Miracle-dz/UniFAR-FTUs huggingface dataset:
A genetic classification of caves and its application in eastern Austria

Abstract Based on existing classifications of caves that often involve descriptive terms, a classification is presented that is based purely on genetic processes. An attribute key is developed that allows the classification of caves by means of cave maps, photographs and reports. This method is applied to a dataset of 6007 caves in a study area in eastern Austria. The area comprises diverse geological units of the Eastern Alps and the southern Bohemian Massif. A total of 94% of the caves could be classified with the surprising result that mechanical weathering and erosion caves are almost as common as solution caves even though the vast majority of caves are developed in carbonate rocks. Field checks confirmed the result and showed that the error is acceptable. The classified caves can also be used as indicator of natural phenomena like gravitational mass movements or vulnerable karst areas by decision-makers non-specialized in cave genesis.
Learning to perceive and recognize a second language: the L2LP model revised

We present a test of a revised version of the Second Language Linguistic Perception (L2LP) model, a computational model of the acquisition of second language (L2) speech perception and recognition. The model draws on phonetic, phonological, and psycholinguistic constructs to explain a number of L2 learning scenarios. However, a recent computational implementation failed to validate a theoretical proposal for a learning scenario where the L2 has less phonemic categories than the native language (L1) along a given acoustic continuum. According to the L2LP, learners faced with this learning scenario must not only shift their old L1 phoneme boundaries but also reduce the number of categories employed in perception. Our proposed revision to L2LP successfully accounts for this updating in the number of perceptual categories as a process driven by the meaning of lexical items, rather than by the learners' awareness of the number and type of phonemes that are relevant in their new language, as the previous version of L2LP assumed. Results of our simulations show that meaning-driven learning correctly predicts the developmental path of L2 phoneme perception seen in empirical studies. Additionally, and to contribute to a long-standing debate in psycholinguistics, we test two versions of the model, with the stages of phonemic perception and lexical recognition being either sequential or interactive. Both versions succeed in learning to recognize minimal pairs in the new L2, but make diverging predictions on learners' resulting phonological representations. In sum, the proposed revision to the L2LP model contributes to our understanding of L2 acquisition, with implications for speech processing in general.
RNAi Dynamics in Juvenile Fasciola spp. Liver Flukes Reveals the Persistence of Gene Silencing In Vitro

Background Fasciola spp. liver fluke cause pernicious disease in humans and animals. Whilst current control is unsustainable due to anthelmintic resistance, gene silencing (RNA interference, RNAi) has the potential to contribute to functional validation of new therapeutic targets. The susceptibility of juvenile Fasciola hepatica to double stranded (ds)RNA-induced RNAi has been reported. To exploit this we probe RNAi dynamics, penetrance and persistence with the aim of building a robust platform for reverse genetics in liver fluke. We describe development of standardised RNAi protocols for a commercially-available liver fluke strain (the US Pacific North West Wild Strain), validated via robust transcriptional silencing of seven virulence genes, with in-depth experimental optimisation of three: cathepsin L (FheCatL) and B (FheCatB) cysteine proteases, and a σ-class glutathione transferase (FheσGST). Methodology/Principal Findings Robust transcriptional silencing of targets in both F. hepatica and Fasciola gigantica juveniles is achievable following exposure to long (200–320 nt) dsRNAs or 27 nt short interfering (si)RNAs. Although juveniles are highly RNAi-susceptible, they display slower transcript and protein knockdown dynamics than those reported previously. Knockdown was detectable following as little as 4h exposure to trigger (target-dependent) and in all cases silencing persisted for ≥25 days following long dsRNA exposure. Combinatorial silencing of three targets by mixing multiple long dsRNAs was similarly efficient. Despite profound transcriptional suppression, we found a significant time-lag before the occurrence of protein suppression; FheσGST and FheCatL protein suppression were only detectable after 9 and 21 days, respectively. Conclusions/Significance In spite of marked variation in knockdown dynamics, we find that a transient exposure to long dsRNA or siRNA triggers robust RNAi penetrance and persistence in liver fluke NEJs supporting the development of multiple-throughput phenotypic screens for control target validation. RNAi persistence in fluke encourages in vivo studies on gene function using worms exposed to RNAi-triggers prior to infection.
Multi-Elemental Profiling of Tibial and Maxillary Trabecular Bone in Ovariectomised Rats

