateral disease), severe hip disorders developed in 36. The positive predictive value of the scintigraphic classification proposed by Conway's group was 97% for the B pathway (absence of lateral column formation) and 85% for the A pathway (presence of lateral column formation). The hyperactivity of the metaphyseal growth plates was a sign of poor prognosis. The sensitivity was only 33%, but the positive predictive value was 92%. This prognostic information was obtained in as few as 5 mo after initial presentation. CONCLUSION This study confirms the high prognostic value of bone scanning in LCP as reported by Conway's group not only in terms of the accuracy of the classification but also in terms of the short time in which the prognostic information can be obtained. Thus, we propose that bone scanning be used as part of routine care for the management of LCP.
Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1

The K1 A/B toxin secreted by virus-infected Saccharomyces cerevisiae strains kills sensitive cells via disturbance of cytoplasmic membrane functions. Despite decades of research, the mechanisms underlying K1 toxicity and immunity have not been elucidated yet. In a novel approach, this study aimed to characterize transcriptome changes in K1-treated sensitive yeast cells in a time-dependent manner. Global transcriptional profiling revealed substantial cellular adaptations in target cells resulting in 1,189 differentially expressed genes in total. Killer toxin K1 induced oxidative, cell wall and hyperosmotic stress responses as well as rapid down-regulation of transcription and translation. Essential pathways regulating energy metabolism were also significantly affected by the toxin. Remarkably, a futile cycle of the osmolytes trehalose and glycogen was identified probably representing a critical feature of K1 intoxication. In silico analysis suggested several transcription factors involved in toxin-triggered signal transduction. The identified transcriptome changes provide valuable hints to illuminate the still unknown molecular events leading to K1 toxicity and immunity implicating an evolutionarily conserved response at least initially counteracting ionophoric toxin action.
A Progressive Vehicle Search System for Video Surveillance Networks

Vehicle search aims to find a specific vehicle appeared in the physical world through surveillance networks. Existing systems usually exploit attributes, like colors and types, or license plate numbers as keywords to find vehicles in the database. However, attribute based search cannot accurately find the target vehicle due to the minor inter-class difference between similar vehicles and the extremely varied environmental factors. Moreover, the license plates usually cannot be correctly recognized in real-world surveillance scenes due to the viewpoints and motion blur. In this paper, we design a progressive vehicle search system, PVSS, for surveillance networks. As a search engine, PVSS contains three main parts: the vehicle crawler, the vehicle indexer, and the vehicle searcher. The vehicle crawler performs vehicle detection and tracking on surveillance videos and sends the cropped vehicle images, camera IDs, and timestamps to the indexer server. The indexer extracts multi-grained visual features, including the appearance features and license plate features, to index the vehicle images in the cameras. In the search stage, given a query vehicle image, the time range, and the spatial scope, the system can search the target vehicle in a progressive manner, i.e., from-coarse-to-fine search with multi-grained features and from-near-to-distant search with the spatiotemporal context. Extensive experiments on the public dataset from a real surveillance network demonstrate the effectiveness of the proposed system.
Genome-Wide Association Study for Adult-Plant Resistance to Stripe Rust in Chinese Wheat Landraces (Triticum aestivum L.) From the Yellow and Huai River Valleys

