Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Biology and Crystallization Communications Serial Femtosecond X-ray Diffraction of 30s Ribosomal Subunit Microcrystals in Liquid Suspension at Ambient Temperature Using an X-ray Free-electron Laser

High-resolution ribosome structures determined by X-ray crystallography have provided important insights into the mechanism of translation. Such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. Here, the application of serial femtosecond X-ray crystallography (SFX) using an X-ray free-electron laser (XFEL) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30S ribosomal subunit microcrystals diffracted to beyond 6 A ˚ resolution, demonstrating the feasibility of using SFX for ribosome structural studies. The ability to collect diffraction data at near-physiological temperatures promises to provide fundamental insights into the structural dynamics of the ribosome and its functional complexes.
Get the Message

Results from three studies demonstrate that victims’ justice-related satisfaction with punishment is influenced by the kind of feedback they receive from offenders after punishment. In contrast to previous studies that found a discrepancy between anticipated and experienced satisfaction from punishment (Carlsmith, Wilson, & Gilbert, 2008), participants were able to accurately predict their satisfaction when made aware of the presence or absence of offender feedback acknowledging the victim’s intent to punish. Results also indicate that victims were most satisfied when offender feedback not only acknowledged the victim’s intent to punish but also indicated a positive moral change in the offender’s attitude toward wrongdoing. These findings indicate that punishment per se is neither satisfying nor dissatisfying but that it is crucial to take its communicative functions and its effects on the offender into account. Implications for psychological and philosophical theories on punishment motives as well as implications for justice procedures are discussed.
Levy-Funded Research Choices by Producers and Society

Commodity levies are used increasingly to fund producer collective goods such as research and promotion. In the present paper we examine theoretical relationships between producer and national benefits from levy-funded research, and consider the implications for the appropriate rates of matching government grants, applied with a view to achieving a closer match between producer and national interests. In many cases the producer and national optima coincide. First, regardless of the form of the supply shift, when product demand is perfectly elastic, or all the product is exported, domestic benefits and costs of levy-funded research all go to producers and they have appropriate incentives. Second, if research causes a parallel supply shift, the producer share of research benefits is the same as their share of costs of a levy, and their incentives are compatible with national interests. In such cases, a matching grant would cause an over-investment in research from a national perspective. However, if demand is less than perfectly elastic, and research causes a pivotal supply shift, the producer share of benefits is smaller than their share of costs of the levy, and they will under-invest in research from a national point of view. A matching grant can be justified in such cases, however the magnitude of the optimal grant is sensitive to market conditions.
Networked vehicles for automated fault detection

Creating fault detection software for complex mechatronic systems (e.g. modern vehicles) is costly both in terms of engineer time and hardware resources. With the availability of wireless communication in vehicles, information can be transmitted from vehicles to allow historical or fleet comparisons. New networked applications can be created that, e.g., monitor if the behavior of a certain system in a vehicle deviates compared to the system behavior observed in a fleet. This allows a new approach to fault detection that can help reduce development costs of fault detection software and create vehicle individual service planning. The COSMO (COnsensus Self-organized MOdeling) methodology described in this paper creates a compact representation of the data observed for a subsystem or component in a vehicle. A representation that can be sent to a server in a backoffice and compared to similar representations for other vehicles. The backoffice server can collect representations from a single vehicle over time or from a fleet of vehicles to define a norm of the vehicle condition. The vehicle condition can then be monitored, looking for deviations from the norm. The method is demonstrated for measurements made on a real truck driven in varied conditions with ten different generated faults. The proposed method is able to detect all cases without prior information on what a fault looks like or which signals to use.
A disconnection-tolerant transport for drive-thru Internet environments

Today's mobile, wireless, and ad-hoc communications often exhibit extreme characteristics challenging assumptions underlying the traditional way of end-to-end communication protocol design in the Internet. One specific scenario is Internet access from moving vehicles on the road as we are researching in the drive-thru Internet project. Using wireless LAN as a broadly available access technology leads to intermittent - largely unpredictable and usually short-lived - connectivity, yet providing high performance while available. To allow Internet applications to deal reasonably well with such intermittent connectivity patterns, we have introduced a supportive drive-thru architecture. A key component is a "session" protocol offering persistent end-to-end communications even in the presence of interruptions. In this paper, we present the design of the persistent connectivity management protocol (PCMP) and report on findings from our implementation.
Squinted TOPS SAR Imaging Based on Modified Range Migration Algorithm and Spectral Analysis