Atomic minerals are the smallest components of bone and the content of Ca, being the most abundant mineral in bone, correlates strongly with the risk of osteoporosis. Postmenopausal women have a far greater risk of suffering from OP due to low Ca concentrations in their bones and this is associated with low bone mass and higher bone fracture rates. However, bone strength is determined not only by Ca level, but also a number of metallic and non-metallic elements in bone. Thus, in this study, the difference of metallic and non-metallic elements in ovariectomy-induced osteoporosis tibial and maxillary trabecular bone was investigated in comparison with sham operated normal bone by laser ablation inductively-coupled plasma mass spectrometry using a rat model. The results demonstrated that the average concentrations of 25Mg, 28Si, 39K, 47Ti, 56Fe, 59Co, 77Se, 88Sr, 137Ba, and 208Pb were generally higher in tibia than those in maxilla. Compared with the sham group, Ovariectomy induced more significant changes of these elements in tibia than maxilla, indicating tibial trabecular bones are more sensitive to changes of circulating estrogen. In addition, the concentrations of 28Si, 77Se, 208Pb, and Ca/P ratios were higher in tibia and maxilla in ovariectomised rats than those in normal bone at all time-points. The present study indicates that ovariectomy could significantly impact the element distribution and concentrations between tibia and maxilla.
A Superfamily of Voltage-gated Sodium Channels in Bacteria*

NaChBac, a six-α-helical transmembrane-spanning protein cloned from Bacillus halodurans, is the first functionally characterized bacterial voltage-gated Na+-selective channel (Ren, D., Navarro, B., Xu, H., Yue, L., Shi, Q., and Clapham, D. E. (2001) Science 294, 2372-2375). As a highly expressing ion channel protein, NaChBac is an ideal candidate for high resolution structural determination and structure-function studies. The biological role of NaChBac, however, is still unknown. In this report, another 11 structurally related bacterial proteins are described. Two of these functionally expressed as voltage-dependent Na+ channels (NaVPZ from Paracoccus zeaxanthinifaciens and NaVSP from Silicibacter pomeroyi). NaVPZ and NaVSP share ∼40% amino acid sequence identity with NaChBac. When expressed in mammalian cell lines, both NaVPZ and NaVSP were Na+-selective and voltage-dependent. However, their kinetics and voltage dependence differ significantly. These single six-α-helical transmembrane-spanning subunits constitute a widely distributed superfamily (NaVBac) of channels in bacteria, implying a fundamental prokaryotic function. The degree of sequence homology (22-54%) is optimal for future comparisons of NaVBac structure and function of similarity and dissimilarity among NaVBac proteins. Thus, the NaVBac superfamily is fertile ground for crystallographic, electrophysiological, and microbiological studies.
NAD-299 ANTAGONISES 5-HT-STIMULATED AND SPIPERONE-INHIBITED [35S]GTPγS BINDING IN CLONED 5-HT1A RECEPTORS

ABSTRACT In Chinese Hamster Ovary (CHO) cells expressing cloned human 5-hydroxy-tryptamine1A (5-HT1A) receptors, (R)-3-N,N-dicyclobutylamino-8-fluoro-[6-3H]-3,4-dihydro-2H-1-benzopyran-5-carboxamide ([3H]NAD-299) exhibited high affinity (Kd = 0.16 nM) and labeled 34% more receptors than 8-hydroxy-2-([2,3-3H]di-n-propylamino)tetralin ([3H]8-OH-DPAT). NAD-299 behaved as a silent antagonist in [35S]GTPγS binding similar to N-tert-butyl-3-(4-(2-methoxyphenyl)-piperazin-1-yl)-2-phenylpropanamide (WAY-100635) and (S)-5-fluoro-8-hydroxy-2-(di-n-propylamino)tetralin ((S)UH-301). 5-HT and 5-carboxamidotryptamine (5-CT) stimulated [35S]GTPγS binding 2.5-fold while spiperone and methiothepin inhibited [35S]GTPγS binding 1.4-fold. Furthermore, NAD-299 antagonised both the 5-HT stimulated and the spiperone inhibited [35S]GTPγS binding to basal levels. The KiL/KiH ratios for spiperone (0.66), methiothepin (0.39), WAY-100635 (0.32), (S)UH-301 (0.94), NAD-299 (1.29), NAN-190 (1.23), (S)pindolol (5.85), ipsapirone (13.1), buspirone (24.6), (±)8-OH-DPAT (47.3), flesinoxan (55.8), 5-HT (200) and 5-CT (389) correlated highly significantly with the intrinsic activity obtained with [35S] GTPγS (r = 0.97).
Filter Pattern Search Algorithms for Mixed Variable Constrained Optimization Problems