Stripe rust (also known as yellow rust), caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), is a common and serious fungal disease of wheat (Triticum aestivum L.) worldwide. To identify effective stripe rust resistance loci, a genome-wide association study was performed using 152 wheat landraces from the Yellow and Huai River Valleys in China based on Diversity Arrays Technology and simple sequence repeat markers. Phenotypic evaluation of the degree of resistance to stripe rust at the adult-plant stage under field conditions was carried out in five environments. In total, 19 accessions displayed stable, high degrees of resistance to stripe rust development when exposed to mixed races of Pst at the adult-plant stage in multi-environment field assessments. A marker–trait association analysis indicated that 51 loci were significantly associated with adult-plant resistance to stripe rust. These loci included 40 quantitative trait loci (QTL) regions for adult-plant resistance. Twenty identified resistance QTL were linked closely to previously reported yellow rust resistance genes or QTL regions, which were distributed across chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4A, 4B, 5B, 6B, 7A, 7B, and 7D. Six multi-trait QTL were detected on chromosomes 1B, 1D, 2B, 3A, 3B, and 7D. Twenty QTL were mapped to chromosomes 1D, 2A, 2D, 4B, 5B, 6A, 6B, 6D, 7A, 7B, and 7D, distant from previously identified yellow rust resistance genes. Consequently, these QTL are potentially novel loci for stripe rust resistance. Among the 20 potentially novel QTL, five (QDS.sicau-2A, QIT.sicau-4B, QDS.sicau-4B.2, QDS.sicau-6A.3, and QYr.sicau-7D) were associated with field responses at the adult-plant stage in at least two environments, and may have large effects on stripe rust resistance. The novel effective QTL for adult-plant resistance to stripe rust will improve understanding of the genetic mechanisms that control the spread of stripe rust, and will aid in the molecular marker-assisted selection-based breeding of wheat for stripe rust resistance.
Turning Away From Averted Gazes: The Effect of Social Exclusion on Gaze Cueing

Past studies showed increased sensitivity to other people’s gaze after social exclusion. In the present research, across two studies, we tested whether social exclusion could affect the basic cognitive phenomenon of gaze-cueing effect, namely, the tendency to redirect visual attention to the same location that other people are looking at. To this purpose, participants were socially excluded or included using the Cyberball manipulation. In Study 1, after the manipulation, participants performed a gaze-cueing task in which an individual’s gaze, oriented rightward or leftward, preceded a peripheral target stimulus requiring a simple categorization response. The gaze direction could be congruent or incongruent with the location of the target. Results revealed a reduced gaze-cueing effect for socially excluded than for socially included participants. In Study 2, where human gazes were replaced by arrow cues, such an interaction between social exclusion and trial congruency disappeared, indicating a specific effect of social stimuli. We interpreted these findings with the notion that excluded participants can perceive an averted gaze as a further sign of social exclusion, thus showing a reduced gaze-cueing effect.
A Simple Model for Predicting the Number and Duration of Rebuffering Events for YouTube Flows

In this paper, we propose a simple model for predicting the number of rebuffering events and their duration in progressive downloads from YouTube. These metrics are necessary to predict the quality perceived by YouTube users. The proposed rebuffering model is based on two thresholds of the amount of data stored by the player buffer: the first threshold is extracted from the results of previous studies, and the second is derived from the experimental results presented in this paper. The proposed model can be easily implemented in simulation tools and we present an example of its use in a Long-Term Evolution simulator in which the mentioned quality metrics have been estimated for different users.
Application of functional genomics in allergy and clinical immunology

Although microarray as a research tool seems to be new, the idea of detection of multiple gene expression during one experiment has been present for many years, perhaps starting with reprobing Northern blots with various probes. More recently, RNase protection assay with multiple probes, differential display and serial analysis of gene expression (SAGE) (1) were used. These techniques, although laborious, allowed expression detection of up to 20 or so genes in one RNA sample. The current response to this demand was cDNA microarray developed by Patrick Brown and his group in 1994 (2, 3). That was based on cDNAs encoding genes of interest synthesized using standard reverse transcription technology and printed on glass slides using an in-house automatic printer. RNA was reverse transcribed using labeled nucleotides and hybridized to cDNA. The intensity of fluorescence was read by a computerized array reader. This system was able to detect expression of 1024 genes in a sample. A commercial response was delivered early by Affymetrics, which developed a chip using 22–25 base oligonucleotides placed on a plastic surface and using 18–30 oligonucleotides per gene assayed. mRNA is reverse transcribed to obtain cDNA. The cDNA is then transcribed with biotin-labeled nucleotides to create biotin-labeled cRNA. Oligonucletide chips are hybridized with biotin-labeled cRNA and the abundance of specific transcript was obtained by reading the chip in a laser scanner. Total fluorescence obtained according to the complex algorithm from sense and missense probes is proportional to gene expression in the original sample. These two technologies (oligonucleotide array and cDNA microarray) have been developed in parallel and may be used in parallel or sequential fashion. Although both have advantages and drawbacks, they set up a standard in whole genome expression assessment. The following paragraph summarizes the basic aspects of both technologies and delivers a comparison of them.
Significant Adhesion Reduction with 4DryField PH after Release of Adhesive Small Bowel Obstruction