For the squinted terrain observation by progressive scans (TOPS) imaging mode, three problems need to be considered: azimuth spectrum aliasing, serious range-azimuth coupling, and azimuth time aliasing after range cell migration correction (RCMC). For these problems, a subaperture imaging algorithm based on the modified range migration algorithm (RMA) combined with spectral analysis (SPECAN) is proposed in this letter. Echo data are properly divided into subapertues so that the 2-D spectrum of each subaperture without aliasing can be obtained; then, the modified RMA is used to perform RCMC; finally, the signal is focused in the Doppler domain by SPECAN and deramping after subaperture recombination. Both simulated and real SAR data in the squinted TOPS mode are used to validate the proposed algorithm.
Effect of osmotic shrinkage and hormones on the expression of Na+/H+ exchanger-1, Na+/K+/2Cl– cotransporter and Na+/K+-ATPase in gill pavement cells of freshwater adapted Japanese eel, Anguilla japonica

SUMMARY It is well-known that gill epithelial cells are important in fish osmoregulation. However, studies on the effect of osmotic stress on the direct cellular responses of the gill epithelial cells are limited. In this paper, we aimed to determine the effects of osmotic hypertonicity, hormones and cellular signaling molecules on the expression of ion transporters in the cultured primary freshwater pavement cells (PVCs), prepared from freshwater-adapted eels (Anguilla japonica). Our data demonstrated that the hypertonic (500 mOsmol l–1) treatment of the isolated PVCs induced cell shrinkage, followed by regulatory volume increase (RVI). Application of blockers (i.e. ouabain, bumetanide and EIPA) demonstrated that Na+/K+-ATPase, Na+/K+/2Cl– cotransporter (NKCC) and Na+/H+ exchanger-1 (NHE-1) were involved in RVI. Western blot analysis of the hypertonic-treated cells revealed a significant induction of NHE-1, NKCC and, α and β subunits of Na+/K+-ATPase. In nonshrunken cultured PVCs, we found that dexamethasone and dibutyryl cAMP treatments significantly stimulated the expression levels of the three ion transporters. Both prolactin and insulin-like growth factor-1, can only induce the expression of NKCC. The effect of thyroid hormone (T3) and dibutyryl cGMP was negligible. In this study, the induction of ion transporter expression was found to be post-transcriptionally regulated as no significant change in mRNA levels was detected. This observation implies that the regulation is rapid and is probably induced via nongenomic actions.
Smartphone-Based Solutions for Fall Detection and Prevention: Challenges and Open Issues

This paper presents a state-of-the-art survey of smartphone (SP)-based solutions for fall detection and prevention. Falls are considered as major health hazards for both the elderly and people with neurodegenerative diseases. To mitigate the adverse consequences of falling, a great deal of research has been conducted, mainly focused on two different approaches, namely, fall detection and fall prevention. Required hardware for both fall detection and prevention are also available in SPs. Consequently, researchers' interest in finding SP-based solutions has increased dramatically over recent years. To the best of our knowledge, there has been no published review on SP-based fall detection and prevention. Thus in this paper, we present the taxonomy for SP-based fall detection and prevention solutions and systematic comparisons of existing studies. We have also identified three challenges and three open issues for future research, after reviewing the existing articles. Our time series analysis demonstrates a trend towards the integration of external sensing units with SPs for improvement in usability of the systems.
Thermal Adaptation of the Archaeal and Bacterial Lipid Membranes

The physiological characteristics that distinguish archaeal and bacterial lipids, as well as those that define thermophilic lipids, are discussed from three points of view that (1) the role of the chemical stability of lipids in the heat tolerance of thermophilic organisms: (2) the relevance of the increase in the proportion of certain lipids as the growth temperature increases: (3) the lipid bilayer membrane properties that enable membranes to function at high temperatures. It is concluded that no single, chemically stable lipid by itself was responsible for the adaptation of surviving at high temperatures. Lipid membranes that function effectively require the two properties of a high permeability barrier and a liquid crystalline state. Archaeal membranes realize these two properties throughout the whole biological temperature range by means of their isoprenoid chains. Bacterial membranes meet these requirements only at or just above the phase-transition temperature, and therefore their fatty acid composition must be elaborately regulated. A recent hypothesis sketched a scenario of the evolution of lipids in which the “lipid divide” emerged concomitantly with the differentiation of archaea and bacteria. The two modes of thermal adaptation were established concurrently with the “lipid divide. ”
Polycyclic Aromatic Hydrocarbon-Induced Changes in Bacterial Community Structure under Anoxic Nitrate Reducing Conditions