Abstract : A new class of algorithms for solving nonlinearly constrained mixed variable optimization problems is presented. This class combines and extends the Audet-Dennis Generalized Pattern Search (GPS) algorithms for bound constrained mixed variable optimization, and their GPS-filter algorithms for general nonlinear constraints. In generalizing existing algorithms, new theoretical convergence results are presented that reduce seamlessly to existing results for more specific classes of problems. While no local continuity or smoothness assumptions are required to apply the algorithm, a hierarchy of theoretical convergence results based on the Clarke calculus is given, in which local smoothness dictate what can be proved about certain limit points generated by the algorithm. To demonstrate the usefulness of the algorithm, the algorithm is applied to the design of a load-bearing thermal insulation system. We believe this is the first algorithm with provable convergence results to directly target this class of problems.
The Association of Socioeconomic Status and Use of Crack/Cocaine With Unprotected Anal Sex in a Cohort of Men Who Have Sex With Men in Rio de Janeiro, Brazil

&NA; Summary: To evaluate the relation between illicit drug use, sexual practices, and socioeconomic status, we analyzed data from the baseline interview of a cohort of 675 men who have sex with men conducted from 1994 to 1999 in Rio de Janeiro, Brazil. Bivariate analyses of factors associated with crack/cocaine use with sex revealed that men who reported crack/cocaine use were significantly (p < .05) more likely than men who did not report drug use to be unemployed (42.7% vs. 29.1%), to have an income of <$250 per month (70.7% vs. 60.9%), to have <8 years of education (69.5% vs. 50.9%), to report bisexual activity (81.7% vs. 41.7%), and to engage in commercial sex (72.0% vs. 37.9%). Multivariate analysis of factors associated with unprotected anal sex with casual male partners in the last 6 months demonstrated that the following variables were associated with this outcome: an income <$250 per month (adjusted odds ratio [AOR] = 1.73, 95% confidence interval [CI]: 1.04‐2.87), less than 8 years of education (AOR = 2.21, CI: 1.38‐3.53), a greater sense of vulnerability (AOR = 2.58, CI: 1.54‐4.33), a willingness to participate in vaccine trials (AOR = 1.91, CI: 1.20‐3.05), and use of crack/cocaine (AOR = 1.91, CI: 1.05‐3.46). Our findings suggest that HIV prevention programs for these men need to address drug use and how drug use may influence sexual behaviors.
Placental Protein 13 Administration to Pregnant Rats Lowers Blood Pressure and Augments Fetal Growth and Venous Remodeling

Reduced first-trimester concentrations of placental protein 13 (PP13) are associated with subsequent development of preeclampsia, a major pregnancy disorder. We previously showed that PP13 has a vasodilatory effect, reduces blood pressure and augments expansive remodeling of the uteroplacental vasculature in pregnant rats. In this study, slow-release osmotic pumps were implanted in gravid rats (on day 8) to provide 1 week of PP13 supplementation. Treatment was associated with a reversible blood pressure reduction that returned to normal on day 15. In addition, PP13 caused venous expansion that is larger in the venous branches closer to the placenta. Then, it increased placental and pup weights. Similar administration of a truncated PP13 variant (DelT221) that is unable to bind carbohydrates (a rare spontaneous mutation associated with a high frequency of severe early preeclampsia among Blacks in South Africa) produced a hypotensive effect similar to the full-length molecule, but without venous remodeling and increased placental and pup weights. These results indicate the importance of PP13 carbohydrate binding for inducing vascular remodeling and improving reproductive outcome. Future studies are needed to determine whether beneficial effects would be evident in animal models of preeclampsia or in women predisposed to the development of preeclampsia.
Quality of emergency rooms and urgent care services: user satisfaction

