Miracle-dz/UniFAR-FTUs huggingface dataset:
Congruent Strain Specific Intestinal Persistence of Lactobacillus plantarum in an Intestine-Mimicking In Vitro System and in Human Volunteers

Background An important trait of probiotics is their capability to reach their intestinal target sites alive to optimally exert their beneficial effects. Assessment of this trait in intestine-mimicking in vitro model systems has revealed differential survival of individual strains of a species. However, data on the in situ persistence characteristics of individual or mixtures of strains of the same species in the gastrointestinal tract of healthy human volunteers have not been reported to date. Methodology/Principal Findings The GI-tract survival of individual L. plantarum strains was determined using an intestine mimicking model system, revealing substantial inter-strain differences. The obtained data were correlated to genomic diversity of the strains using comparative genome hybridization (CGH) datasets, but this approach failed to discover specific genetic loci that explain the observed differences between the strains. Moreover, we developed a next-generation sequencing-based method that targets a variable intergenic region, and employed this method to assess the in vivo GI-tract persistence of different L. plantarum strains when administered in mixtures to healthy human volunteers. Remarkable consistency of the strain-specific persistence curves were observed between individual volunteers, which also correlated significantly with the GI-tract survival predicted on basis of the in vitro assay. Conclusion The survival of individual L. plantarum strains in the GI-tract could not be correlated to the absence or presence of specific genes compared to the reference strain L. plantarum WCFS1. Nevertheless, in vivo persistence analysis in the human GI-tract confirmed the strain-specific persistence, which appeared to be remarkably similar in different healthy volunteers. Moreover, the relative strain-specific persistence in vivo appeared to be accurately and significantly predicted by their relative survival in the intestine-mimicking in vitro assay, supporting the use of this assay for screening of strain-specific GI persistence.
Solving the problem of antidepressant selection in Lithuania.

PURPOSE To ascertain the opinion of psychiatrists of the factors those determine antidepressants selection. MATERIAL AND METHODS An original questionnaire of 30 questions, which deals with reliance of antidepressants selection according to the subtype of depression, was represented for a quarter of all Lithuanian psychiatrists. RESULTS Respondents for depression with obsession 36% chose paroxetine. It is interesting that despite the controversial opinion about the TCAprescribing according to their side effects profile and safety to use, our respondent chose amitriptyline for the melancholic depression with suicidal thoughts (50.2%) and for the anesthetic depression (28%). In some cases there is no unanimous opinion among the psychiatrists--data scattering was received in selection, the respondents chose different antidepressants from different groups in similar frequency. For the treatment of the adynamic depression--7.6%--amitriptyline, 12.1%--citalopram, 10.6%--reboxetine, 10.6%--venlafaxine, for the anxious depression--15.2%--amitriptyline, about 20%--citalopram, 15.2%--mirtazapin, for the anesthetic depression 14.3%--escitalopram, 9%--sertraline, 8.3%--venlafaxine. There is no clear tendency or prevailing antidepressant. CONCLUSIONS Psychopathological peculiarity of depression can be one of the most important criteria in antidepressant selection. However, in many cases, the subtype of depression is ascertained empirically and based solely on the personal experience and clinical practice of the psychiatrist. There are no clear diagnostic criteria or practical guidelines for the reliable verification of the psychopathological subtype of depression, which would allow for the selection of a more adequate and prompt treatment for the patient.
Type A viral hepatitis. New developments in an old disease.

IN recent years, our understanding of the nature and diversity of viruses causing hepatitis in human beings has been sharply increased.1 Those agents now include the viruses of hepatitis A (classic short-incubation infectious hepatitis) and hepatitis B (long-incubation serum hepatitis), one or more still-undefined viruses responsible for "non-A,non-B hepatitis," and the recently recognized delta virus. Among these types of hepatitis, each of which occurs commonly within the United States, hepatitis A is uniquely and primarily transmitted by the fecal—oral route and thus possesses an unequaled potential for epidemic spread. Although it is relatively benign and never eventuates in chronic hepatitis, .
How Do I Model State? Let Me Count the Ways

There is nothing like a disagreement concerning an arcane technical matter to bring out the best (and worst) in software architects and developers. As every reader knows from experience, it can be hard to get to the bottom of what exactly is being debated. One reason for this lack of clarity is often that different people care about different aspects of the problem. In the absence of agreement concerning the problem, it can be difficult to reach an agreement about the solutions.
Optimal Time Selection for the Polarisation and Depolarisation Current Measurement for Power Transformer Insulation Diagnosis

