Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleic Acids Research

We present a computer method to determine nucleic acid secondary structures. It is based on three steps: 1) the search for all possible helical regions relied on a mathematical approach derived from the convolution theorem; it uses a tetradimensional complex vector representation of the bases along the sequence; 2) a 'tree' search for a set of minimum free energy structures, by the aid of an approximate energy evaluation to reduce the computer time requirements; 3) the exact calculation and refinement of the energies. A method to introduce the experimental data and reach an arrangement between them and the free energy minimization criterion is shown. In order to demonstrate the confidence of the program a test on four RNA sequences is performed. The method has computer time requirement proportional to N, where N is the length of the sequence and retrieves a set of optimal free energy structures. INTRODUCTION The importance of the role of secondary and tertiary RNA structure in biological processes is grown in the last years (1 -3 ) . It is now generally assumed that primary sequence carries the information required for its actual three-dimensional folding. Predicting secondary structure first and then proceeding on to tertiary structure can be supposed to be a fruitful, if not infallible, approach. With the increase in length and number of the determinated nucleic acid sequences, there has been a growing need for algorithms that can efficiently search for the more probable secondary structures. Several methods have been developed to this aim by minimizing the free energy (4—17). Some of these methods predict only one optimal free energy structure for each nucleotide sequence. Alternate equivalent and suboptimal free energy structures are not identified despite their possible biological significance. The methods capable of identifying more than one optimal secondary structure generally require user intervention and/or external constraints (7,11,13). The computer programs based on all these methods generally require a computational time proportional to N, and memory requirements of the order of N, where N is the number of nucleotides in the sequence. The experimental (enzymatic, chemical) data, if considered are generally introduced in the programs as constraints. Here we present an algorithm able to select a set of optimal free energy structures, with computer time requirement proportional to N, and with the possibility of introducing a gradual competition between the experimental data and the free energy content of the structure.
Outer membrane protein profiles of Haemophilus pleuropneumoniae

Outer membrane protein profiles of Haemophilus pleuropneumoniae were examined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Cells were disrupted by sonication, and outer membrane-enriched fractions were prepared by differential centrifugation and selective solubilization of the inner membrane with sodium N-lauroyl sarcosinate. Colony type, growth medium, time of harvest, and in vitro or in vivo passage had no appreciable effect on the protein profiles of the strains examined. Seven patterns were distinguished among the reference strains of the nine capsular serotypes. These patterns were based on the mobility of the major outer membrane proteins migrating in the 39,000- to 44,000-molecular-weight region of the gel, a 16K to 16.5K protein, and a heat-modifiable 29K protein. Strains of serotypes 1 and 9 had identical outer membrane protein profiles, as did strains of serotypes 2 and 6. The reference strains of the remaining five serotypes each had a distinct pattern. The outer membrane protein profiles of 95 field isolates belonging to serotypes 1, 5, 7, and 9 from swine in the midwestern United States were determined and compared with the reference patterns. The results indicate that the population of H. pleuropneumoniae is clonal, with three predominant clones distinguished by both serotype and outer membrane protein profile responsible for the majority of H. pleuropneumoniae disease occurring in swine in the United States.
Humoral immune response to herpes simplex virus type 2 glycoproteins in patients receiving a glycoprotein subunit vaccine

