Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for lateral transfer and recombination in OspC variation in Lyme disease Borrelia

The ospC gene was amplified by the polymerase chain reaction from each of 76 Lyme disease Borrelia strains. Restriction fragment length polymorphism (RFLP) analysis demonstrated 33 distinct RFLP types; two additional RFLP types were identified from published ospC sequences. For each RFLP type, at least one ospC gene was sequenced and the degree of sequence relatedness examined by construction of an ospC gene tree. The genes were extremely diverse, with sequence identity ranging from 74.4% to 99.0%; the majority of changes are localized within the central portion of the molecule. A comparison of ospC sequences suggests that recombination occurs frequently between ospC alleles; this genetic exchange is proposed to be mediated by lateral transfer of ospC sequences. Evidence indicates that recombination occurs between ospC genes from the same Borrelia species (i.e. B. afzelii and B. garinii) as well as between different Borrelia species (i.e. B. afzelii and B. garinii, B. burgdorferi and genogroup DN127).
Spatial Variability of Field Microtopography and Its Influence on Irrigation Performance

Surface irrigation is the main irrigation method,which is most widely used in the world.Surface irrigation performance is affected by field length,field width,field microtopography,inflow rate,soil infiltration,crops,and so on.Field microtopography is among the most important factors affecting the performance of basin irrigation system due to its influence on the advance and recession processes.It can direct the irrigation design and management to systematically analyze their effects on the basin irrigation performances by numerical simulation.
The New ARTIST 5 for all Digisondes

Beginning in December 2007, UMLCAR is conducting a network-wide upgrade of the Automatic Real-Time Ionogram Scaler with True height (ARTIST), the ionogram autoscaling software developed for Digisondes. The new ARTIST Version 5 revamps classic, well-seasoned ARTIST 4 techniques for the modern computers and programming environments. It also implements new approaches developed to strengthen the ARTIST persona. Special attention has been directed to the characterization of the Autoscaling Confidence Level (ACL) and provision of the uncertainty bounds for the automatically scaled characteristics and derived electron density profiles in order to properly ingest them in assimilative ionospheric models. The new SAO.XML format for ionogram-derived data is used to report ARTIST 5 data. The paper describes progress in the ionogram autoscaling research at UMLCAR that has culminated into release of the ARTIST 5 upgrade.
Electrocardiogram of the athlete. Alterations simulating those of organic heart disease.

Routine medical evaluations of well-trained endurance athletes frequently disclose electrocardiographic abnormalities suggestive of organic heart disease. First- and second-degree atrioventricular (AV) block, altered ventricular conduction, criteria for atrial enlargement or ventricular hypertrophy, and repolarization abnormalities are commonly found. On the basis of such abnormal tracings, the athlete may be advised to refrain from his customary strenuous exertion, even though the results of physical examination are normal and there is no history suggesting cardiovascular disease. In fact, such athletes are usually quite fit for the activity for which they train so vigorously. The electrocardiographic findings probably reflect the anatomic and electrophysiologic effects of training on the cardiovascular system. It is important for physicians to recognize these changes as normal variants when seen in well-trained athletes.
Molecular Phylogeny of a RING E3 Ubiquitin Ligase, Conserved in Eukaryotic Cells and Dominated by Homologous Components, the Muskelin/RanBPM/CTLH Complex

