Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Photodynamic Therapy on the Virulence Factors of Staphylococcus aureus

Staphylococcus aureus is a Gram-positive bacterium that is present in the human microbiota. Nevertheless, these bacteria can be pathogenic to the humans. Due to the increasing occurrence of antibiotic-resistant S. aureus strains, new approaches to control this pathogen are necessary. The antimicrobial photodynamic inactivation (PDI) process is based in the combined use of light, oxygen, and an intermediary agent (a photosensitizer). These three components interact to generate cytotoxic reactive oxygen species that irreversibly damage vital constituents of the microbial cells and ultimately lead to cell death. Although PDI is being shown to be a promising alternative to the antibiotic approach for the inactivation of pathogenic microorganisms, information on effects of photosensitization on particular virulence factors is strikingly scarce. The objective of this work was to evaluate the effect of PDI on virulence factors of S. aureus and to assess the potential development of resistance of this bacterium as well as the recovery of the expression of the virulence factors after successive PDI cycles. For this, the photosensitizer 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetra-iodide (Tetra-Py+-Me) and six strains of S. aureus [one reference strain, one strain with one enterotoxin, two strains with three enterotoxins and two methicillin resistant strains (MRSA) – one with five enterotoxins and the other without enterotoxins] were used. The effect of photosensitization on catalase activity, beta hemolysis, lipases, thermonuclease, enterotoxins, coagulase production, and resistance/susceptibility to methicillin was tested. To assess the development of resistance after successive cycles of treatment, three strains of S. aureus (ATCC 6538, 2065 MA, and SA 3 MRSA) were used. The surviving colonies of a first cycle of PDI were collected from the solid medium and subjected to further nine consecutive cycles of PDI. The results indicate that the expression of some external virulence factors is affected by PDI and enterotoxin producing strains were more susceptible to PDI than non-toxigenic strains. The surviving bacteria did not develop resistance. PDI, contrarily to traditional antibiotics, inhibited the expression of virulence factors, efficiently inactivating either highly virulent strains and low virulent S. aureus strains, inactivating also antibiotic susceptible and resistant strains, without development of photoresistance after at least 10 consecutive cycles of treatment, and so this therapy may become a strong promising alternative to antibiotics to control pathogenic microorganisms.
Dynamic coupling of excitatory and inhibitory responses in the medial nucleus of the trapezoid body

The neuronal representation of acoustic amplitude modulations is an important prerequisite for understanding the processing of natural sounds. We investigated this representation in the medial nucleus of the trapezoid body (MNTB) of the Mongolian gerbil using sinusoidal amplitude modulations (SAM). Depending on the SAM’s carrier frequency (fC) MNTB cells either increase or decrease their discharge rates, indicating underlying excitatory and inhibitory/suppressive mechanisms. As natural sounds typically are composed of multiple spectral components we investigated how stimuli containing two spectral components are represented in the MNTB, especially when they have opposing effects on the discharge rate. Three conditions were compared: SAM stimuli (1) with rate‐increasing fC, (2) with rate‐increasing fC and an additional unmodulated rate‐decreasing pure tone, and (3) with rate‐decreasing fC and an unmodulated, rate‐increasing pure tone. We found that responses under all three conditions showed comparable strength of phase‐locking. Adding a rate‐decreasing tone to a rate‐increasing SAM increased phase‐locking for modulation frequencies (fAM) of ≤ 600 Hz. A comparison of two possible coding strategies – phase‐locking vs. envelope reproduction – indicates that both strategies are realized to different degrees depending on the fAM. We measured latencies for following modulations in rate‐increasing and rate‐decreasing SAMs using a modified reverse correlation approach. Although latencies varied between 2.5 and 5 ms between cells, a decrease in rate consistently followed an increase in rate with a delay of about 0.2 ms in each cell. These results suggest a temporally precise representation of rate‐increasing and rate‐decreasing stimuli at the level of the MNTB during dynamic stimulation.
iPack: in-Network Packet Mixing for High Throughput Wireless Mesh Networks

A major barrier for the adoption of wireless mesh networks is severe limits on throughput. Many in-network packet mixing techniques at the network layer [1], [2], [3] as well as the physical layer [4], [5], [6] have been shown to substantially improve throughput. However, the optimal mixing algorithm that maximizes throughput is still unknown. In this paper, we propose iPack, an algorithm for in-network generation of composite packets that integrates coding at two different layers of the protocol stack: XOR-based network coding and physical layer superposition coding. Using extensive simulations, we find that the throughput gain of the joint coding iPack algorithm is 30% more than the better performer of network coding and superposition coding in a wide range of scenarios, and automatically takes advantage of the best available coding opportunities. In a typical wireless mesh network when more traffic is between the clients and access points, the average throughput improvement of iPack, our joint optimization scheduler, can be 324%, while there can be little gain (less than 10%) if network coding alone is used. We also validate our results by implementing iPack on a small-scale testbed based on GNU Radio.
Reference metadata extraction from scientific papers