Non-destructive dielectrometry measurement techniques such as polarisation and depolarisation current (PDC) measurement is gaining popularity in power industry to evaluate the insulation condition of transformers. Due to nature of the polarisation species involved in transformer insulation, a perfect PDC measurement would take a very long time, to allow all the interfacial polarisation species to be relaxed. Test duration of 10,000s charging and 10,000s discharging has been considered a reasonable compromise in the context of power transformer insulation. However, in a practical field situation power utilities usually cannot afford such a long measurement time due to economical factors. The authors of this paper explore the possibility of further reducing the PDC measurement time to meet the preference of power industries. Since polarisation and depolarisation are reverse process to each other; it would be possible to estimate oil and paper conductivity from short duration measurements. An experimental investigation has been performed on a distribution transformer and on a model transformer to estimate and compare the accuracy of conductivity computation with different charging and discharging times. These test data helps to decide on the optimal PDC test duration. To help extrapolation of PDC data from short duration to longer duration (i.e. 10,000s), both the current difference and charge difference methods have been adopted. The results from these methods have been critically analysed in this paper.
Neutrophil Granulocyte–committed Cells Can Be Driven to Acquire Dendritic Cell Characteristics

Polymorphonuclear granulocytes (PMNs) are thought to fulfill their role in host defense primarily via phagocytosis and release of cytotoxic compounds and to be inefficient in antigen presentation and stimulation of specific T cells. Dendritic cells (DCs), in contrast, are potent antigen-presenting cells with the unique capacity to initiate primary immune responses. We demonstrate here that highly purified lactoferrin-positive immediate precursors of end-stage neutrophilic PMN (PMNp) can be reverted in their functional maturation program and driven to acquire characteristic DC features. Upon culture with the cytokine combination granulocyte/macrophage colony-stimulating factor plus interleukin 4 plus tumor necrosis factor α, they develop DC morphology and acquire molecular features characteristic for DCs. These molecular changes include neo-expression of the DC-associated surface molecules cluster of differentiation (CD)1a, CD1b, CD1c, human leukocyte antigen (HLA)-DR, HLA-DQ, CD80, CD86, CD40, CD54, and CD5, and downregulation of CD15 and CD65s. Additional stimulation with CD40 ligand induces also expression of CD83 and upregulates CD80, CD86, and HLA-DR. The neutrophil-derived DCs are potent T cell stimulators in allogeneic, as well as autologous, mixed lymphocyte reactions (MLRs), whereas freshly isolated neutrophils are completely unable to do so. In addition, neutrophil-derived DCs are at least 10,000 times more efficient in presenting soluble antigen to autologous T cells when compared to freshly isolated monocytes. Also, in functional terms, these neutrophil-derived DCs thus closely resemble “classical” DC populations.
Adaptive Probabilistic Trajectory Optimization via Efficient Approximate Inference

Robotic systems must be able to quickly and robustly make decisions when operating in uncertain and dynamic environments. While Reinforcement Learning (RL) can be used to compute optimal policies with little prior knowledge about the environment, it suffers from slow convergence. An alternative approach is Model Predictive Control (MPC), which optimizes policies quickly, but also requires accurate models of the system dynamics and environment. In this paper we propose a new approach, adaptive probabilistic trajectory optimization, that combines the benefits of RL and MPC. Our method uses scalable approximate inference to learn and updates probabilistic models in an online incremental fashion while also computing optimal control policies via successive local approximations. We present two variations of our algorithm based on the Sparse Spectrum Gaussian Process (SSGP) model, and we test our algorithm on three learning tasks, demonstrating the effectiveness and efficiency of our approach.
An efficient many-core architecture for Elliptic Curve Cryptography security assessment

Elliptic Curve Cryptography (ECC) is a popular tool to construct public-key crypto-systems. The security of ECC is based on the hardness of the elliptic curve discrete logarithm problem (ECDLP). Implementing and analyzing the performance of the best known methods to solve the ECDLP is useful to assess the security of ECC and choose security parameters in practice. We present a novel many-core hardware architecture implementing the parallel version of Pollard's rho algorithm to solve the ECDLP. This architecture results in a speed-up of almost 300% compared to the state of the art and we use it to estimate the monetary cost of solving the Certicom ECCp-131 challenge using FPGAs.
Intracranial haemorrhage in haemophilia

