Miracle-dz/UniFAR-FTUs huggingface dataset:
An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins

Two-component signal transduction systems with membrane-embedded sensor histidine kinases are believed to recognize environmental signals and transduce this information over the cellular membrane to influence the activity of a transcription factor to which they are mated. The YycG sensor kinase of Bacillus subtilis, containing two transmembrane helices, is subject to a complicated activity-control circuit involving two other proteins with N-terminal transmembrane helices, YycH and YycI. Truncation studies of YycH and YycI demonstrated that the individual transmembrane helices of these proteins are sufficient to adjust YycG activity, indicating that this control is achieved at the membrane level. A replica exchange molecular dynamics computational approach generated in silico structural models of the transmembrane helix complex that informed mutagenesis studies of the YycI transmembrane helix supporting the accuracy of the in silico model. The results predict that signal recognition by any of the extracellular domains of the sensor histidine kinase YycG or the associated proteins YycH and YycI is transmitted across the cellular membrane by subtle alterations in the positions of the helices within the transmembrane complex of the three proteins.
A Case-Control Study Estimating Accident Risk for Alcohol, Medicines and Illegal Drugs

Background The aim of the present study was to assess the risk of having a traffic accident after using alcohol, single drugs, or a combination, and to determine the concentrations at which this risk is significantly increased. Methods A population-based case-control study was carried out, collecting whole blood samples of both cases and controls, in which a number of drugs were detected. The risk of having an accident when under the influence of drugs was estimated using logistic regression adjusting for gender, age and time period of accident (cases)/sampling (controls). The main outcome measures were odds ratio (OR) for accident risk associated with single and multiple drug use. In total, 337 cases (negative: 176; positive: 161) and 2726 controls (negative: 2425; positive: 301) were included in the study. Results Main findings were that 1) alcohol in general (all the concentrations together) caused an elevated crash risk; 2) cannabis in general also caused an increase in accident risk; at a cut-off of 2 ng/mL THC the risk of having an accident was four times the risk associated with the lowest THC concentrations; 3) when ranking the adjusted OR from lowest to highest risk, alcohol alone or in combination with other drugs was related to a very elevated crash risk, with the highest risk for stimulants combined with sedatives. Conclusion The study demonstrated a concentration-dependent crash risk for THC positive drivers. Alcohol and alcohol-drug combinations are by far the most prevalent substances in drivers and subsequently pose the largest risk in traffic, both in terms of risk and scope.
A COMPARISON OF THE EFFECTS OF PARTIAL AND TOTAL LATERAL FRONTAL LESIONS ON TEST PERFORMANCE BY MONKEYS 1

3 monkeys with sulous principals lesions (P group), 3 with lateral frontal lesions sparing sulcus principals (NP group), 3 with total lateral frontal lesions (T group) and 3 unoperated Ss (U group) were compared on retention of simultaneous visual discrimination and acquisition of (a) delayed alternation, (b) auditory discrimination, (c) 2 successive visual discriminations, and (d) discrimination reversal. The groups did not differ on the visual tasks. On alternation both the P and T groups were severely impaired, the T group being poorer. On auditory discrimination only the T group was markedly impaired. Alternation results lend themselves to a focus-field description. Both focus-field and mass action descriptions are consistent with the auditory discrimination findings. Lesions of granular cortex on the lateral aspect of the frontal lobe are consistently followed by the delayed response deficit but cortical lesions elsewhere in the frontal lobe are not (Pribram, 1955b; Pribram, Kruger, Robinson, & Berman, 1955), Within lateral
Vaccination and Tick-borne Encephalitis, Central Europe

Tick-borne encephalitis is a disease of the brain caused by a virus found in many parts of Europe as well as central and eastern Asia. As the name indicates, the virus is spread by tick bites. The number of people infected each year varies according to complex interactions involving the ticks’environment, the weather, and human socioeconomic and vaccination status. To determine how well vaccine protects against the disease, researchers compared the number of cases in 3 neighboring countries in which vaccination coverage differs but many other factors remain the same: Austria (where more than three quarters of the population are vaccinated) and Slovenia and the Czech Republic (where less than one quarter of the population are vaccinated). They found far fewer cases in Austria, indicating that vaccination is an excellent way to prevent this disease.
Institutional boundaries and common-pool resource management: A comparative analysis of water management programs in California