Bibliographical information of scientific papers is of great value since the Science Citation Index is introduced to measure research impact. Most scientific documents available on the web are unstructured or semi-structured, and the automatic reference metadata extraction process becomes an important task. This paper describes a framework for automatic reference metadata extraction from scientific papers. Our system can extract title, author, journal, volume, year, and page from scientific papers in PDF. We utilize a document metadata knowledge base to guide the reference metadata extraction process. The experiment results show that our system achieves a high accuracy.
Payments for Environmental Services in a Policymix: Spatial and Temporal Articulation in Mexico

Government based Payments for Ecosystem Services (PES) have been criticized for not maximizing environmental effectiveness through appropriate targeting, while instead prioritizing social side-objectives. In Mexico, existing literature on how the Payments for Ecosystem Services-Hydrological program (PSA-H) has targeted deforestation and forest degradation shows that both the process of identifying the eligible areas and the choice of the selection criteria for enrolling forest parcels have been under the influence of competing agendas. In the present paper we study the influence of the PSA-H multi-level governance on the environmental effectiveness of the program–the degree to which forest at high risk of deforestation is enrolled- building from a “policyscape” framework. In particular, we combine governance analysis with two distinct applications of the policyscape framework: First, at national level we assess the functional overlap between the PSA-H and other environmental and rural programs with regard to the risk of deforestation. Second, at regional level in the states of Chiapas and Yucatan, we describe the changing policy agenda and the role of technical intermediaries in defining the temporal spatialization of the PSA-H eligible and enrolled areas with regard to key socio-economic criteria. We find that, although at national level the PSA-H program has been described as coping with both social and environmental indicators thanks to successful adaptive management, our analysis show that PSA-H is mainly found in communities where deforestation risk is low and in combination with other environmental programs (protected areas and forest management programs). Such inertia is reinforced at regional level as a result of the eligible areas’ characteristics and the behaviour of technical intermediaries, which seek to minimise transaction costs and sources of uncertainty. Our project-specific analysis shows the importance of integrating the governance of a program in the policyscape framework as a way to better systematize complex interactions at different spatial and institutional scales between policies and landscape characteristics.
Efficient cache architectures for reliable hybrid voltage operation using EDC codes

Semiconductor technology evolution enables the design of sensor-based battery-powered ultra-low-cost chips (e.g., below 1 €) required for new market segments such as body, urban life and environment monitoring. Caches have been shown to be the highest energy and area consumer in those chips. This paper proposes a novel, hybrid-operation (high Vcc, ultra-low Vcc), single-Vcc domain cache architecture based on replacing energy-hungry bitcells (e.g., 10T) by more energy-efficient and smaller cells (e.g., 8T) enhanced with Error Detection and Correction (EDC) features for high reliability and performance predictability. Our architecture is proven to largely outperform existing solutions in terms of energy and area.
The ability of early changes in motivation to predict later antidepressant treatment response

Introduction Baseline values and early changes of emotional reactivity, cognitive speed, psychomotor function, motivation, and sensory perception have not been studied to any extent in unipolar depression, although they could help to characterize different dimensions of illness that are harder to capture by clinicians, give new insights on how patients improve, and offer new early clinical markers for later treatment response. Methods About 1,565 adult outpatients with major depressive disorder receiving agomelatine completed the clinician-rated 16-item quick inventory of depressive symptoms, Clinical Global Impression, and Multidimensional Assessment of Thymic States (MAThyS) rating scales at inclusion, Week 2 and Week 6. The MAThyS includes a 20-item self-rated visual analog scale (from inhibition [0] to activation [10], with [5] representing the usual state) leading to five a priori dimensions (emotional reactivity, cognitive speed, psychomotor function, motivation, and sensory perception). Results All MAThyS dimension scores increased from inclusion to Week 2 and from inclusion to Week 6 (P<0.001). Improvement was around 2 points (out of 10) for motivation, 1.5 points for psychomotor function, and 0.5 points for other dimensions. Motivation showed a trend to being more severely impaired at inclusion in future nonresponders (t=1.25, df=1,563, P=0.10). Its improvement at Week 2 was the most discriminating MAThyS dimension between future responders and nonresponders, and represents the best predictor of future response, with the highest area under the receptor operating characteristic curve (area under curve =0.616, 95% confidence interval [0.588–0.643], P<0.001). Finally, improvements in motivation correlated the most strongly with clinician-rated 16-item quick inventory of depressive symptoms improvement (r=−0.491, df=1,563, P<0.001). Conclusion Motivation had the most capacity for early improvement, the best predictive value for response, and the largest global margin of progress in depressed outpatients. Assessing the evolution of self-reported motivation over time in major depressive disorder could offer an interesting complementary approach to predict response.
Crop identification with Sentinel-2 satellite imagery in Finland

