Miracle-dz/UniFAR-FTUs huggingface dataset:
A brainstem area mediating cerebrovascular and EEG responses to hypoxic excitation of rostral ventrolateral medulla in rat

1 We sought to identify the medullary relay area mediating the elevations of regional cerebral blood flow (rCBF) and synchronization of the electroencephalogram (EEG) in the rat cerebral cortex elicited by hypoxic excitation of reticulospinal sympathoexcitatory neurons of the rostral ventrolateral medulla (RVLM). 2 In anaesthetized spinalized rats electrical stimulation of RVLM elevated rCBF (laser‐Döppler flowmetry) by 31 ± 6 %, reduced cerebrovascular resistance (CVR) by 26 ± 8 %, and synchronized the EEG, increasing the power of the 5–6 Hz band by 98 ± 25 %. Stimulation of a contiguous caudal region, the medullary cerebral vasodilator area (MCVA), had comparable effects which, like responses of RVLM, were replicated by microinjection of L‐glutamate (5 nmol, 20 nl). 3 Microinjection of NaCN (300 pmol in 20 nl) elevated rCBF (17 ± 5 %) and synchronized the EEG from RVLM, but not MCVA, while nicotine (1.2 nmol in 40 nl) increased rCBF by 13 ± 5 % and synchronized the EEG from MCVA. In intact rats nicotine lowered arterial pressure only from MCVA (101 ± 3 to 52 ± 9 mmHg). 4 Bilateral electrolytic lesions of MCVA significantly reduced, by over 59 %, elevations in rCBF and, by 78 %, changes in EEG evoked from RVLM. Bilateral electrolytic lesions of RVLM did not affect responses from MCVA. 5 Anterograde tracing with BDA demonstrated that RVLM and MCVA are interconnected. 6 The MCVA is a nicotine‐sensitive region of the medulla that relays signals elicited by excitation of oxygen‐sensitive reticulospinal neurons in RVLM to reflexively elevate rCBF and slow the EEG as part of the oxygen‐conserving (diving) reflex initiated in these neurons by hypoxia or ischaemia.
Artifact-free quantification of free 3-chlorotyrosine, 3-bromotyrosine, and 3-nitrotyrosine in human plasma by electron capture-negative chemical ionization gas chromatography mass spectrometry and liquid chromatography-electrospray ionization tandem mass spectrometry.

Halogenation and nitration of biomolecules have been proposed as key mechanisms of host defense against bacteria, fungi, and viruses. Reactive oxidants also have the potential to damage host tissue, and they have been implicated in disease. In the current studies, we describe specific, sensitive, and quantitative methods for detecting three stable markers of oxidative damage: 3-chlorotyrosine, 3-bromotyrosine, and 3-nitrotyrosine. Our results indicate that electron capture-negative chemical ionization-gas chromatography/mass spectrometry (EC-NCI GC/MS) is 100-fold more sensitive than liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-MS/MS) for analyzing authentic 3-chlorotyrosine, 3-bromotyrosine, and 3-nitrotyrosine. Using an isotopomer of tyrosine to evaluate artifactual production of the analytes during sample preparation and analysis, we found that artifact generation was negligible with either technique. However, LC-MS/MS proved cumbersome for analyzing multiple samples because it required 1.5 h of run and equilibration time per analysis. In contrast, EC-NCI GC/MS required only 5 min of run time per analysis. Using EC-NCI GC/MS, we were able to detect and quantify attomole levels of free 3-chlorotyrosine, 3-bromotyrosine, and 3-nitrotyrosine in human plasma. Our results indicate that EC-NCI GC/MS is a sensitive and specific method for quantifying free 3-chlorotyrosine, 3-bromotyrosine, and 3-nitrotyrosine in biological fluids in a single, rapid analysis and that it avoids generating any of the analytes ex vivo.
The prognostic value of time needed on dialysis in patients with delayed graft function.