Policymakers and academics often identify institutional boundaries as one of the factors that shape the capacity of jurisdictions to manage natural resources such as water, forests, and scenic lands. This article examines two key bodies of literature-common-pool resource management theory and local public economy theory-to explain how the boundaries of political jurisdictions affect natural resource management. Two empirical methods were used to test hypotheses from the literature, using a study of water management programs in California. The results demonstrate that institutional boundaries that coincide with natural resources are likely to be associated with the implementation of more effective resource management programs. At the same time, where jurisdictions can control through coordination, they can also facilitate more effective resource management where jurisdictions do not match resource boundaries. © 2004 by the Association for Public Policy Analysis and Management.
Efficient Spatio-Temporal Tactile Object Recognition with Randomized Tiling Convolutional Networks in a Hierarchical Fusion Strategy

Robotic tactile recognition aims at identifying target objects or environments from tactile sensory readings. The advancement of unsupervised feature learning and biological tactile sensing inspire us proposing the model of 3T-RTCN that performs spatio-temporal feature representation and fusion for tactile recognition. It decomposes tactile data into spatial and temporal threads, and incorporates the strength of randomized tiling convolutional networks. Experimental evaluations show that it outperforms some state-of-the-art methods with a large margin regarding recognition accuracy, robustness, and fault-tolerance; we also achieve an order-of-magnitude speedup over equivalent networks with pretraining and finetuning. Practical suggestions and hints are summarized in the end for effectively handling the tactile data.
Bioinformatics - a practical guide to the analysis of genes and proteins

Foreword (Lee Hood). Preface. Contributors. PART ONE: BIOLOGICAL DATABASES. 1. Sequence Databases (Rolf Apweiler). 2. Mapping Databases (Peter S. White and Tara C. Matise). 3. Information Retrieval from Biological Databases (Andreas D. Baxevanis). 4. Genomic Databases (Tyra G. Wolfsberg). PART TWO: ANALYSIS AT THE NUCLEOTIDE LEVEL. 5. Predictive Methods Using DNA Sequences (Enrique Blanco and Roderic Guigo). 6. Predictive Methods Using RNA Sequences (David Mathews and Michael Zuker). 7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry). PART THREE: ANALYSIS AT THE PROTEIN LEVEL. 8. Predictive Methods Using Protein Sequences (Yanay Ofran and Burkhard Rost). 9. Protein Structure Prediction and Analysis (David Wishart). 10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright). PART FOUR: INFERRING RELATIONSHIPS. 11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis). 12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton). 13. Sequence Assembly and Finishing Methods (Nancy F. Hansen, Pamela Jacques Thomas and Gerard G. Bouffard). 14. Phylogenetic Analysis (Fiona S. L. Brinkman). 15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis). 16. Using DNA Microarrays to Assay Gene Expression (John Quackenbush). 17. Proteomics and Protein Identification (Mark R. Holmes, Kevin R. Ramkissoon and Morgan C. Giddings). PART FIVE: DEVELOPING TOOLS. 18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein). Appendices. Glossary. Index.
Determining orbits for the Milky Way's dwarfs

We calculate orbits for the Milky Way dwarf galaxies with proper motions, and compare these to subhalo orbits in a high-resolution cosmological simulation. We use the simulation data to assess how well orbits may be recovered in the face of measurement errors, a time-varying triaxial gravitational potential and satellite-satellite interactions. For present measurement uncertainties, we recover the apocentre r a and pericentre r p to ~ 40 per cent. With improved data from the Gaia satellite we should be able to recover r a and r p to ~ 14 per cent, respectively. However, recovering the 3D positions and orbital phase of satellites over several orbits is more challenging. This owes primarily to the non-sphericity of the potential and satellite interactions during group infall. Dynamical friction, satellite mass-loss and the mass evolution of the main halo play a more minor role in the uncertainties. We apply our technique to nine Milky Way dwarfs with observed proper motions. We show that their mean apocentre is lower than the mean of the most massive subhaloes in our cosmological simulation, but consistent with the most massive subhaloes that form before z = 10. This lends further support to the idea that the Milky Way's dwarfs formed before reionization.
Lowered serum total L-carnitine levels are associated with obesity at term pregnancy