European Union member countries are obligated to control the validity of Common Agricultural Policy subsidy applications. Each member country performs manual inspection for at least 5% of these subsidy applications. This is both expensive and a considerable administrative burden. According to European Union, the crop type identification process in Common Agricultural Policy could be carried out using remote sensing or orthophoto imagery for an alternative to physical inspections by competent authorities. Automated crop type identification would reduce the costs significantly. This master’s thesis addressed the crop identification with optical Sentinel-2 satellite imagery in Finland. The aim was to investigate whether it was possible to reliably identify the crop growing in land parcels by using machine learning classification methods. This thesis presented an automated approach of identifying crops. Multiple different machine learning classification algorithms were trained and tested to find out the most suitable processing method, time period and classification algorithm by utilizing the land parcels obtained from the Finnish Agency for Rural Affairs. The developed processing method and most of the tested classification algorithms were able to perform relatively well in crop identification in cloudy growth period 2017 of Finland. Therefore, the developed method could be applied to different use cases and cloudy weather conditions. The further development and training of the classification algorithms could make it possible to utilize this approach in Finland as well as in other EU countries for the Common Agricultural Policy control and possibly in numerous other tasks.
A Viterbi-based non-coherent DBPSK-demodulator with 1-bit quantization and digital differential decoding for AWGN channels

In this paper, we present a non-coherent differential binary phase-shift keying demodulation scheme with a 1-bit analogue-digital-converter, based on a novel likelihood-decoding scheme. It needs very little resources in both, the analogue and the digital domain. This is useful for simple receivers operating under frequency-flat channel conditions. The demodulation scheme was integrated in a complete transceiver based on a FPGA platform connected to a 60 GHz analogue frontend. In addition to the presented simulations, we measured the real system behavior in an office environment and showed a stable HD video transmission over a 60 GHz line-of-sight link.
Sunset Time and the Health Effects of Social Jetlag Evidence from US Time Zone Borders

This paper uses a spatial regression discontinuity design to identify the health effects of the misalignment between social and biological time induced by different sunset times and the fact that social schedules are not responsive to solar cues. Exploiting the discontinuity in the timing of natural light provided by the existence of time zones, we find that being exposed to more light in the evening has negative effects on sleep duration, increases obesity and diabetes prevalence, and the likelihood of reporting any cognitive impairment. Our results suggest that sleep is the main mechanisms explaining the effects on health and cognitive outcomes.
A quantitative study of neutrality in GP boolean landscapes

Neutrality of some boolean parity fitness landscapes is investigated in this paper. Compared with some well known contributions on the same issue, we define some new measures that help characterizing neutral landscapes, we use a new sampling methodology, which captures some features that are disregarded by uniform random sampling, and we introduce new genetic operators to define the neighborhood of tree structures. We compare the fitness landscape induced by two different sets of functional operators (SNand and SXorNot). The different characteristics of the neutral networks seem to justify the different difficulties of these landscapes for genetic programming.
An assessment of satellite-based agricultural water productivity over the Indian region

ABSTRACT The preliminary analysis of agricultural water productivity (AWP) over India using satellite data were investigated through productivity mapping, water use (actual evapotranspiration (ETa)/effective rainfall (Reff) mapping and water productivity mapping. Moderate Resolution Imaging Spectroradiometer data was used for generating agricultural land cover (MCD12Q1 at 500 m), gross primary productivity (GPP; MOD17A2 at 1 km), and ETa (MOD16A2 at 1 km). Reff was estimated at 10 km using the United States Department of Agriculture soil conservation service method from daily National Oceanic and Atmospheric Administration Climate Prediction Center rainfall data. Six years’ (2007–2012) data were analysed from June to October. The seasonal AWP and rainwater productivity (RWP) were estimated using the ratios of seasonal GPP (kg C m−2) and water use (mm) maps. The average AWP and RWP ranges from 1.10–1.30 kg Cm−3 and 0.94–1.0 kg C m−3, respectively, with no significant annual variability but a wide spatial variability over India. The highest AWP was observed in northern India (1.22–1.80 kg C m−3) and lowest in western India (0.81–1.0 kg C m−3). Large variations in AWP (0.69–1.80 kg C m−3) were observed in Himachal Pradesh, Jammu and Kashmir, northeastern states (except Assam), Kerala, and Uttaranchal. The low GPP of these areas (0.0013–0.13 kg C m−2) with low seasonal total ETa (<101 mm) and Reff (<72 mm) making the AWP high that do not correspond to high productivity but possible water stress. Gujarat, Rajasthan, Maharashtra, Madhya Pradesh, Jharkhand, and Karnataka showed low AWP (0.73–1.13 kg C m−3) despite having high ETa (261–558 mm) and high Reff (287–469 mm), indicating significant scope for improving productivity. The highest RWP was observed in northern parts and Indo-Gangetic plains (0.80–1.6 kg C m−3). The 6 years’ analysis reveals the status of AWP, leading to appropriate interventions to better manage land and water resources, which have great importance in global food security analysis.
Extending the automated zoning procedure to reconcile incompatible zoning systems