Serial serum specimens from 22 herpes simplex virus (HSV)-seronegative recipients of an HSV type 2 (HSV-2) glycoprotein subunit vaccine were analyzed by radioimmunoprecipitation and polyacrylamide gel electrophoresis for the development of antibodies to HSV-2 gB, gD, and g80, a complex of gC and gE. Volunteers received 50 (n = 12) or 100 micrograms (n = 10) of vaccine at days 0, 28, and 140; sera were drawn weekly for 8 weeks and again at days 140, 147, and 365. Among seronegative volunteers, antibody to gB was detected 2 weeks after the first dose, while antibodies to g80 and gD were detected after the second dose (day 35). Antibodies to nonglycosylated HSV-specific proteins were not detected. A dose-response effect between recipients of 50- and 100-micrograms doses was observed in the proportion of vaccine recipients seroconverting to g80 and in the proportion of recipients retaining antibodies to both gD and g80 over time. Diminishing complement-independent neutralizing antibody titers occurred after the second dose and were associated with loss or reduction of detectable antibody to gD. Volunteers who were seropositive for HSV-1-specific antibody (n = 11) were also enrolled in the trial and received 50-micrograms doses of vaccine. Vaccination resulted in conversion to HSV-2 complement-independent neutralizing antibody specificity or indeterminant specificity in 10 of 11 volunteers. These shifts were accompanied by changes in the radioimmunoprecipitation and polyacrylamide gel electrophoresis profile. These changes, which were apparent by 14 days after the first vaccine dose, included de novo appearance or increased levels of antibody to g80 and increased levels of antibody to gD and gB. These studies document the immunogenicity of solubilized glycoproteins gB, gD, gC, and, possibly, gE in humans.
The Differential Relationship Between Finger Gnosis, and Addition and Subtraction: An fMRI Study

The impact of fingers on numerical cognition has received a great deal of attention recently. One sub-set of these studies focus on the relation between finger gnosis (also called finger sense or finger gnosia), the ability to identify and individuate fingers, and mathematical development. Studies in this subdomain have reported mixed findings so far. While some studies reported that finger gnosis correlates with or predicts mathematics abilities in younger children, others failed to replicate these results. The current study explores the relationship between finger gnosis and two arithmetic operations—addition and subtraction. Twenty-four second to third graders participated in this fMRI study. Finger sense scores were negatively correlated with brain activation measured during both addition and subtraction. Three clusters, in the left fusiform, and left and right precuneus were found to negatively correlate with finger gnosis both during addition and subtraction. Activation in a cluster in the left inferior parietal lobule (IPL) was found to negatively correlate with finger gnosis only for addition, even though this cluster was active both during addition and subtraction. These results suggest that the arithmetic fact retrieval may be linked to finger gnosis at the neural level, both for addition and subtraction, even when behavioral correlations are not observed. However, the nature of this link may be different for addition compared to subtraction, given that left IPL activation correlated with finger gnosis only for addition. Together the results reported appear to support the hypothesis that fingers provide a scaffold for arithmetic competency for both arithmetic operations.
Evaluation of CD14 in host defence

An extensive search for the cell membrane targets for lipopolysaccharide (LPS), the major causative agent of Gram‐negative septic shock, resulted in the identification of CD14 as the major endotoxin ‘receptor’. Besides recognition of LPS, several new aspects of its biological functions have been described recently. In this review the different CD14 forms, their most important biological and biochemical features, signalling properties, cellular and subcellular distribution and association with different diseases are discussed in detail, showing that these molecules posses several unique biological functions and further proving their central role in innate immunity.
Multi-device Map-aided Fingerprint-based Indoor Positioning using Ray Tracing

The objective of this work is to investigate potential accuracy improvements in the fingerprint–based indoor positioning processes, by imposing map-constraints into the positioning algorithms in the form of a–priori knowledge. In our approach, we propose the introduction of a Route Probability Factor (RPF), which reflects the possibility of a user, to be located on one position instead of all others. The RPF does not only affect the probabilities of the points along the pre-defined frequent routes, but also influences all the neighbouring points that lie at the proximity of each frequent route. The outcome of the evaluation process, indicates the validity of the RPF approach, demonstrated by the significant reduction of the positioning error.
A novel human-robot interaction system based on 3D mapping and virtual reality

Aiming at improving the level of the Human-Robot Interaction (HRI), a novel HRI system based on 3D mapping and virtual reality (VR) is proposed, in the background of rescue robots. In the HRI system, the rescue robot constructs a 3D map in the complex post-disaster environment based on a multi-line LiDAR and an inertial measurement unit (IMU) in real time. The map is represented using 3D-NDT, which is incrementally transmitted to the VR system. In the VR side, the human operator uses interactive devices to generate commands to control the robot's movement remotely, in order to perform the rescue task. Using the proposed HRI system, the operator can obtain a strong sense of immersion, thus can better understand the robot's working environment. In addition, as a new way of human-robot interaction, the HRI system provides new ideas to improve the natural level of the interaction between the robot and the human operator.
Histamine Pharmacology and New CNS Drug Targets

