Miracle-dz/UniFAR-FTUs huggingface dataset:
Decoding of generic mental representations from functional MRI data using word embeddings

Several different groups have demonstrated the feasibility of building forward models of functional MRI data in response to concrete stimuli such as pictures or video, and of using these models to decode or reconstruct stimuli shown while acquiring test fMRI data. In this paper, we introduce an approach for building forward models of conceptual stimuli, concrete or abstract, and for using these models to carry out decoding of semantic information from new imaging data. We show that this approach generalizes to topics not seen in training, and provides a straightforward path to decoding from more complex stimuli such as sentences or paragraphs.
Feeding in darkness eliminates dependent growth suppression

KEYWORDS: Arctic charr, Feeding, Growth, Social interactions Growth performance of Arctic charr, Salvelinus alpinus, is depressed at low (<20 kg m ~) stocking densities and growth has been reported to reach a maximum when fish are stocked at densities of 50-70 kg m -3 (Wallace et al., 1988; Baker and Ayles, 1990; Jorgensen et al., 1993). Growth rates may, however, be high when fish are stocked at densities in excess of 100 kg m -3, provided that good water quality can be maintained (Wallace et al., 1988; Jcrgensen et al., 1993). The causes of growth depression of charr stocked at low densities are not known, but it has been suggested that aggressive behaviour, the formation of territories and the establishment of dominance hierarchies may be contributory factors (Jobling and Wandsvik, 1983; Jobling, 1985; Wallace et al., 1988; Brown et al., 1992). In a recent study, however, Jorgensen et aL (1993) did not find evidence that despotism, and the establishment of clear-cut dominance hierarchies, was a major factor contributing to growth suppression of the fish stocked at the lowest density (15 kg m-3). In this latter study, locomotory activity, food intake and growth rates were depressed in all individuals held at low stocking density. Food was offered continuously, and in excess, and, thus, the reasons for the growth suppression in these fish are still not clear. In the present report, data are presented showing that feeding in darkness eliminates the negative effects of low stocking density on growth in Arctic charr. In the current experiment, eight groups of individually tagged (FTF-69 fingerling tags, Floy Tag & Mfg), hatchery-reared Arctic charr with an initial average weight of 28 g were held in 90 1, circular tanks for a period of 44 days. Four groups were held under continuous light conditions and the remaining four under short-day (8L:16D) conditions. For groups held under both light regimes, the numbers of fish in two tanks were 25 and in the other two tanks 100. This corresponded to an initial stocking density of 10 and 36 kg m -3, respectively. All groups were fed in excess for 16 h each day on commercial dry pellets (FK Start, 2.5 mm), using automatic disc feeders. Feeding was carried out during the time of the day in which the short-day groups (8L:16D) experienced darkness. Water temperature was maintained at 8.0 °C. One week after the establishment of the groups (day 7), live weights of individual fish were recorded, and measurements were repeated on day 44. Specific growth rates (SGR, % day -1) were calculated as [(lnWT -- InWt) • 100]" (T - t) -~, where Wt and WT represent fish weights at the start (day 7) and the end of the experiment (day 44), respectively, and T - t represents the number of days between weighings. * Author to whom correspondence should be addressed. 0967-6120 © 1993 Chapman & Hall
From Multidrug- to Extensively Drug-Resistant Tuberculosis: Upward Trends as Seen from a 15-Year Nationwide Study