This paper concerns the problem of matching incompatible zonal geographies, for example in the context of comparing census outputs over time. The automated zoning procedure (AZP) proposed by Openshaw (1977) is reviewed and extended to permit its application to the intersection of two zonal systems. A population stress statistic is proposed which may be used in the extended AZP algorithm in order to maximise the match between two zonal geographies. An implementation of this approach is described, and illustrated by reference to UK Census data.
Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2

Signal transduction events are often mediated by small protein domains such as SH2 (Src homology 2) domains that recognize phosphotyrosines (pY) and flanking sequences. In case of the SHP-2 receptor tyrosine phosphatase an N-terminal SH2 domain binds and inactivates the phosphatase (PTP) domain. The pY-peptide-binding site on the N-terminal SH2 domain does not overlap with the PTP binding region. Nevertheless, pY-peptide binding causes domain dissociation and phosphatase activation. Comparative multi-nanosecond molecular dynamics simulations on the N-SH2 domain in ligand-bound and free states have been performed to study the allosteric mechanism that leads to domain dissociation upon pY-peptide binding. Significant ligand-dependent differences in the conformational flexibility of regions that are involved in SH2-PTP domain association have been observed. The results support a mechanism of signal transduction where SH2-peptide binding modulates the domain flexibility and reduces its capacity to fit into the entrance of the PTP catalytic domain of SHP-2.
Photoinitiated Polymerization: Advances, Challenges, and Opportunities

The use of photoinitiated polymerization is continuously growing in industry as reflected by the large number of applications in not only conventional areas such as coatings, inks, and adhesives but also high-tech domains, optoelectronics, laser imaging, stereolithography, and nanotechnology. In this Perspective, the latest developments in photoinitiating systems for free radical and cationic polymerizations are presented. The potential use of photochemical methods for step-growth polymerization is also highlighted. The goal is, furthermore, to show approaches to overcome problems associated with the efficiency, wavelength flexibility, and environmental and safety issues in all photoinitiating systems for different modes of activation. Much progress has been made in the past 10 years in the preparation of complex and nano-structured macromolecules by using photoinitiated polymerizations. Thus, the new and emerging applications of photoinitiated polymerizations in the field of biomaterials, surface modific.
Bundled execution of recurring traces for energy-efficient general purpose processing

Technology scaling has delivered on its promises of increasing device density on a single chip. However, the voltage scaling trend has failed to keep up, introducing tight power constraints on manufactured parts. In such a scenario, there is a need to incorporate energy-efficient processing resources that can enable more computation within the same power budget. Energy efficiency solutions in the past have typically relied on application specific hardware and accelerators. Unfortunately, these approaches do not extend to general purpose applications due to their irregular and diverse code base. Towards this end, we propose BERET, an energy-efficient co-processor that can be configured to benefit a wide range of applications. Our approach identifies recurring instruction sequences as phases of “temporal regularity” in a program's execution, and maps suitable ones to the BERET hardware, a three-stage pipeline with a bundled execution model. This judicious off-loading of program execution to a reduced-complexity hardware demonstrates significant savings on instruction fetch, decode and register file accesses energy. On average, BERET reduces energy consumption by a factor of 3–4X for the program regions selected across a range of general-purpose and media applications. The average energy savings for the entire application run was 35% over a single-issue in-order processor.
Low-overhead Secure Network Coding based on Chaotic Sequence

A minimum overhead secure network coding based on chaotic sequence is presented in this paper. And only the source need to be modified, intermediate nodes implement a classical distributed ne twork code. So the proposed scheme is applied to all the linear network coding. Combine the chaotic sequence with original source information vector, because of the high randomness and the sensitivity to initial state of chaotic sequence, the presented network code is "One-Time Pad (OTP)". So the secure network coding achieves complete secrecy. This scheme requires only one noisy symbol to be embedded in the original information symbol vector to achieve complete secrecy. The theoretical analysis confirm that this sch eme can achieve the information-theoretic security condition and the signalling overhead to obtain complete security is minimized, while the atta cker has limited wiretapping ability.