Intracranial bleeding has long been regarded as particularly lethal in haemophilia and is currently the most common cause of death among haemophiliacs in Finland (Ikkala, 1960), in Sweden (Blomback, 1962), and in New South Wales (Kerr, 1963). It appears that intracranial haemorrhage has not been influenced by modem therapy to the same extent as post-operative or traumatic bleeding at other sites, which were formerly the most common causes of death (Birch, 1937). This trend is illustrated in Table I which shows the distribution of causes of death among 106 haemophiliacs in New South Wales between 1900 and 1962. Even allowing for incomplete ascertainment of deaths during the earlier years of this century, the threefold increase in fatal intracranial bleeding since 1940 contrasts with reduced mortality from most other types of haemorrhage during the same period.
Space-time codes over PN sequences for DS/CDMA systems

This paper considers the application of space-time coding techniques in DS/CDMA communication systems with multiple transmit antennas. Space-time codes are constructed over the set of possible pseudo noise (PN) sequences rather than standard 2-D signals. Several design examples of these codes with different sequences and slates are presented and possible methods of implementation are suggested. Simulation results indicate that the proposed space-time coded systems provide a significant performance improvement over the reference transmit diversity system. The performance improvement is more pronounced when two receive antennas are employed and grows as the data alphabet M grows.
Ensembl comparative genomics resources

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl. org.
Infrastructure for Data Processing in Large-Scale Interconnected Sensor Networks

With the price of wireless sensor technologies diminishing rapidly we can expect large numbers of autonomous sensor networks being deployed in the near future. These sensor networks will typically not remain isolated but the need of interconnecting them on the network level to enable integrated data processing will arise, thus realizing the vision of a global "sensor Internet. " This requires a flexible middleware layer which abstracts from the underlying, heterogeneous sensor network technologies and supports fast and simple deployment and addition of new platforms, facilitates efficient distributed query processing and combination of sensor data, provides support for sensor mobility, and enables the dynamic adaption of the system configuration during runtime with minimal (zero-programming) effort. This paper describes the global sensor networks (GSN) middleware which addresses these goals. We present GSN's conceptual model, abstractions, and architecture, and demonstrate the efficiency of the implementation through experiments with typical high-load application profiles. The GSN implementation is available from http://gsn.sourceforge. net/.
A new coumarin from stem bark of Calophyllum wallichianum

Abstract A phytochemical study carried out on the plant, Calophyllum wallichianum has led to the isolation of a new coumarin, wallimarin T (1) and a known coumarin, calanolide E (2) along with two common triterpenes, friedelin (3) and stigmasterol (4). The structures of these compounds were elucidated with the aid of spectroscopic analyses such as FT-IR, GC-MS, and NMR. MIC assay against the Bacillus bacteria were conducted on the extracts and this gave MIC values ranging from 0.313 to 1.25 mg/mL. Compound 2 was weakly inhibitory towards the Bacilli strains with MIC values ranging from 0.25–0.50 mg/mL. Wallimarin T (1) was not active towards all four bacteria. Overall, the extracts exhibited weak bactericidal properties whereas compound 2 was not bactericidal on the tested bacteria. The hexane and chloroform extracts of the plant were found to be inhibitors to the growth of Bacillus megaterium, Bacillus cereus, Bacillus pumilus and Bacillus subtilis.
Open Access Research Article the Effect of Marathon on Mrna Expression of Anti-apoptotic and Pro-apoptotic Proteins and Sirtuins Family in Male Recreational Long-distance Runners

Background: A large body of evidence shows that a single bout of strenuous exercise induces oxidative stress in circulating human lymphocytes leading to lipid peroxidation, DNA damage, mitochondrial perturbations, and protein oxidation. In our research, we investigated the effect of physical load on the extent of apoptosis in primary cells derived from blood samples of sixteen healthy amateur runners after marathon (a.m.). Results: Blood samples were collected from ten healthy amateur runners peripheral blood mononuclear cells (PBMCs) were isolated from whole blood and bcl-2, bax, heat shock protein (HSP)70, Cu-Zn superoxide dismutase (SOD), Mn-SOD, inducible nitric oxide synthase (i-NOS), SIRT1, SIRT3 and SIRT4 (Sirtuins) RNA levels were determined by Northern Blot analysis. Strenuous physical load significantly increased HSP70, HSP32, Mn-SOD, Cu-Zn SOD, iNOS, GADD45, bcl-2, forkhead box O (FOXO3A) and SIRT1 expression after the marathon, while decreasing bax, SIRT3 and SIRT4 expression (P < 0.0001). Conclusion: These data suggest that the physiological load imposed in amateur runners during marathon attenuates the extent of apoptosis and may interfere with sirtuin expression. Background Apoptosis, or programmed cell death, is a normal physiological function essential for the homeostasis of immuno haemopoietic tissues. This process occurs via specific sig-naling pathways, eventually leading to DNA fragmentation , nuclear condensation, proteolysis and cell fragmentation [1]. An important regulatory event in the apoptotic process is the activation of caspases, a family of cysteine proteases, which regulate two major and relatively distinct pathways, the extrinsic and intrinsic pathways. The extrinsic pathway known also as mitochondrial pathway involves pro-and anti-apoptotic members of the bcl-2 family of proteins [2,3].
Cytotoxic T Cells Reactive to an Immunodominant Leukemia-associated Antigen can be Specifically Primed and Expanded by Combining a Specific Priming Step With Nonspecific Large-scale Expansion