Background Emergence of extensively drug-resistant tuberculosis (XDR-TB) represents an enormous challenge to Public Health globally. Methods Progression towards XDR-TB was investigated in Belgium, a country with a typically low TB incidence, by analyzing the magnitude, characteristics, and treatment success of multidrug-resistant tuberculosis (MDR-TB) through a population-based study from 1994 to 2008. Results Among the 174 MDR-TB patients, 81% were foreign-born, 48% of these being asylum seekers. Although the number of MDR-TB patients remained stable through the study period at around 15 new cases annually, frequencies of resistance of the patients’ first MDR-TB isolate to second-line drugs increased, as well as the total number of antibiotics it was resistant to (p<0.001). XDR-TB cases were detected from 2002 onwards. For 24 patients, additional resistance to several second-line drugs was acquired during treatment. Molecular-guided investigations indicated little to no contribution of in-country clonal spread or exogenous re-infection. The increase of pre-XDR and XDR cases could be attributed to rising proportions of patients from Asia and Central and Eastern Europe (p<0.001) and an increase in the isolation of Beijing strains in these groups (p<0.001). Despite augmented resistance, the treatment success rate improved from 63.0% to 75.8% (p = 0.080) after implementation in 2005 of improved surveillance measures and therapeutic access. Conclusions Increasing severity in drug resistance patterns leading to more XDR- and “panresistant” TB cases in a country with a low TB incidence like Belgium represents a strong alert on worsening situations in other world regions and requires intense public health measures.
Sequence Diversity of rulA among Natural Isolates of Pseudomonas syringae and Effect on Function of rulAB-Mediated UV Radiation Tolerance

ABSTRACT The rulAB locus confers tolerance to UV radiation and is borne on plasmids of the pPT23A family in Pseudomonas syringae. We sequenced 14 rulA alleles from P. syringae strains representing seven pathovars and found sequence differences of 1 to 12% within pathovar syringae, and up to 15% differences between pathovars. Since the sequence variation withinrulA was similar to that of P. syringaechromosomal alleles, we hypothesized that rulAB has evolved over a long time period in P. syringae. A phylogenetic analysis of the deduced amino acid sequences of rulAresulted in seven clusters. Strains from the same plant host grouped together in three cases; however, strains from different pathovars grouped together in two cases. In particular, the rulAalleles from P. syringae pv. lachrymans and P. syringae pv. pisi were grouped but were clearly distinct from the other sequenced alleles, suggesting the possibility of a recent interpathovar transfer. We constructed chimeric rulABexpression clones and found that the observed sequence differences resulted in significant differences in UV (wavelength) radiation sensitivity. Our results suggest that specific amino acid changes in RulA could alter UV radiation tolerance and the competitiveness of theP. syringae host in the phyllosphere.
Detection of testosterone administration based on the carbon isotope ratio profiling of endogenous steroids: international reference populations of professional soccer players

Background and objectives: The determination of the carbon isotope ratio in androgen metabolites has been previously shown to be a reliable, direct method to detect testosterone misuse in the context of antidoping testing. Here, the variability in the 13C/12C ratios in urinary steroids in a widely heterogeneous cohort of professional soccer players residing in different countries (Argentina, Italy, Japan, South Africa, Switzerland and Uganda) is examined. Methods: Carbon isotope ratios of selected androgens in urine specimens were determined using gas chromatography/combustion/isotope ratio mass spectrometry (GC-C-IRMS). Results: Urinary steroids in Italian and Swiss populations were found to be enriched in 13C relative to other groups, reflecting higher consumption of C3 plants in these two countries. Importantly, detection criteria based on the difference in the carbon isotope ratio of androsterone and pregnanediol for each population were found to be well below the established threshold value for positive cases. Conclusions: The results obtained with the tested diet groups highlight the importance of adapting the criteria if one wishes to increase the sensitivity of exogenous testosterone detection. In addition, confirmatory tests might be rendered more efficient by combining isotope ratio mass spectrometry with refined interpretation criteria for positivity and subject-based profiling of steroids.
Fault friction parameters inferred from the early stages of afterslip following the 2003 Tokachi‐oki earthquake