Ubiquitination is an essential post-translational modification that regulates signalling and protein turnover in eukaryotic cells. Specificity of ubiquitination is driven by ubiquitin E3 ligases, many of which remain poorly understood. One such is the mammalian muskelin/RanBP9/CTLH complex that includes eight proteins, five of which (RanBP9/RanBPM, TWA1, MAEA, Rmnd5 and muskelin), share striking similarities of domain architecture and have been implicated in regulation of cell organisation. In budding yeast, the homologous GID complex acts to down-regulate gluconeogenesis. In both complexes, Rmnd5/GID2 corresponds to a RING ubiquitin ligase. To better understand this E3 ligase system, we conducted molecular phylogenetic and sequence analyses of the related components. TWA1, Rmnd5, MAEA and WDR26 are conserved throughout all eukaryotic supergroups, albeit WDR26 was not identified in Rhizaria. RanBPM is absent from Excavates and from some sub-lineages. Armc8 and c17orf39 were represented across unikonts but in bikonts were identified only in Viridiplantae and in O. trifallax within alveolates. Muskelin is present only in Opisthokonts. Phylogenetic and sequence analyses of the shared LisH and CTLH domains of RanBPM, TWA1, MAEA and Rmnd5 revealed closer relationships and profiles of conserved residues between, respectively, Rmnd5 and MAEA, and RanBPM and TWA1. Rmnd5 and MAEA are also related by the presence of conserved, variant RING domains. Examination of how N- or C-terminal domain deletions alter the sub-cellular localisation of each protein in mammalian cells identified distinct contributions of the LisH domains to protein localisation or folding/stability. In conclusion, all components except muskelin are inferred to have been present in the last eukaryotic common ancestor. Diversification of this ligase complex in different eukaryotic lineages may result from the apparently fast evolution of RanBPM, differing requirements for WDR26, Armc8 or c17orf39, and the origin of muskelin in opisthokonts as a RanBPM-binding protein.
Primary Biliary Cirrhosis Associated with Systemic Sclerosis: Diagnostic and Clinical Challenges

Patients with primary biliary cirrhosis (PBC) often have concurrent limited systemic sclerosis (SSc). Conversely, up to one-fourth of SSc patients are positive for PBC-specific antimitochondrial antibodies (AMA). The mechanisms responsible for the co-occurrence of these diseases are largely unknown. Genetic, epigenetic, environmental, and infectious factors appear to be important for the pathogenesis of the disease, but the hierarchy of events are not well defined. Patients with SSc and PBC have an increased morbidity and mortality compared with the general population, but whether the presence of both diseases in an affected individual worsens the prognosis and/or outcome of either disease is not clear. Some case reports suggested that the presence of SSc in PBC patents is associated with a more favorable prognosis of the liver disease, whereas others report an increased mortality in patients with PBC and SSc compared to patients with PBC alone. This paper discusses the features of patients with PBC-associated SSc. Our aims are to clarify some of the pathogenetic, diagnostic, and clinical challenges that are currently faced in the routine management of these patients. We also intend to provide some practical hints for practitioners that will assist in the early identification of patients with PBC-associated SSc.
Animal exposure, sensitization, and allergic symptoms in first-year veterinary medicine students

The AllergoVet study longitudinally examines the influence of animal exposure on the development of sensitization and allergic diseases among veterinary medicine students. In this group, contact to animals usually existed long before the study began. Therefore, the aim of this analysis was to investigate lifelong animal species-specific exposure and the prevalence of sensitizations and allergic symptoms already existing before the start of the study. Questionnaire data, including exposure history, were summarized to determine the duration and intensity of animal-related exposure as well as the prevalence of allergic symptoms to animals. Serologically, specific IgE was determined against ubiquitous inhalant allergens (atopy screen sx1) and against animal allergens using ImmunoCAP. The association between animal-specific sensitization, allergic symptoms, and exposure was analyzed using Fisher’s exact test or Cochran-Armitage trend test. All study participants (n = 313) had previous contact with animals, with dogs mentioned most frequently (91.1%) followed by cats (89.5%) and horses (72.2%). Sensitization to ubiquitous allergens (positive sx1 value) was detected in 38.4% of subjects. Approximately 11%, 7%, and 5% were sensitized to cats, dogs, and horses, respectively. Only a small proportion of these sensitizations were associated with self-reported symptoms (41% for cat, 9% for dog, and 13% for horse). While no significant association between animal-specific exposure and sensitization was found for cats and horses, a clear trend emerged for dogs. With increasing duration of exposure to dogs, the number of dog-specific sensitizations decreased significantly (p = 0.0069). Furthermore, a decreasing trend in sx1 sensitization was noted with increasing cat (p = 0.0288) and dog (p = 0.0107) exposure. None of the subjects who grew up on a farm (n = 40) had any sensitization to animals. The sensitization prevalence determined among first-year students in veterinary medicine roughly corresponds to that in the general population. Most animal sensitizations were not clinically relevant. In this collective, a protective effect of increasing exposure to animals in childhood and adolescence was found on sensitization, which was particularly pronounced during contact with dogs.
Piracetam Improves Activated Blood Flow and Facilitates Rehabilitation of Poststroke Aphasic Patients