INTRODUCTION We hypothesize that in patients with delayed graft function (DGF), the need for a longer time needed on dialysis (TND) post-kidney transplant is associated with poorer long-term function and an increase in complications. METHODS This was a retrospective chart review involving collaboration between Western University (WU) Renal Transplant Program of London, Ontario and the Saskatchewan renal transplant program (SRTP). A total of 774 patients (567 WU and 207 SRTP) received kidney transplants between 2004 and 2011, of which 83 patients with deceased donor transplants (59 WU and 24 SRTP) developed DGF, defined as the need for dialysis in the first week posttransplant. RESULTS Patients with DGF were divided into three groups depending on TND [group 1: <7 days (n = 52), group 2: 7-14 days (n = 13) and group 3 (n = 18): >14 days]. The creatinine clearance (CrCl) at 30 days (42.5, 33.8, 20.0 cc/min; P < 0.001) and 1 year (56.7, 49.2, 37.3 cc/min, P = 0.031) were significantly different between the three groups. Multivariate regression analysis identified length of TND posttransplant (β = -0.5, P < 0.001) and donation after cardiac death (DCD) donor (β = 19.5, P < 0.001) as the most significant predictors of CrCl at 1 year in these patients with DGF. DCD kidneys with DGF had a higher CrCl at 1 year and fewer readmissions in the first year compared with non-DCD kidneys with DGF. DISCUSSION Our study suggests that increased TND is associated with worse CrCl at 1 year. The data also support the hypothesis of a different mechanism for DGF in DCD and non-DCD kidneys.
Influence of pH on stored human platelets

BACKGROUND: During storage at room temperature, platelets (PLTs) undergo several changes, a process known as PLT storage lesion. The pH is one of the variables changing and has been suggested to be a good surrogate marker for the quality of PLT concentrates. It is unknown whether the pH decrease as such induces the PLT storage lesion or that the deterioration of the PLTs results in the pH decrease. In this study, the responses of PLTs to applied pH values were investigated.
UCHIME improves sensitivity and speed of chimera detection

Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Internal Transcribed Spacer) to assess diversity or compare populations. Undetected chimeras may be misinterpreted as novel species, causing inflated estimates of diversity and spurious inferences of differences between populations. Detection and removal of chimeras is therefore of critical importance in such experiments. Results: We describe UCHIME, a new program that detects chimeric sequences with two or more segments. UCHIME either uses a database of chimera-free sequences or detects chimeras de novo by exploiting abundance data. UCHIME has better sensitivity than ChimeraSlayer (previously the most sensitive database method), especially with short, noisy sequences. In testing on artificial bacterial communities with known composition, UCHIME de novo sensitivity is shown to be comparable to Perseus. UCHIME is >100× faster than Perseus and >1000× faster than ChimeraSlayer. Contact: robert@drive5.com Availability: Source, binaries and data: http://drive5.com/uchime. Supplementary information: Supplementary data are available at Bioinformatics online.
Validation of the Rome III criteria for the diagnosis of irritable bowel syndrome in secondary care.

BACKGROUND & AIMS There are few validation studies of existing diagnostic criteria for irritable bowel syndrome (IBS). We conducted a validation study of the Rome and Manning criteria in secondary care. METHODS We collected complete symptom, colonoscopy, and histology data from 1848 consecutive adult patients with gastrointestinal symptoms at 2 hospitals in Hamilton, Ontario; the subjects then underwent colonoscopy. Assessors were blinded to symptom status. Individuals with normal colonoscopy and histopathology results, and no evidence of celiac disease, were classified as having no organic gastrointestinal disease. The reference standard used to define the presence of true IBS was lower abdominal pain or discomfort in association with a change in bowel habit and no organic gastrointestinal disease. Sensitivity, specificity, and positive and negative likelihood ratios, with 95% confidence intervals, were calculated for each diagnostic criteria. RESULTS In identifying patients with IBS, sensitivities of the criteria ranged from 61.9% (Manning) to 95.8% (Rome I), and specificities from 70.6% (Rome I) to 81.8% (Manning). Positive likelihood ratios ranged from 3.19 (Rome II) to 3.39 (Manning), and negative likelihood ratios from 0.06 (Rome I) to 0.47 (Manning). The level of agreement between diagnostic criteria was greatest for Rome I and Rome II (κ = 0.95), and lowest for Manning and Rome III (κ = 0.59). CONCLUSIONS Existing diagnostic criteria perform modestly in distinguishing IBS from organic disease. There appears to be little difference in terms of accuracy. More accurate ways of diagnosing IBS, avoiding the need for investigation, are required.
Regional structural characteristics of bovine periodontal ligament samples and their suitability for biomechanical tests