[1] We use subdaily GPS time series of positions in the first 5 hours following the 2003 Tokachi-oki earthquake (Mw = 8.0) located offshore of Hokkaido, Japan, to estimate frictional parameters for the afterslip zone on the subduction interface. The data show little motion immediately after the earthquake with sudden acceleration at about 1.2 hours after the main shock. This coincides with the largest aftershock (M = 7.4), followed by gradual deceleration. We assume that early afterslip is the response of a fault patch to instantaneous stress perturbations caused by the main shock and the largest aftershock. Early afterslip is modeled with a spring-slider system obeying a rate- and state-dependent friction law. We develop and apply an inversion method to estimate friction parameters, Dc, aσ, and (a − b)σ, where σ is effective normal stress. The estimated 95% confidence intervals of Dc, aσ, and (a − b)σ are 2.6 × 10−4 to 1.8 × 10−3 m, 0.29 to 0.43 MPa, and 0.214 to 0.220 MPa, respectively. Estimated Dc is 10 to 103 times larger than typical laboratory values. Estimated aσ and (a − b)σ values suggest that a and a − b are smaller than typical laboratory values and/or the pore pressure on the plate boundary is significantly elevated above the hydrostatic value. Our analyses show that the model can reproduce the observed GPS data and that the timing of the rapid acceleration of postseismic deformation is controlled by the frictional properties of the fault and stress change from the main shock, not by the timing of the largest aftershock.
Effect of Diatom Silica Content on Copepod Grazing, Growth and Reproduction

Diatoms are often a major food source for zooplankton and contribute significantly to vertical POC flux through sinking of dead cells, aggregates and zooplankton fecal pellets. The silica content of diatoms varies among different species and within a species growing under different environmental conditions and physiological status. However, to-date there has been no investigation of the effect of diatom silica content on zooplankton grazing, growth and reproduction. We conducted a series of experiments using the diatom Thalassiosira weissflogii with different silica content achieved by growth under high and low light and these cells were fed to a copepod, Parvocalanus crassirostris. Our results show that this copepod strongly preferred cells with low silica content over high silica-containing cells, with the ingestion rate on low silica diatoms being 2-3 times higher than that on high silica diatoms. Fecal pellet production rate was significantly higher for copepods feeding on highly silicified cells. Furthermore, copepod growth rate (measured as an increase in wet weight), egg production rate and hatching success were all severely compromised under a high silica diatom diet. Females of P. crassirostris feeding on a low silica diatom diet produced an average 90 eggs during a one day incubation, while those fed with high silica diatoms produced only 11 eggs per day. Similarly, the hatching success during a 3-day period was 82 ± 17% and 23 ± 36% for the low and high silica diatom treatments, respectively, with zero success observed in ~65% of the females feeding on high Si diatoms. Our findings have important ecological implications for the biological pump and may alter our previous view of the role of diatoms in planktonic food webs and the role of the degree of silicification in controlling amount of POC flux to deeper waters.
Validation of algorithms to detect distant metastases in men with prostate cancer using routine registry data in Denmark

Objective Among patients with prostate cancer, diagnostic codes for bone metastases in the Danish National Registry of Patients have a sensitivity of 44%. In an attempt to improve the sensitivity of registry-based identification of metastases from prostate cancer, we tested a series of algorithms, combining elevated prostate-specific antigen (PSA) levels, use of antiresorptive therapy, and performed bone scintigraphy. Patients and methods We randomly selected 212 men diagnosed with prostate cancer in 2005–2010 in the Central Denmark Region with prespecified PSA values, antiresorptive therapy, and bone scintigraphy who did not have a registry-based diagnostic code indicating presence of distant metastases. We defined three candidate algorithms for bone metastases: 1) PSA >50 μg/L and bone scintigraphy, 2) PSA >50 μg/L and antiresorptive therapy, and 3) PSA ≤50 μg/L with antiresorptive therapy or bone scintigraphy. An algorithm for distant metastasis site other than bone was defined as PSA >50 μg/L alone. Medical chart review was used as the reference standard to establish the presence or absence of metastases. Validity was expressed as a positive predictive value (PPV) or a negative predictive value, based on whether the algorithms correctly classified metastases compared with the reference standard. Results We identified 113 men with evidence of metastases according to the candidate algorithms, and 99 men without evidence of metastases according to the candidate algorithm. The PPVs of PSA >50 μg/L were 0.10 (95% confidence interval [CI] 0.04–0.19) for bone metastases and 0.14 (95% CI 0.07–0.24) for nonbone metastases, regardless of receipt of antiresorptive therapy or presence of bone scintigraphy. The PPVs for any metastases were 0.16 (95% CI 0.06–0.32) for PSA >50 μg/L and 0.28 (95% CI 0.14–0.47) for PSA >50 μg/L with bone scintigraphy. Adding antiresorptive treatment to the algorithm did not improve PPV. All negative predictive values approached 1.00. Conclusion Algorithms based on elevated PSA, antiresorptive therapy, or bone scintigraphy are not suitable for supplementing diagnostic codes to identify additional cases of distant metastases among men with prostate cancer. However, it is possible that in this setting, medical chart review is not a gold standard to identify metastases.
Spatial Fisher Vectors for Image Categorization