Objective To evaluate the quality of emergency rooms and urgent care services according to the satisfaction of their users. Methods A cross-sectional descriptive study with a quantitative approach. The sample comprised 136 users and was drawn at random. Data collection took place between October and November 2012 using a structured questionnaire. Results Participants were mostly male (64.7%) aged less than 30 years (55.8%), and the predominant level of education was high school (54.4%). Among the items evaluated, those that were statistically associated with levels of satisfaction with care were waiting time, confidence in the service, model of care, and the reason for seeking care related to acute complaints, cleanliness, and comfortable environment. Conclusion Accessibility, hospitality, and infrastructure were considered more relevant factors for patient satisfaction than the cure itself.
A pixel‐based semi‐stochastic algorithm for the registration of geophysical images

The availability of overlapping geophysical data produced by different sensors provides complementary information about the investigation area. However, joint interpretation of these geophysical images is challenging. One common problem is the registration of the images that is necessary to compare features appearing in dissimilar datasets. Measurements in archeological geophysics are often performed by handheld devices therefore, the actual location of the measurement could be different from the planned one. These offsets are localized and essentially random. Consequently, it is impossible to correct them following usual deterministic approaches. This paper presents a novel registration method between geophysical images produced from different prospecting methods. We developed a semi‐stochastic, iterative registration algorithm that applies random local transformations in small randomly selected regions of the processed image. The algorithm uses the mutual information of the images as similarity measure due to its suitability in images of different modalities. We use a pair of images to train the algorithm and tune its parameters. Afterwards, we test the method with nine different pairs of geophysical images from various locations and characteristics. The results, in all cases, show a significant increase of the mutual information in comparison with the registration through geographical coordinates.
Computational emergence and computational emotion

Presents an analysis of the issues pertaining to computational emergence and emotion in (cognitive) agent systems whether their ecology is carbon or silicon-based. We consider how a developing computational theory of cognition can be used to monitor and manage interactions with and within complex systems and so harness unwanted and emergent states and behaviours before the computational system becomes dysfunctional. A comparison is made between these emergent computational states and emotional states. The opening scenario provides a global systems context for the interaction between man and the cyber-domain. The final focus of the paper weaves these threads together in a consideration of the nature of goals, emotion and philosophical issues related to (computational) modelling.
The engineering geology of playas, salt playas and salinas

The terminology used by engineering geologists to describe the various inland saline basin environments has evolved separately from that of other disciplines. This reflects their different interests, but it has meant that, in the published literature, the same terms (e.g. sabkha, playa, salina and numerous local terms) are used to describe different landforms. This note focuses on the characteristic hazards (aggressive saline ground, salt weathering, low bearing capacity and flooding) and their environmental controls. In doing so, the note describes how the severity of the geotechnical risks varies between the different basin types, largely controlled by the position of the groundwater table and, to a lesser extent, the presence of evaporite bedrock within the catchment or region (i.e. the source of salts for surface water and aerosols).
A new pressure-controlled colon delivery capsule for chronotherapeutic treatment of nocturnal asthma

The purpose of this study was to prepare a pressure-controlled colon delivery capsule (PCDC) containing theophylline (TPH) dispersion in a lipid matrix as a chronotherapeutic drug delivery system for the treatment of nocturnal asthma. The system was made by film coating using Eudragit S100- based formula over the sealed-hard gelatin capsules containing the drug-lipid dispersion. The lipid formula was composed mainly of Gelucire 33/01 (G33) with different ratios of surfactants (1–10%). The efficiency of the prepared system was evaluated in vitro for its ability to withstand both the gastric and intestinal medium. In addition, the drug plasma concentrations were monitored after single administration to Beagle dogs and compared to that obtained after administration of a reference marketed, generic, sustained-release TPH tablets, Avolen® SR. It was found that the optimum lipid formula was GL2 containing 90% G33 and 10% Labrasol. The film-coated capsules showed complete resistance to both the acidic environment (pH 1.2) for 2 hours and phosphate buffer pH 6.8 for 3 hours at 37°C. In vivo evaluation of the TPH-based PCDCs showed longer lag time compared TO the marketed formula followed by sudden increase in TPH blood levels, which recommends the high potential of this system as a chronotherapeutic drug delivery for nocturnal asthma. The prepared PCDCs exhibited a significantly higher Cmax and Tmax and a nonsignificantly different AUC compared with Avolen® SR. Higher TPH blood levels from 1 to 8 hours postadministration was detected in the case of the prepared PCDCs.
Primary Sjögren Syndrome in Spain: Clinical and Immunologic Expression in 1010 Patients