Abstract Objective: This study aims to compare the serum total l-carnitine concentrations of obese and non-obese pregnant women and to identify the role of l-carnitine in both maternal and fetal weight gain during pregnancy. Method: This study reviews 118 healthy women with singleton term pregnancy (≥37 weeks). The characteristics of the recruited subjects were analyzed according to their pre-pregnancy body mass index (BMI). Results: The women with pre-pregnancy BMI < 18.5 kg/m2 had significantly higher serum l-carnitine levels whereas the women with BMI > 29.9 kg/m2 at term pregnancy had significantly lower serum l-carnitine levels (p = 0.001 for both). The neonates born to women with BMI > 29.9 kg/m2 at term pregnancy had significantly longer height and wider head circumference (p = 0.001 for both). Serum total l-carnitine levels correlated significantly and negatively with pre-pregnancy body weight, pre-pregnancy BMI, pregnancy body weight, pregnancy BMI and serum triglyceride levels (r = −0.397, p = 0.001; r = −0.357, p = 0.001; r = −0.460, p = 0.001; r = −0.463, p = 0.001 and r = −0.216, p = 0.019, respectively). There was a significant and positive correlation between l-carnitine and HDL values (r = 0.243, p = 0.008). Conclusions: The crucial role of l-carnitine in pregnancy metabolism suggests that nutritional supplementation of this amino acid can be offered to women who are either overweight or obese at the beginning of the pregnancy.
Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences.

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup. The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genes is strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D. sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D. nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous.
Compassion in care: A qualitative study of older people with a chronic disease and nurses

This article describes compassion as perceived within the relationship between nurses and older persons with a chronic disease. The aim of the study is to understand the benefit of compassion for nursing practice within the context of long-term care. The design of the study involves a qualitative analysis of in-depth interviews with nurses and patients in three different care-settings. Results show the nature of compassion in seven dimensions: attentiveness, listening, confronting, involvement, helping, presence and understanding. Analysis of the data also shows in what way opinions of participants relate to issues raised in a previous literature study, for example the difference between pity and compassion. The conclusion states that compassion is a valuable process which motivates patients as well as nurses to cooperate in achieving relevant outcomes of care. The discussion involves some methodological issues. For one thing, further confirmation of the dimensions found is recommended.
Hearing Loss After Spinal Anesthesia Is Related to Needle Size

Audiograms were performed preoperatively and 2 days postoperatively in 28 patients given spinal anesthesia for transurethral resection of the prostate. In 14 patients 22-gauge and in 14 patients 26-gauge spinal needles were used. Hearing loss of 10 dB or more at any frequency was observed in 13 of 14 patients in the 22-gauge group and in 4 of 14 patients in the 26-gauge group. There was a statistically significant reduction in hearing level in the low-frequency range in patients in whom the 22-gauge needle was used. Hearing loss was unilateral at five frequencies and bilateral at one frequency.No cases of postspinal headache occurred. Audiometry may be a more sensitive indication of cerebrospinal fluid leak than postspinal headache.
Electroconvulsive Therapy for Major Depression in the Oldest Old: Effects of Medical Comorbidity on Post-Treatment Survival.

This is a longitudinal study of 65 patients who were 80 years old or older at the time they were hospitalized for depression. Thirty-seven were treated with ECT and 28 with medication. Survival after 1, 2, and 3 years in the ECT group was 73.0%, 54.1%, and 51.4%, respectively. Survival after 1, 2, and 3 years in the non-ECT group was 96.4%, 90.5%, and 75.0%, respectively. The relatively high mortality rate in the ECT group in this study suggests that patients over 80 who undergo ECT have more severe physical illness than those who can be treated successfully with medication. Medical comorbidity is a major determinant of long-term outcome of depression in the oldest old.
TOWARDS CYCLIC LOAD MODELING OF REINFORCED CONCRETE

The need for accurate methods of analysis of reinforced concrete structures under general loading conditions has been brought to the fore by structural failures sustained during the Northridge and Kobe earthquakes. This paper presents an alternative method by which finite element analysis procedures can be made to provide accurate simulations of reinforced concrete subjected to reversed cyclic loads. Emphasis is placed on developing simple, numerically stable formulations. Plastic offset strains are defined for concrete and reinforcement, and these are incorporated into the analysis through the use of prestrain forces. The elastic components of strain are then used to define effective secant stiffness factors. To provide a record of plastic offsets, and of maximum strain experienced during previous loading, strain envelopes are defined using a Mohr's circle construction. Provisional constitutive models are presented for the concrete, although further work is required in this area. An analysis of a shearwall shows the procedure to be stable and compliant and to provide reasonably accurate simulations of behavior. The results of a pilot series of panel tests are used to identify the aspects of concrete modeling that are in need of further study and refinement.
From the seismic cycle to long‐term deformation: linking seismic coupling and Quaternary coastal geomorphology along the Andean megathrust