Mechanical testing of the periodontal ligament requires a practical experimental model. Bovine teeth are advantageous in terms of size and availability, but information is lacking as to the anatomy and histology of their periodontium. The aim of this study, therefore, was to characterize the anatomy and histology of the attachment apparatus in fully erupted bovine mandibular first molars. A total of 13 teeth were processed for the production of undecalcified ground sections and decalcified semi‐thin sections, for NaOH maceration, and for polarized light microscopy. Histomorphometric measurements relevant to the mechanical behavior of the periodontal ligament included width, number, size and area fraction of blood vessels and fractal analysis of the two hard–soft tissue interfaces. The histological and histomorphometric analyses were performed at four different root depths and at six circumferential locations around the distal and mesial roots. The variety of techniques applied provided a comprehensive view of the tissue architecture of the bovine periodontal ligament. Marked regional variations were observed in width, surface geometry of the two bordering hard tissues (cementum and alveolar bone), structural organization of the principal periodontal ligament connective tissue fibers, size, number and numerical density of blood vessels in the periodontal ligament. No predictable pattern was observed, except for a statistically significant increase in the area fraction of blood vessels from apical to coronal. The periodontal ligament width was up to three times wider in bovine teeth than in human teeth. The fractal analyses were in agreement with the histological observations showing frequent signs of remodeling activity in the alveolar bone – a finding which may be related to the magnitude and direction of occlusal forces in ruminants. Although samples from the apical root portion are not suitable for biomechanical testing, all other levels in the buccal and lingual aspects of the mesial and distal roots may be considered. The bucco‐mesial aspect of the distal root appears to be the most suitable location.
Phylogenetic associations of human and simian T-cell leukemia/lymphotropic virus type I strains: evidence for interspecies transmission

Homologous env sequences from 17 human T-leukemia/lymphotropic virus type I (HTLV-I) strains from throughout the world and from 25 simian T-leukemia/lymphotropic virus type I (STLV-I) strains from 12 simian species in Asia and Africa were analyzed in a phylogenetic context as an approach to resolving the natural history of these related retroviruses. STLV-I exhibited greater overall sequence variation between strains (1 to 18% compared with 0 to 9% for HTLV-I), supporting the simian origin of the modern viruses in all species. Three HTLV-I phylogenetic clusters or clades (cosmopolitan, Zaire, and Melanesia) were resolved with phenetic, parsimony, and likelihood analytical procedures. Seven phylogenetic clusters of STLV-I were resolved with the most primitive (deeply rooted) divergence involving several STLV-I strains from Asian primate species. Combined analysis of HTLV-I and STLV-I revealed that neither STLV-I clusters nor HTLV-I clusters recapitulated host species specificity; rather, multiple clades from the same species were closer to clades from other species than to each other. We interpret these evolutionary associations as support for the occurrence of multiple discrete interspecies transmissions of ancestral viruses between primate species (including human) that led to recognizable phylogenetic clades that persist in modern species. Geographic concordance of divergent host species that harbor closely related viruses reinforces that physical feasibility for hypothesized interspecies virus transmission in the past and in the present.
Point matching as a classification problem for fast and robust object pose estimation

We propose a novel approach to point matching under large viewpoint and illumination changes that are suitable for accurate object pose estimation at a much lower computational cost than state-of-the-art methods. Most of these methods rely either on using ad hoc local descriptors or on estimating local affine deformations. By contrast, we treat wide baseline matching of key points as a classification problem, in which each class corresponds to the set of all possible views of such a point. Given one or more images of a target object, we train the system by synthesizing a large number of views of individual key points and by using statistical classification tools to produce a compact description of this view set. At run-time, we rely on this description to decide to which class, if any, an observed feature belongs. This formulation allows us to use a classification method to reduce matching error rates, and to move some of the computational burden from matching to training, which can be performed beforehand. In the context of pose estimation, we present experimental results for both planar and non-planar objects in the presence of occlusions, illumination changes, and cluttered backgrounds. We show that the method is both reliable and suitable for initializing real-time applications.
Regulation of Autoimmune Diabetes by Complete Freund’s Adjuvant Is Mediated by NK Cells

Autoimmune (type 1) diabetes results from a loss of β cells that is mediated by self-reactive T cells. Previous studies have shown that a single injection of CFA prevents diabetes in nonobese diabetic (NOD) mice, but the mechanism(s) of protection remain unknown. We show here that NOD mice immunized with CFA have a markedly reduced incidence of diabetes and that this reduced incidence is associated with a decrease in the number of β cell-specific, autoreactive CTL. In addition, the adoptive transfer of diabetes into syngeneic NOD/SCID recipients was prevented by CFA immunization, and the protective effects of CFA were lost when cells expressing the NK cell marker, asialo GM1, were removed from both donor cells and recipient mice. Returning a population of CD3−DX5+ cells to the adoptive transfer restored the protective effects of CFA. Therefore, NK cells mediate the protective effects of CFA possibly through the down-regulation of autoreactive CTL and stimulation of NK cells represents a novel approach to the prevention of autoimmune diabetes.
A Methodology for Designing the Control of Energy Harvesting Sensor Nodes