Background and Purpose In a prospective, double-blind, placebo-controlled study, it was investigated whether piracetam improves language recovery in poststroke aphasia assessed by neuropsychological tests and activation PET measurement of cerebral blood flow. Methods Twenty-four stroke patients with aphasia were randomly allocated to 2 groups: 12 patients received 2400 mg piracetam twice daily, 12 placebo. Before and at the end of the 6-week treatment period in which both groups received intensive speech therapy, the patients were examined neuropsychologically and studied with H215O PET at rest and during activation with a word-repetition task. Blood flow was analyzed in 14 language-activated brain regions defined on reconstructed surface views from MRI coregistered to the PET images. Results Before treatment, both groups were comparable with respect to performance in language tasks and to type and severity of aphasia. In the piracetam group, increase of activation effect was significantly higher (P <0.05) in the left transverse temporal gyrus, left triangular part of inferior frontal gyrus, and left posterior superior temporal gyrus after the treatment period compared with the initial measures. The placebo group showed an increase of activation effect only in the left vocalization area. In the test battery, the piracetam group improved in 6 language functions, the placebo group only in 3 subtests. Conclusions Piracetam as an adjuvant to speech therapy improves recovery of various language functions, and this effect is accompanied by a significant increase of task-related flow activation in eloquent areas of the left hemisphere.
’Well, it literally stops me from having a life when it’s really bad': a nested qualitative interview study of patient views on the use of self-management treatments for the management of recurrent sinusitis (SNIFS trial)

Objective To explore the experience and perceptions of illness, the decision to consult a general practitioner and the use of self-management approaches for chronic or recurrent sinusitis. Design Qualitative semistructured interview study. Setting UK primary care. Participants 32 participants who had been participating in the ‘SNIFS’ (Steam inhalation and Nasal Irrigation For recurrent Sinusitis) trial in the South of England. Method Thematic analysis of semistructured telephone interviews. Results Participants often reported dramatic impact on both activities and their quality of life. Participants were aware of both antibiotic side effects and resistance, but if they had previously been prescribed antibiotics, many patients believed that they would be necessary for the future treatment of sinusitis. Participants used self-help treatments for short and limited periods of time only. In the context of the trial, steam inhalation used for recurrent sinusitis was described as acceptable but is seen as having limited effectiveness. Nasal irrigation was viewed as acceptable and beneficial by more patients. However, some participants reported that they would not use the treatment again due to the uncomfortable side effects they experienced, which outweighed any symptom relief, which may have resulted had they continued. Conclusions Steam inhalation is acceptable but seen as having limited effectiveness. Nasal irrigation is generally acceptable and beneficial for symptoms, but detailed information on the correct procedure and potential benefits of persisting may increase acceptability and adherence in those patients who find it uncomfortable. Trial registration number ISRCTN 88204146.
Influence of the Change in Oxidation Number of Mn on Magnetic Properties of  ${\rm BaTi}_{{1}-{x}}{\rm Mn}_{x}{\rm O}_{3}$