: We introduce an extension of bag-of-words image representations to encode spatial layout. Using the Fisher kernel framework we derive a representation that encodes the spatial mean and the variance of image regions associated with visual words. We extend this representation by using a Gaussian mixture model to encode spatial layout, and show that this model is related to a soft-assign version of the spatial pyramid representation. We also combine our representation of spatial layout with the use of Fisher kernels to encode the appearance of local features. Through an extensive experimental evaluation, we show that our representation yields state-of-the-art image categorization results, while being more compact than spatial pyramid representations. In particular, using Fisher kernels to encode both appearance and spatial layout re-sults in an image representation that is computationally efﬁcient, compact, and yields excellent performance while using linear classiﬁers.
Antibiotic Resistance Pattern and Phylogenetic Analysis of Commensal Escherichia coli Isolated from Poultry

In the present investigation a total of 40 isolates of Escherichia coli from healthy poultry birds were investigated for antibiotic resistance pattern and distribution of various phylogroups in different age groups of birds. All the isolates showed green metallic sheen on Eosin Methylene Blue agar plate and were confirmed by various biochemical test. Genotypic confirmation by 16S rRNA gene revealed an amplicon of 662bp in all Escherichia coli isolates. The antibiogram pattern showed high distribution of resistance to multiple drugs among all the isolates with at least each isolate being resistant to three or more antibiotics. The antibiogram results showed that 100% of the isolates were resistant to penicillin, oxacillin and nalidixic acid. Resistance level was more than 50% for doxycycline (97.5), tetracycline (90%), erythromycin (85%), rifampicin (80%) and trimethoprim (75%). The study revealed that amikacin and levofloxacin were the most effective drugs. Out of the four main phylogenetic groups (A, B1, B2, and D), only two phylogroups viz A and B1 were obtained by multiplex PCR with a prevalence of 62.5% and 37.5% respectively.
ORILAM, a three‐moment lognormal aerosol scheme for mesoscale atmospheric model: Online coupling into the Meso‐NH‐C model and validation on the Escompte campaign

[1] Classical aerosol schemes use either a sectional (bin) or lognormal approach. Both approaches have particular capabilities and interests: the sectional approach is able to describe every kind of distribution, whereas the lognormal one makes assumption of the distribution form with a fewer number of explicit variables. For this last reason we developed a three-moment lognormal aerosol scheme named ORILAM to be coupled in three-dimensional mesoscale or CTM models. This paper presents the concept and hypothesis of a range of aerosol processes such as nucleation, coagulation, condensation, sedimentation, and dry deposition. One particular interest of ORILAM is to keep explicit the aerosol composition and distribution (mass of each constituent, mean radius, and standard deviation of the distribution are explicit) using the prediction of three-moment (m0, m3, and m6). The new model was evaluated by comparing simulations to measurements from the Escompte campaign and to a previously published aerosol model. The numerical cost of the lognormal mode is lower than two bins of the sectional one.
Preferences of Louisiana agronomic crop producers and crop consultants regarding sources of information related to agricultural production