During the last decade, the identification of a number of novel drug targets led to the development of promising new compounds which are currently under evaluation for their therapeutic prospective in CNS related disorders. Besides the established pleiotropic regulatory functions in the periphery, the interest in the potential homeostatic role of histamine in the brain was revived following the identification of H3 and H4 receptors some years ago. Complementing classical CNS pharmacology, the development of selective histamine receptor agonists, antagonists, and inverse agonists provides the lead for the potential exploitation of the histaminergic system in the treatment of brain pathologies. Although no CNS disease entity has been associated directly to brain histamine dysfunction until now, the H3 receptor is recognized as a drug target for neuropathic pain, sleep‐wake disorders, including narcolepsy, and cognitive impairment associated with attention deficit hyperactivity disorder, schizophrenia, Alzheimer’s, or Parkinson's disease, while the first H3 receptor ligands have already entered phase I–III clinical trials. Interestingly, the localization of the immunomodulatory H4 receptor in the nervous system exposes attractive perspectives for the therapeutic exploitation of this new drug target in neuroimmunopharmacology. This review focuses on a concise presentation of the current “translational research” approach that exploits the latest advances in histamine pharmacology for the development of beneficial drug targets for the treatment of neuronal disorders, such as neuropathic pain, cognitive, and sleep‐wake pathologies. Furthermore, the role of the brain histaminergic system(s) in neuroprotection and neuroimmunology/inflammation remains a challenging research area that is currently under consideration.
Stability of Harassment in Children: Analysis of the Canadian National Longitudinal Survey of Children and Youth Data

No longitudinal information about bullying and peer harassment among Canadian children currently exists. In the present study, the author examined the stability of bullying and harassment. The sample consisted of two cohorts of children aged 10-11 years (n = 2,798) and 12-13 years (n = 1,946) drawn from the Canadian National Longitudinal Survey of Children and Youth, which is a stratified random sample of households in Canada. The author analyzed children's reports of bullying and harassment from 1994 to 2001 using cross-sectional time-series analyses. The results show that children who were not bullied or harassed in one cycle were unlikely to report being bullied or harassed at a subsequent cycle. About half of children who reported being bullied or harassed in a previous cycle also reported being bullied or harassed in a subsequent cycle. The author concludes that some children may be resilient, whereas others are vulnerable to ongoing bullying and harassment from their peers.
Trešās paaudzes Universitātes sistēmdinamikas modeļa izstrāde RTU vajadzībām

Inovatīvais 21. gadsimts izvirza jaunas prasības universitātēm: tās ir ne vien izglītības iestādes, bet arī pētniecības un inovāciju ieviesanas centri. Jaunās funkcijas universitātēm liek veikt būtiskas izmaiņas savās vadības sistēmās. Pētījuma novitātes elements ir saistīts ar 3. paaudzes universitātes koncepcijas realizēsanu augstskolas modelī. Raksta mērķis ir izstrādāt 3. paaudzes universitātes stratēģiskās plānosanas sistēmdinamikas modeli. Pētījuma rezultāti ir pārbaudīti un ieviesti RTU. Ir secināts, ka universitātes attīstība ir atkarīga no spējām attīstīt inovatīvas tehnoloģijas, un mazo valstu augstskolām pastāv izaugsmes robežas.
An unusual structure in the floor of the fourth ventricle of the Golden Hamster (Mesocricetus Auratus)