We prepared BaTi<sub>1-x</sub>Mn<sub>x</sub>O<sub>3</sub> samples (x = 0 and 0.05) by standard solid-state reaction at 700°C and 900°C in an Ar ambient to change oxidation number of Mn dopants. The fabricated samples were then studied structural characterization and electronic structures by means of X-ray diffraction and absorption, and Raman scattering and electron-spin-resonance spectrometers. We found oxidation numbers 2+ and 3+ of Mn ions coexisting in BaTi<sub>1-x</sub>Mn<sub>x</sub>O<sub>3</sub> with x = 0.05, where the Mn<sup>2+</sup>/Mn<sup>3+</sup> ratio is about one for the sample annealed at 700°C. These Mn ions prefer locating at the Ti site in the tetragonal BaTiO<sub>3</sub> host lattice. In particular, there is a change in the oxidation number of Mn<sup>2+</sup> → Mn<sup>3+</sup> when the annealing temperature changes from 700°C to 900°C. Their magnetic properties are accordingly changed. Meanwhile, annealing pure BaTiO<sub>3</sub> in an Ar ambient at 700°C and 900°C does not lead to ferromagnetic (FM) order; they are almost diamagnetic. With the obtained results, we believe that FM order in Mn-doped BaTiO<sub>3</sub> annealed in an Ar ambient is associated with exchange interactions of Mn<sup>2+</sup> ions mediated by oxygen vacancies rather than associated with Mn<sup>3+</sup> ions.
The Dantzig selector: Statistical estimation when P is much larger than n

In many important statistical applications, the number of variables or parameters p is much larger than the number of observations n. Suppose then that we have observations y=Xβ+z, where β∈Rp is a parameter vector of interest, X is a data matrix with possibly far fewer rows than columns, n≪p, and the zi’s are i.i. d. N(0, σ^2). Is it possible to estimate β reliably based on the noisy data y?
A Differential Model of the Baroreflex Control of the Cardiovascular System During a Tilt Test

In this paper, a differential model of the cardiovascular system and its baroreflex control is presented. This simplified model of the circulation includes the left heart, arterial and venous compartments, the afferent baroreceptor pathway, the sympathetic and vagal efferent activities and excitation-contraction coupling at the cardiac muscle level. The model is used to simulate the interactions among the baroreflex control loop, the pulsating heart and the effector during a graded orthostatic tilt. There is a satisfactory agreement between the model and experimental results illustrated through heart rate variability analysis. Experimental data on heart rate control can then be explained fairly well by a rather simple action of the sympathetic-parasympathetic system on the heart rate. The output of the proposed model are usually measured cardiovascular signals. An objective is to use it in model-based signal processing in order to assess the short-term control of cardiovascular system.
Reactivation Kinetics of HIV-1 and Susceptibility of Reactivated Latently Infected CD4+ T Cells to HIV-1-Specific CD8+ T Cells

ABSTRACT The “shock and kill” model of human immunodeficiency virus type 1 (HIV-1) eradication involves the induction of transcription of HIV-1 genes in latently infected CD4+ T cells, followed by the elimination of these infected CD4+ T cells by CD8+ T cells or other effector cells. CD8+ T cells may also be needed to control the spread of new infection if residual infected cells are present at the time combination antiretroviral therapy (cART) is discontinued. In order to determine the time frame needed for CD8+ T cells to effectively prevent the spread of HIV-1 infection, we examined the kinetics of HIV transcription and virus release in latently infected cells reactivated ex vivo. Isolated resting, primary CD4+ T cells from HIV-positive (HIV+) subjects on suppressive regimens were found to upregulate cell-associated HIV-1 mRNA within 1 h of stimulation and produce extracellular virus as early as 6 h poststimulation. In spite of the rapid kinetics of virus production, we show that CD8+ T cells from 2 out of 4 viremic controllers were capable of effectively eliminating reactivated autologous CD4+ cells that upregulate cell-associated HIV-1 mRNA. The results have implications for devising strategies to prevent rebound viremia due to reactivation of rare latently infected cells that persist after potentially curative therapy. IMPORTANCE A prominent HIV-1 cure strategy termed “shock and kill” involves the induction of HIV-1 transcription in latently infected CD4+ T cells with the goal of elimination of these cells by either the cytotoxic T lymphocyte response or other immune cell subsets. However, the cytotoxic T cell response may also be required after curative treatment if residual latently infected cells remain. The kinetics of HIV-1 reactivation indicate rapid upregulation of cell-associated HIV-1 mRNA and a 5-h window between transcription and virus release. Thus, HIV-specific CD8+ T cell responses likely have a very short time frame to eliminate residual latently infected CD4+ T cells that become reactivated after discontinuation of antiretroviral therapy following potentially curative treatment strategies.
Feasibility of esophageal stent fixation with an over-the-scope-clip for malignant esophageal strictures to prevent migration