Identification of dominant leukemia-associated neoantigens and favoring specific priming and subsequent expansion of T cells reactive to these antigens might harbor therapeutic potential. Here, a new strategy combines a specific T-cell activation step using tumor lysate-pulsed bone marrow-derived dendritic cells with a nonspecific large-scale expansion method. The leukemia cell line C1498 transduced with a potentially immunodominant antigen (ovalbumin) was used to track expansion and functionality of antigen-specific cytotoxic T cell (CTL), both in vitro and in vivo. Three times more leukemia-specific CTL could be generated when compared with the respective controls. CTL generated after increasing the antigen-specific T-cell precursor frequency in vitro cured up to 80% of mice bearing leukemia with the respective antigen (P<0.005, as compared with controls). Alternatively, the yield of CTL reactive to a immunodominant neoantigen increased by factor 2 to 6 when T-cell donors were immunized with dendritic cell presenting the respective antigen. However, increasing the leukemia-reactive precursor frequency to a clinically exploitable level will be the key for the design of successful T-cell therapy trials.
Visual and auditory affect recognition in singly diagnosed mentally retarded patients, mentally retarded patients with autism and normal young children.

Five groups were tested for facial and postural affect recognition by use of word and tonal prompts. Group 1 contained normal young children. Groups 2 and 3 were moderately retarded and Groups 4 and 5 were severely retarded. Retardation was complicated by autism in Groups 3 and 5. There were eight conditions. In Condition 1, happy, sad and angry faces were displayed simultaneously in each of 18 trials, with the subjects prompted verbally to point to one of the affects (e.g., the angry face) in a given trial. In Condition 2, full figures (with facial features omitted) were used instead of the faces, and emotion was conveyed by use of body position and muscle tone. The same procedure was followed as before. Conditions 3 and 4 were repeated of 1 and 2, except that descriptive word prompts were used (e.g., point to the yelling picture). Conditions 5 and 6 were the same as 1 and 2, except that affective voice intonations were used instead of word prompts. The subjects had to identify the voice tones by using affective words (e.g., happy) in Condition 7, and descriptive words (e.g., laughing) in Condition 8. An analysis of the error data indicated that retarded subjects had particular difficulty recognizing angry stimuli with both affective and descriptive word prompting. In addition, they tended to confuse happy with angry voice tones.
Classification of Intrinsically Disordered Regions and Proteins

1.1. Uncharacterized Protein Segments Are a Source of Functional Novelty Over the past decade, we have observed a massive increase in the amount of information describing protein sequences from a variety of organisms.1,2 While this may reflect the diversity in sequence space, and possibly also in function space,3 a large proportion of the sequences lacks any useful function annotation.4,5 Often these sequences are annotated as putative or hypothetical proteins, and for the majority their functions still remain unknown.6,7 Suggestions about potential protein function, primarily molecular function, often come from computational analysis of their sequences. For instance, homology detection allows for the transfer of information from well-characterized protein segments to those with similar sequences that lack annotation of molecular function.8−10 Other aspects of function, such as the biological processes proteins participate in, may come from genetic- and disease-association studies, expression and interaction network data, and comparative genomics approaches that investigate genomic context.11−17 Characterization of unannotated and uncharacterized protein segments is expected to lead to the discovery of novel functions as well as provide important insights into existing biological processes. In addition, it is likely to shed new light on molecular mechanisms of diseases that are not yet fully understood. Thus, uncharacterized protein segments are likely to be a large source of functional novelty relevant for discovering new biology.
State estimation over a network: Packet-dropping analysis and design

In this paper, we consider discrete-time state estimation over a network. Two scenarios are investigated. In the first scenario, we assume the sensor sends its measurement packet across a packet-dropping network, and we find minimum packet arrival rate that guarantees certain performance at the remote estimator. In the second scenario, we assume the network does not drop any data packet but the sensor has the freedom to send its current measurement data or not. We look for the optimal measurement data sending rate at the sensor which provides the optimal tradeoff between the sending cost at the sensor and the error at the estimator. Examples are provided to illustrate the theories and algorithms developed.