Although bacterial anaerobic degradation of mono-aromatic compounds has been characterized in depth, the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene has only started to be understood in sulfate reducing bacteria, and little is known about the anaerobic degradation of PAHs in nitrate reducing bacteria. Starting from a series of environments which had suffered different degrees of hydrocarbon pollution, we used most probable number (MPN) enumeration to detect and quantify the presence of bacterial communities able to degrade several PAHs using nitrate as electron acceptor. We detected the presence of a substantial nitrate reducing community able to degrade naphthalene, 2-methylnaphthalene (2MN), and anthracene in some of the sites. With the aim of isolating strains able to degrade PAHs under denitrifying conditions, we set up a series of enrichment cultures with nitrate as terminal electron acceptor and PAHs as the only carbon source and followed the changes in the bacterial communities throughout the process. Results evidenced changes attributable to the imposed nitrate respiration regime, which in several samples were exacerbated in the presence of the PAHs. The presence of naphthalene or 2MN enriched the community in groups of uncultured and poorly characterized organisms, and notably in the Acidobacteria uncultured group iii1-8, which in some cases was only a minor component of the initial samples. Other phylotypes selected by PAHs in these conditions included Bacilli, which were enriched in naphthalene enrichments. Several nitrate reducing strains showing the capacity to grow on PAHs could be isolated on solid media, although the phenotype could not be reproduced in liquid cultures. Analysis of known PAH anaerobic degradation genes in the original samples and enrichment cultures did not reveal the presence of PAH-related nmsA-like sequences but confirmed the presence of bssA-like genes related to anaerobic toluene degradation. Altogether, our results suggest that PAH degradation by nitrate reducing bacteria may require the contribution of different strains, under culture conditions that still need to be defined.
The Earliest Phases of Star Formation (EPoS): a Herschel key project - The thermal structure of low-mass molecular cloud cores

Context. The temperature and density structure of molecular cloud cores are the most important physical quantities that determine the course of the protostellar collapse and the properties of the stars they form. Nevertheless, density profiles often rely either on the simplifying assumption of isothermality or on observationally poorly constrained model temperature profiles. The instruments of the Herschel satellite provide us for the first time with both the spectral coverage and the spatial resolution that is needed to directly measure the dust temperature structure of nearby molecular cloud cores. Aims. With the aim of better constraining the initial physical conditions in molecular cloud cores at the onset of protostellar collapse, in particular of measuring their temperature structure, we initiated the guaranteed time key project (GTKP) "The Earliest Phases of Star Formation" (EPoS) with the Herschel satellite. This paper gives an overview of the low-mass sources in the EPoS project, the Herschel and complementary ground-based observations, our analysis method, and the initial results of the survey. Methods. We study the thermal dust emission of 12 previously well-characterized, isolated, nearby globules using FIR and submm continuum maps at up to eight wavelengths between 100 mu m and 1.2 mm. Our sample contains both globules with starless cores and embedded protostars at different early evolutionary stages. The dust emission maps are used to extract spatially resolved SEDs, which are then fit independently with modified blackbody curves to obtain line-of-sight-averaged dust temperature and column density maps. Results. We find that the thermal structure of all globules (mean mass 7 M-circle dot) is dominated by external heating from the interstellar radiation field and moderate shielding by thin extended halos. All globules have warm outer envelopes (14-20 K) and colder dense interiors (8-12 K) with column densities of a few 10(22) cm(-2). The protostars embedded in some of the globules raise the local temperature of the dense cores only within radii out to about 5000 AU, but do not significantly affect the overall thermal balance of the globules. Five out of the six starless cores in the sample are gravitationally bound and approximately thermally stabilized. The starless core in CB 244 is found to be supercritical and is speculated to be on the verge of collapse. For the first time, we can now also include externally heated starless cores in the L-smm/L-bol vs. T-bol diagram and find that T-bol <25 K seems to be a robust criterion to distinguish starless from protostellar cores, including those that only have an embedded very low-luminosity object.
Multilevel Passenger Screening Strategies for Aviation Security Systems

Passenger prescreening is a critical component of aviation security. This paper introduces the Multilevel Allocation Problem (MAP), which models the screening of passengers and baggage in a multilevel aviation security system. A passenger is screened by one of several classes, each of which corresponds to a set of procedures using security screening devices, where passengers are differentiated by their perceived risk levels. Each class is defined in terms of its fixed cost (the overhead costs), its marginal cost (the additional cost to screen a passenger), and its security level. The objective of MAP is to assign each passenger to a class such that the total security is maximized subject to passenger assignments and budget constraints. This paper shows that MAP is NP-hard, introduces two dynamic programming algorithms for solving MAP in pseudo-polynomial time, and introduces a Greedy heuristic that obtains approximate solutions to MAP that use no more than two classes. Examples are constructed using data extracted from the Official Airline Guide (OAG). Analysis of the examples suggests that fewer security classes for passenger screening may be more effective and that using passenger risk information can lead to more effective security screening strategies.
A quantitative study of the effects of cholinergic drugs on carotid chemoreceptors in the cat.