Abstract Background and study aims Fixation of an esophageal self-expandable metal stent (SEMS) with an over-the-scope-clip (OTSC) system for a benign stricture to prevent migration has been reported. However, the efficacy of SEMS fixation with an OTSC for malignant esophageal stricture remains unclear. The aim of this retrospective study was to evaluate the feasibility of SEMS fixation with an OTSC for a malignant esophageal stricture. Patients and methods Twelve patients who underwent esophageal SEMS placement and fixation with an OTSC for a malignant esophageal stricture were included in this retrospective study. The primary endpoint was technical success. The secondary endpoint was clinical success, which was defined as an improvement of at least 1 grade in the dysphagia score 1 week after SEMS placement or changes in the dysphagia score from before SEMS placement to 1 week after SEMS placement. Results The technical success rate was 100 %. The clinical success rate was 92.3 %. In 6 mild stricture cases in which a standard peroral endoscope could be used, no migration of the SEMS was observed. The median dysphagia score before and at 1 week after SEMS placement was 3 (range 2 – 4) and 0 (0 – 4), respectively, which indicated improvement at 1 week after SEMS placement compared with before SEMS placement (P = 0.002). There were no adverse events associated with placement of SEMS and deployment of an OTSC. Conclusions SEMS fixation with an OTSC is feasible for prevention of migration due to a malignant esophageal stricture.
The (in-) validity of the WSSUS assumption in vehicular radio channels

The assumption of wide-sense-stationarity (WSS) and uncorrelated scattering (US) of wireless propagation channels is widespread for the design and analysis of wireless propagation channels. However, the assumption is only valid within a limited range. In this paper, we investigate the extension of this range not only in time (WSS), but also in frequency (US), for measured vehicular propagation channels. We do this by using the collinearity of the local scattering function, which is a bounded spectral distance metric, and thus allows us to set an indicative threshold, which in turn enables a WSS and a US test. We prove that the fading process in vehicular communications is strongly non-WSS, which agrees with results previously reported in the literature. Furthermore, for the first time (to the authors' knowledge), we show their non-US behavior as well, mainly in scenarios with rich scattering. The dimensions of the minimum stationarity region are on the order of 40 ms in time and 40MHz in frequency.
Exploring Correlated Subspaces for Efficient Query Processing in Sparse Databases

Sparse data are becoming increasingly common and available in many real-life applications. However, relatively little attention has been paid to effectively model the sparse data and existing approaches such as the conventional "horizontal¿ and "vertical¿ representations fail to provide satisfactory performance for both storage and query processing, as such approaches are too rigid and generally do not consider the dimension correlations. In this paper, we propose a new approach, named HoVer, to store and conduct query for sparse data sets in an unmodified RDBMS, where HoVer stands for horizontal representation over vertically partitioned subspaces. According to the dimension correlations of sparse data sets, a novel mechanism has been developed to vertically partition a high-dimensional sparse data set into multiple lower-dimensional subspaces, and all the dimensions are highly correlated intrasubspace and highly unrelated intersubspace, respectively. Therefore, original data objects can be represented by the horizontal format in respective subspaces. With the novel HoVer representation, users can write SQL queries over the original horizontal view, which can be easily rewritten into queries over the subspace tables. Experiments over synthetic and real-life data sets show that our approach is effective in finding correlated subspaces and yields superior performance for the storage and query of sparse data.