Measurement of interseismic strain along subduction zones reveals the location of both locked asperities, which might rupture during megathrust earthquakes, and creeping zones, which tend to arrest such seismic ruptures. The heterogeneous pattern of interseismic coupling presumably relates to spatial variations of frictional properties along the subduction interface and may also show up in the fore‐arc morphology. To investigate this hypothesis, we compiled information on the extent of earthquake ruptures for the last 500 years and uplift rates derived from dated marine terraces along the South American coastline from central Peru to southern Chile. We additionally calculated a new interseismic coupling model for that same area based on a compilation of GPS data. We show that the coastline geometry, characterized by the distance between the coast and the trench; the latitudinal variations of long‐term uplift rates; and the spatial pattern of interseismic coupling are correlated. Zones of faster and long‐term permanent coastal uplift, evidenced by uplifted marine terraces, coincide with peninsulas and also with areas of creep on the megathrust where slip is mostly aseismic and tend to arrest seismic ruptures. We conclude that spatial variations of frictional properties along the megathrust dictate the tectono‐geomorphological evolution of the coastal zone and the extent of seismic ruptures along strike.
Identification of a Conserved B-Cell Epitope on Duck Hepatitis A Type 1 Virus VP1 Protein

Background The VP1 protein of duck hepatitis A virus (DHAV) is a major structural protein that induces neutralizing antibodies in ducks; however, B-cell epitopes on the VP1 protein of duck hepatitis A genotype 1 virus (DHAV-1) have not been characterized. Methods and Results To characterize B-cell epitopes on VP1, we used the monoclonal antibody (mAb) 2D10 against Escherichia coli-expressed VP1 of DHAV-1. In vitro, mAb 2D10 neutralized DHAV-1 virus. By using an array of overlapping 12-mer peptides, we found that mAb 2D10 recognized phages displaying peptides with the consensus motif LPAPTS. Sequence alignment showed that the epitope 173LPAPTS178 is highly conserved among the DHAV-1 genotypes. Moreover, the six amino acid peptide LPAPTS was proven to be the minimal unit of the epitope with maximal binding activity to mAb 2D10. DHAV-1–positive duck serum reacted with the epitope in dot blotting assay, revealing the importance of the six amino acids of the epitope for antibody-epitope binding. Competitive inhibition assays of mAb 2D10 binding to synthetic LPAPTS peptides and truncated VP1 protein fragments, detected by Western blotting, also verify that LPAPTS was the VP1 epitope. Conclusions and Significance We identified LPAPTS as a VP1-specific linear B-cell epitope recognized by the neutralizing mAb 2D10. Our findings have potential applications in the development of diagnostic techniques and epitope-based marker vaccines against DHAV-1.
A Multipartite Version of the Turan Problem - Density Conditions and Eigenvalues

In this paper we propose a multipartite version of the classical Turan problem of determining the minimum number of edges needed for an arbitrary graph to contain a given subgraph. As it turns out, here the non-trivial problem is the determination of the minimal edge density between two classes that implies the existence of a given subgraph. We determine the critical edge density for trees and cycles as forbidden subgraphs, and give the extremal structure. Surprisingly, this critical edge density is strongly connected to the maximal eigenvalue of the graph. Furthermore, we give a sharp upper and lower bound in general, in terms of the maximum degree of the forbidden graph.
An RCT on treatment of palatally displaced canines with RME and/or a transpalatal arch.

AIM To investigate the effect of rapid maxillary expansion (RME) and/or transpalatal arch (TPA) therapy in combination with deciduous canine extraction on the eruption of palatally displaced canines (PDCs). SUBJECTS AND METHODS Hundred and twenty subjects were enrolled in an RCT based on PDCs diagnosed on panoramic radiographs and they were randomly assigned to one of four study groups. Three treatment groups (TGs) (RME followed by TPA therapy plus extraction of deciduous canines, RME/TPA/EC group, 40 subjects; TPA therapy plus extraction of deciduous canines, TPA/EC group, 25 subjects; extraction of deciduous canines, EC group, 25 subjects) were analyzed. A control group (CG, 30 subjects) received no orthodontic treatment. Prevalence rates of eruption of PDCs in the three TGs were compared with the CG at T2. Predictive features at T1 for successful canine eruption were tested in the three TGs. RESULTS AND DISCUSSION The prevalence of canine eruption was 80 per cent for the RME/TPA/EC group, 79 per cent for the TPA/EC group, 62.5 per cent for the EC group, versus 28 per cent in the CG, with statistically significant differences between all the groups, with the exception of the comparison between RME/TPA/EC and TPA/EC. Predictive pretreatment variables for the success of treatment were less severe sectors of canine displacement, prepubertal stages of skeletal maturity, and an open root apex of PDCs. CONCLUSIONS The use of a TPA in absence of RME can be equally effective than the RME/TPA combination in PDC cases not requiring maxillary expansion, thus reducing the burden of treatment for the patient.