The dissemination of information related to agronomic crop production is crucial to the success of the agriculture industry in Louisiana. This information is distributed by various sources and through multiple methods. The primary purpose of this study was to determine the preferences of Louisiana agronomic crop producers and crop consultants in regard to acquiring information related to their agricultural operations. A secondary purpose was to determine how agronomic crop producers perceived selected LSU AgCenter information sources on accuracy, awareness and frequency of use. Data for the study were obtained through surveys completed by 176 agronomic crop producers and 32 crop consultants. The data were analyzed to determine perceptions of the two groups of various information sources on issues of usefulness, frequency of use and the preferences to particular sources. The participants’ perceptions of selected LSU AgCenter information sources were also analyzed for awareness, frequency of use and accuracy. The majority of agronomic crop producers were white (99.4%). Their average age was 48.6 years, and they had been farming agronomic crops for an average of 25.2 years. The majority of the crop consultants in the study were white (100%), male (96.9%) and college graduates (96.9%). The findings indicated that both groups actively used many of the information sources featured in the study. Consultants were the most preferred source for agronomic crop producers followed closely by sources affiliated with the LSU AgCenter. For
Risks worth taking: Safety agreements among discordant gay couples

Abstract As HIV research and prevention efforts increasingly target gay men in relationships, situational factors such as couple serostatus and agreements about sex become central to examinations of risk. Discordant gay couples are of particular interest because the risk of HIV infection is seemingly near-at-hand. Yet, little is known about their sexual behaviors, agreements about sex, and safer sex efforts. The present study utilized longitudinal semi-structured, qualitative interviews to explore these issues among 12 discordant couples. Findings show that nearly every couple had agreements about reducing the likelihood of HIV transmission from one partner to the other. Negotiating these agreements involved establishing a level of acceptable risk, determining condom use, and employing other risk-reduction techniques, such as seropositioning and withdrawal. For half of the couples, these agreements did not involve using condoms; only two couples reported consistent condom use. Despite forgoing condoms, however, none reported seroconversion over the course of data collection. Additional issues are raised where long-term HIV prevention is concerned. Future prevention efforts with discordant couples should work with, rather than fight against, the couple's decision to use condoms and endeavor to complement and accentuate their other safer sex efforts.
Effect of preceding stimulation on sound localization and its representation in the auditory midbrain

Prior stimulation can influence the perception of sound source location. Some psychophysical sound localization procedures differ in the amount of prior stimulation, which may affect measures of localization accuracy. If and how particularly the number of preceding stimuli affects sound localization and the neural representation of sound source position has not been investigated so far and will be the focus of the present report. We trained Mongolian gerbils in a left/right discrimination task where the target stimulus was preceded by silence or followed a number of reference stimuli. Localization thresholds decreased with the number of references presented before the target stimulus. The smallest thresholds were found after the presentation of a train of 5 reference stimuli and after silence. We recorded from units in the inferior colliculus (IC) of anaesthetized gerbils using virtual‐acoustic space stimuli mimicking the ones used in the behavioural task and applied signal detection theory to compare behavioural and neurometric thresholds. We found that neurometric thresholds based on spike rate information of single units covered a wide range of threshold values but only neurometric thresholds that were based on responses of small populations of IC units reached consistently thresholds we also observed in the behavioural experiment. Unlike behavioural thresholds, however, neurometric thresholds were independent of the number of reference stimuli suggesting that processing stages downstream from the IC might better reflect the effect of prior stimulation.
RTP: robust tenant placement for elastic in-memory database clusters

In the cloud services industry, a key issue for cloud operators is to minimize operational costs. In this paper, we consider algorithms that elastically contract and expand a cluster of in-memory databases depending on tenants' behavior over time while maintaining response time guarantees. We evaluate our tenant placement algorithms using traces obtained from one of SAP's production on-demand applications. Our experiments reveal that our approach lowers operating costs for the database cluster of this application by a factor of 2.2 to 10, measured in Amazon EC2 hourly rates, in comparison to the state of the art. In addition, we carefully study the trade-off between cost savings obtained by continuously migrating tenants and the robustness of servers towards load spikes and failures.