We conducted the current study to characterize the clinical presentation of primary Sjögren syndrome (SS) in a large cohort of Spanish patients and to determine whether epidemiologic, clinical, and analytical features modulate disease expression. Patients were from the GEMESS Study group, which was formed in 2005 and included 12 Spanish reference centers. By March 2007, the database included 1010 consecutive patients, recruited since 1994, both incident and prevalent cases. The cohort included 937 women and 73 men (ratio, 13:1), with a mean age of 53 years at diagnosis and 59 years at inclusion in the registry. Multivariate analysis showed that male patients had a lower frequency of thyroiditis, Raynaud phenomenon, and antinuclear antibodies. Young-onset patients had a low degree of sicca involvement (xerostomia and parotid enlargement) and a high frequency of immunologic markers (anti-Ro/SS-A and low C4 levels). Patients with disease duration of more than 10 years had a higher prevalence of xerophthalmia, parotid enlargement, lung involvement, and peripheral neuropathy in comparison with incident cases. The subset of patients with anti-Ro/La antibodies had the highest prevalence of most systemic, hematologic, and immunologic alterations (higher frequency of Raynaud phenomenon, altered parotid scintigraphy, positive salivary gland biopsy, peripheral neuropathy, thrombocytopenia, and rheumatoid factor). Hypocomplementemia was associated with a higher frequency of vasculitis and lymphoma, and cryoglobulins with a higher frequency of parotid enlargement, vasculitis, and leukopenia. Epidemiologic, clinical, and analytical features have a significant impact on the clinical presentation of primary SS, influencing the results of the main diagnostic tests, the prevalence and diversity of extraglandular involvement, and the frequency of the main immunologic markers. Primary SS should be considered as a systemic autoimmune disease that can express in many guises beyond sicca involvement. Abbreviations: ANA = antinuclear antibodies, CNS = central nervous system, RF = rheumatoid factor, SS = Sjögren syndrome.
The LIM-Homeodomain Gene Family in the DevelopingXenopus Brain: Conservation and Divergences with the Mouse Related to the Evolution of the Forebrain

A comparative analysis of LIM-homeodomain (LIM-hd) expression patterns in the developing stage 32 Xenopus brain is presented. x-Lhx2, x-Lhx7, andx-Lhx9 were isolated and their expression, together with that of x-Lhx1 and x-Lhx5,was analyzed in terms of prosomeric brain development and LIM-hd combinatorial code and compared with mouse expression data. The results show an almost complete conservation of expression patterns in the diencephalon. The Lhx1/5 and Lhx2/9subgroups label the pretectum/ventral thalamus/zona limitans versus the dorsal thalamus, respectively, in alternating stripes of expression in both species. Conversely, strong divergences in expression patterns are observed between the telencephalon of the two species for Lhx1/5 andLhx2/9. Lhx7 exhibits particularly conservative patterns and is proposed as a medial ganglionic eminence marker. The conservation of diencephalic segments is proposed to mirror the conservative nature of diencephalic structures across vertebrates. In contrast, the telencephalic divergences are proposed to reflect the emergence of significant novelty in the telencephalon (connectivity changes) at the anamniote/amniote transition. Moreover, the data allow the new delineation of pallial and subpallial domains in the developing frog telencephalon, which are compared with mouse subdivisions. In the pallium, the mouse combinatorial expression of LIM-hd is notably richer than in the frog, again possibly reflecting evolutionary changes in cortical connectivity.