During the course of a neurophysiological investigation of the electrical activity of subcortical structures in the golden hamster (Mesocricetus aura tus ) , it became necessary to prepare serial sections of the brain of this animal in order to identify accurately the loci from which activity had been recorded. Systematic examination of these sections disclosed a formation in the floor of the 4th ventricle in the region of the facial colliculus which we have been unable to find reported in previous studies of the anatomy of the brains of hamsters (Buchanan and Hill, '49; Auer, '50) or of other mammals (Huber et al., '43). The purpose of this communication is to describe this structure and i ts apparent neural connections. METHODS
Paralisia Cerebral: Fundamentos para Pais e Cuidadores

Um aspecto que nao pode ser ignorado e o impacto da paralisia cerebral na dinâmica interna da familia, devido ao fato de que seus membros sao confrontados com uma realidade diferente que exige adaptacoes e modificacoes diarias. A forma como os pais, cuidadores e membros da familia se ajustam e crucial para o futuro da crianca e das pessoas envolvidas. Devido as dificuldades dos pais e cuidadores de criancas com paralisia cerebral em adquirir conhecimentos sobre as definicoes, classificacoes e diferencas causadas pela deficiencia, este trabalho tem como objetivo apresentar esclarecimentos teoricos e praticos sobre paralisia cerebral. Para tanto, organizou-se um texto explicativo dos principais motivos que causam as alteracoes na postura e movimento das criancas com deficiencia, pois e sabido que o conhecimento dos pais pode interferir no cuidado e na educacao, considerando que os pais desempenham um papel essencial como educadores de seus filhos, especialmente durante os primeiros anos de formacao, e que isso proporcionara a todos oportunidades de participacao, aprendizado e crescimento.
[Studies on the chemical constitutents in herb of Verbena officinalis].

OBJECTIVE To isolate and identify the chemical constituents from Verbena officinalis. METHOD The compounds were isolated by means of chromatography and the structures were determined on the basis of physical and spectral analysis. RESULT Four compounds were isolated and identified as apigenin (I), 4'-hydroxywogonin (II), verbenalin (III) and hastatoside (IV). CONCLUSION Compounds I and II were obtained from the genus for the first time.
Conversion from cyclosporin to FK 506 after liver transplantation

Thirty-seven liver-grafted patients with steroid-resistant acute or chronic graft rejection or with cyclosporin-related complications were converted from CyA to FK 506. The clinical outcome of the patients primarily depended on the degree of liver dysfunction present at initiation of FK 506 treatment. In patients switched to FK 506 for treatment of acute or early chronic graft rejection, CyA nephrotoxicity, or CyA malabsorption, the FK 506 therapy was associated with a clear improvement in the clinical course. In contrast, in patients with advanced chronic graft rejection, a lower response rate to the conversion in immunosuppression was observed. The lower response rate was associated with a higher patient mortality. These studies demonstrate that FK 506 represents a valuable alternative immunosuppressant for liver-grafted patients. The conversion from CyA to FK 506 should take place before serious — and potentially irreversible — disturbances in liver function are observed.
Taking into account indirect jumps or calls in continuous control-flow checking

Control-flow checking (CFC) is one of the main approaches to monitor the behavior of a microprocessor-based system without specific assumptions on error models (e.g., single bit flips). Many approaches have been proposed and evaluated, but none takes explicitly into account the possibility of indirect jumps or calls for which destination addresses are not hard-coded. This paper discusses first the need for an approach taking care of such sequence breaks. Then an approach is proposed to enhance current control-flow checking schemes.
Improving the efficiency of BDD-based operators by means of partitioning

Binary decision diagrams (BDD's) are a state-of-the-art core technique for the symbolic representation and manipulation of Boolean functions, relations and finite sets. Many computer-aided design (CAD) applications resort to them, but size and time efficiency restrict their applicability to medium-small designs. We concentrate on complex operators used in symbolic manipulation. We analyze and optimize their performance by means of new dynamic partitioning strategies. We propose a novel quick algorithm for the estimation of cofactor size, and a technique to choose splitting variables according to their discrimination power, so that their cofactors may be optimized by different variable orderings (tending to the more flexible FBDDs). Furthermore, we analyze time efficiency and the impact of hashing/caching on BDD-based operators. We finally include an experimental observation of memory usage and running time for operators applied in symbolic manipulation.
The incidence and consequences of falls in stroke patients during inpatient rehabilitation: factors associated with high risk.