1. Conflicting qualitative evidence exists concerning the effects on chemoreceptor activity of some drugs which influence the cholinergic system. Quantitative evidence has been obtained in the present study which should resolve the conflict. 2. Experiments were performed in pentobarbitone‐anaesthetized cats in which the activity of chemoreceptor units in the sinus nerve was used to assess chemoreceptor responses. The effects of drugs on responses to I.A. ACH and NaCN were determined from dose‐response data obtained from several animals and expressed as mean dose ratios 3. The chemoreceptor response to ACh was slightly inhibited by atropine, alpha‐ and beta‐bungarotoxin and HC‐3, almost completely suppressed by mecamylamine, and markedly potentiated by physostigmine. 4. Concomitant responses to NaCN were unaffected by atropine, beta‐bungarotoxin, mecamylamine or physostigmine. There was a slight inhibition following alpha‐bungarotoxin and a potentiation after HC‐3. 5. The results do not support the theory that ACh is an excitatory sensory transmitter in the carotid body.
Probabilistic Combination of Features for Music Classification

We describe an approach to the combination of music similarity feature spaces in the context of music classification. The approach is based on taking the product of posterior probabilities obtained from separate classifiers for the different feature spaces. This allows for a different influence of the classifiers per song and an overall classification accuracy improving those resulting from individual feature spaces alone. This is demonstrated by combining spectral and rhythmic similarity for classification of ballroom dance music.
VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data

This work is in line with an on-going effort tending toward a computational (quantitative and refutable) understanding of human neuro-cognitive processes. Many sophisticated models for behavioural and neurobiological data have flourished during the past decade. Most of these models are partly unspecified (i.e. they have unknown parameters) and nonlinear. This makes them difficult to peer with a formal statistical data analysis framework. In turn, this compromises the reproducibility of model-based empirical studies. This work exposes a software toolbox that provides generic, efficient and robust probabilistic solutions to the three problems of model-based analysis of empirical data: (i) data simulation, (ii) parameter estimation/model selection, and (iii) experimental design optimization.
An empirical study on the efficiency of graphical vs. textual representations in requirements comprehension

Graphical representations are used to visualise, specify, and document software artifacts in all stages of software development process. In contrast with text, graphical representations are presented in two-dimensional form, which seems easy to process. However, few empirical studies investigated the efficiency of graphical representations vs. textual ones in modelling and presenting software requirements. Therefore, in this paper, we report the results of an eye-tracking experiment involving 28 participants to study the impact of structured textual vs. graphical representations on subjects' efficiency while performing requirement comprehension tasks. We measure subjects' efficiency in terms of the percentage of correct answers (accuracy) and of the time and effort spend to perform the tasks. We observe no statistically-significant difference in term of accuracy. However, our subjects spent more time and effort while working with the graphical representation although this extra time and effort does not affect accuracy. Our findings challenge the general assumption that graphical representations are more efficient than the textual ones at least in the case of developers not familiar with the graphical representation. Indeed, our results emphasise that training can significantly improve the efficiency of our subjects working with graphical representations. Moreover, by comparing the visual paths of our subjects, we observe that the spatial structure of the graphical representation leads our subjects to follow two different strategies (top-down vs. bottomup) and subsequently this hierarchical structure helps developers to ease the difficulty of model comprehension tasks.
Seasonal variation of human semen parameters: A retrospective study in Italy

Introduction: Human infertility is a common condition secondary to many primary or secondary causes. As for these latter, different seasonal and climatic patterns have been hypothesized to play a role. The aim of this study was to assess the presence of a possible seasonal pattern in the functional parameters of semen samples maintained in a large tertiary center database. Materials and methods: The reports of spermograms of 5188 consecutive subjects, collected at the Center for Reproductive Incapacity of the University Hospital of Parma during a 11-year period (2003–2014), were retrospectively analyzed. The reports included sperm motility, volume, and number, as well as pH, swelling and eosin tests. Data of different parameters were analyzed by season of sample collection. The ANOVA test was used for the evaluation of continuous variables, after Log transformation in case of a non-normal distribution, while χ2 test was used for categorical variables. Moreover, logistic regression analysis was performed, to identify factors independently associated with normal sperm motility. Results: Compared with the other seasons of the year, a higher sperm motility was found during the summer. Moreover, the prevalence of samples with a normal sperm pH (7.2–8) was higher during the spring, whilst the volume of sperm was higher in winter. Logistic regression analysis showed that normal sperm motility (>40%) was independently associated with spring (1.227; 95% CI 1.077–1.507, p = 0.005), summer (2.031; 95% CI 1.689–2.442, p < 0.001), swelling test (1.953; 95% CI 1.670–2.284, p < 0.001), eosin test (2.804; 95% CI 2.477–3.174, p < 0.001), pH (0.507; 95% CI 0.346–0.743, p < 0.001), LOG-number (2.949; 95% CI 2.470–3.522, p < 0.001) and LOG-volume (2.216; 95% CI 1.696–2.894, p < 0.001) of semen. Conclusion: This study suggests the existence of a positive relationship between some semen parameters and seasons.