Abstract Background Peritoneal adhesions reoccur in up to 100% of cases, possibly causing complications like pain, secondary female infertility, and small bowel obstruction. The latter has a mortality rate of up to 15% during hospitalization. This study investigates if recurrence of peritoneal adhesions can be prevented by prophylactic use of the starch-based medical device 4DryField. Methods The course of 40 patients with surgery for intestinal obstruction and, partially, second intervention was analyzed. In both operations, adhesion severity and extent were scored 0 (no adhesions) to III (massive/dense and vascular adhesions) and 0 (no adhesions) to III (extensive, covering more than approximately 25 × 25 cm), respectively. To prevent recurrence of adhesions all patients were treated with 4DryField gel (60 mL saline solution per 5 g powder), evenly distributed on the whole impaired intestine (including anastomoses) before abdominal closure. Follow-up was up to 1.5 years in a 3 to 6 months' interval. Results Eight patients had relaparotomies on postoperative days 1 to 155. In the first operation, median adhesion severity score was III, median adhesion extent II. In redo-surgeries, significantly lower scores were detected (median adhesion severity: 0, p = 0.0003; median adhesion extent: 0, p = 0.0009). No adverse events related to the product were observed. One patient had later redo-surgery in another hospital due to recurrence of adhesions, one patient suffered from flatulence. All other patients were free of adhesion-related symptoms during follow-up. Conclusion Based on the high severity of diseases and the significant reduction of adhesion severity and extent in redo-surgeries, 4DryField gel is a promising adjunct for adhesion prevention in bowel surgery. The favorable results should be confirmed in prospective randomized trials.
A Clonal Lineage of VanA-Type Enterococcus faecalis Predominates in Vancomycin-Resistant Enterococci Isolated in New Zealand

ABSTRACT Avoparcin was used as a feed additive in New Zealand broiler production from 1977 until June 2000. We report here on the effects of the usage and discontinuation of avoparcin on the prevalence of vancomycin-resistant enterococci (VRE) in broilers. Eighty-two VRE isolates were recovered from poultry fecal samples between 2000 and mid-2001. VRE isolates were only obtained from broiler farms that were using, or had previously used, avoparcin as a dietary supplement. Of these VRE isolates, 73 (89%) were VanA-type Enterococcus faecalis and nine (11%) were VanA-type Enterococcus faecium. All E. faecalis isolates were found to have an identical or closely related pulsed-field gel electrophoresis (PFGE) pattern of SmaI-digested DNA and were susceptible to both ampicillin and gentamicin. The PFGE patterns of the nine E. faecium isolates were heterogeneous. All VRE contained both the vanA and ermB genes, which, regardless of species or PFGE pattern, resided on the same plasmid. Eighty-seven percent of the VRE isolates also harbored the tet(M) gene, while for 63 and 100%, respectively, of these isolates, the avilamycin and bacitracin MICs were high (≥256 μg/ml). Five of eight vancomycin-resistant E. faecalis isolates recovered from humans in New Zealand revealed a PFGE pattern identical or closely related to that of the E. faecalis poultry VRE isolates. Molecular characterization of Tn1546-like elements from the VRE showed that identical transposons were present in isolates from poultry and humans. Based on the findings presented here, a clonal lineage of VanA-type E. faecalis dominates in VRE isolated from poultry and humans in New Zealand.