OBJECTIVES To determine the incidence of falls on a stroke rehabilitation unit; to assess the frequency and nature of injuries; and to identify risk factors predictive of falls, functional outcomes, and impairments. DESIGN Retrospective cohort study. SETTING An inpatient stroke rehabilitation unit. PARTICIPANTS Two hundred thirty-eight consecutive stroke patient admissions. INTERVENTIONS Incident reports completed on patients who experienced a fall while on the unit were reviewed and resultant injuries categorized (abrasions, lacerations, fractures). MAIN OUTCOME MEASURES Stroke impairments and admission functional assessments, FIM instrument, Berg Balance Scale (BBS), and Chedoke-McMaster (CM) Stroke Impairment Inventory of fallers were compared with nonfallers. RESULTS Of the 238 patients, 88 (37%) experienced at least 1 fall, and almost half of these (45 patients [19%]) experienced at least 2 falls. A total of 180 falls were reported over the 5-year period. Of the 180 reported falls, 33% occurred when patients were using their wheelchairs. Injuries occurred in 22% of the reported falls. These consisted of contusions (49%) and abrasions (41%), primarily of the upper (30.8%) and lower (25.6%) extremities. Only 1 fracture was reported. Fallers tended to have lower admission BBS scores (50% of patients with a score <30 fell vs 18% with a score >30, P <.01) and a lower score on the admission arm, leg, and foot components of the CM (P <.05). Patients who fell were also more likely to be apraxic (P <.014) and suffer from cognitive deficits (P <.01). Repeat fallers had lower admission FIM scores (P <.01) when compared with nonfallers. CONCLUSION Although patients undergoing stroke rehabilitation experienced a significant number of falls, the incidence of serious injury was small. Patients who experienced at least 1 fall had significantly lower BBS, FIM, and CM arm, leg, and foot scores compared with nonfallers. These data suggest that groups of stroke patients who are at risk for falls within the rehabilitation setting can be identified by using a variety of impairment and functional assessments. This information may be potentially useful for designing interventions directed at reducing fall frequency among stroke survivors.
Polymerized ragweed antigen E. I. Preparation and immunologic studies.

Glutaraldehyde treatment of partially purified ragweed AgE was done to provide cross-linked proteins of this material. The ragweed preparation contained a high concentration of antigen E. The glutaraldehyde treatment produced aggregates of ragweed antigen E that were fractionated through Sepharose 6B, 4B and Sephadex G-200 to prepare polymers of two molecular weight ranges, the first approximately 0.2 to 4 million and the second 4 to 20 million. These materials reacted completely with antibody against ragweed antigen E but required higher concentrations to neutralize antibody as the molecular weight of polymerized ragweed increased. The polymerized ragweed did not show antigenic deletion nor were new antigenic determinants definitively shown. The polymerized ragweed was at least as antigenic in animal studies as ragweed antigen E and the polymerized ragweed antigen with a molecular weight range of approximately 0.2 to 4 million showed evidence of possibly greater antigenicity than the monomeric ragweed antigen E.
Architecture Recovery Based on Design Rule Hierarchy

Software clustering techniques have been extensively studied for the purpose of retrieving a high-level structure of a software system. While prior work has been effective for legacy systems, we observe that a key feature of modern software architectures has not been exploited to improve architecture recovery from code. In this paper, we contribute new architecture recovery techniques based on design rule theory. The rationale is that modern software architecture often features architecture-level design rules that are implemented as special program constructs, such as abstract interfaces. These design rules decouple the rest of the system into components, rather than belonging to one of them. We contribute a family of architecture recovery techniques based on this rationale, enabling the combination of design rule based clustering with other clustering techniques, and the splitting of a large system into subsystems. We evaluated our approach both quantitatively and qualitatively, using eight subjects including open source and real industrial software projects. Keywords-Architecture Recovery, Design Rule, Modularity, Reverse Engineering