Sensor nodes equipped with renewable energy sources are capable of recharging their batteries and supporting data collection and transmission indefinitely. Energy and data management of these types of systems is challenging primarily due to the variability of renewable energy sources and transmission channels. This paper explores a methodology for designing the control of such systems. The goal is to jointly control the energy usage and data sampling rate to maximize the long-term performance of the system subject to the constraints imposed by the available energy and data. The design of this control is based on estimates of the large deviations of the energy stored in the battery and of the queued data. A low-complexity control policy is proposed that does not depend on the instantaneous charge of the battery and data backlog and almost maximizes the long-term data transmission rate. Moreover, the results show that one can decouple the analysis of the energy and of the data queue without much loss in performance.
Change in sex ratio, disease course and age at diagnosis in Oslo MS patients through seven decades

Objectives – To study changes in sex ratio, disease course, time from onset to diagnosis and age at diagnosis by year of birth in a well‐defined population of multiple sclerosis (MS) patients. Materials and methods – Based on the Oslo MS Registry patients born from 1910 to 1980 with residence in Oslo at time of diagnosis were studied. Data were analyzed by 10‐year intervals based on year of birth. Results – The female to male ratio increased significantly from 1.48 to 2.30 through seven decades. Also, the ratio of initial relapsing–remitting (RR‐MS) to primary progressive (PP‐MS) disease course increased significantly from 1.93 to 16.00. The time from onset to diagnosis and the mean age at diagnosis declined significantly during the same period. Conclusions – This study shows that there has been a change in MS sex ratio, disease course and age at diagnosis through a period of seven decades, suggesting an environmental factor mainly affecting women at a younger age and causing a RR‐MS disease course.
Suicide and non-suicide mortality after self-harm in Taipei City, Taiwan.

BACKGROUND Most previous studies of long-term mortality risk following self-harm have been conducted in Western countries with few studies from Asia. AIMS To investigate suicide and non-suicide mortality after non-fatal self-harm in Taipei City, Taiwan. METHOD Prospective cohort study (median follow-up 3.3 years) of 7601 individuals presenting to hospital with self-harm (January 2004 to December 2006). Standardised mortality ratios (SMRs) for suicide and non-suicide mortality were calculated. RESULTS Suicide risk in the year following self-harm was over 100 times higher than in the general population (SMR = 119.6, 95% CI 99.6-142.5). Males and middle-aged and older adults had the highest subsequent risk of suicide. Compared with people who took an overdose, individuals who used hanging or charcoal burning in their index episode had the highest risk of suicide. For non-suicide mortality the SMRs were 6.7 (95% CI 5.7-7.8) in the first year and 4.4 (95% CI 3.9-4.9) during the whole follow-up period. CONCLUSIONS Patterns of increased all-cause and suicide mortality following an episode of self-harm are similar in Taipei City to those seen in Western countries. Designing better aftercare following non-fatal self-harm, particularly for those with underlying physical disorders or who have used lethal self-harm methods, should be a priority for suicide prevention programmes in Asia.
Analysis of Phase Interrogated SPR Fiber Optic Sensors With Bimetallic Layers

An effective analytical model combining geometrical optics with the transfer-matrix theory for stratified optical media is applied to investigate the sensing properties of tapered optical fiber surface plasmon resonance (SPR) sensors incorporating Ag-Au bimetallic layers, particularly in the context of phase interrogation. The performance of the sensing structures is studied as a function of the tapering parameters and thickness of the metallic layers. It is shown that the Ag-Au bimetallic combination is capable of improving the resolution and tuning working region of SPR fiber-optic sensors and that by tapering the sensing structures enhanced sensitivity can be achieved when phase interrogation is considered.
Vinasse: an alternative to lime sulphur for flower thinning?

Thinning trials with vinasse in comparison to lime sulphur were carried out for 4 years at different sites in South Tyrol. Beside the thinning effect, the influence on fruit quality, phytotoxic damage on the leaves and the return bloom of treated trees were evaluated. Depending on the dosage the vinasse treatments showed a good thinning effect, but russetting and leave damages were significantly higher in comparison to lime sulphur. Return bloom of vinasse treated trees was lower than of those treated with lime sulphur. In conclusion, vinasse treatments can not substitute lime sulphur for flower thinning in organic apple orchards.
Anti-PGL-1 Positivity as a Risk Marker for the Development of Leprosy among Contacts of Leprosy Cases: Systematic Review and Meta-analysis

Background There is no point of care diagnostic test for infection with M. Leprae or for leprosy, although ELISA anti PGL-1 has been considered and sometimes used as a means to identify infection. Methods A systematic review of all cohort studies, which classified healthy leprosy contacts, at entry, according to anti-PGL1 positivity, and had at least one year follow up. The outcome was clinical diagnosis of leprosy by an experienced physician. The meta-analysis used a fixed model to estimated OR for the association of PGL-1 positivity and clinical leprosy. A fixed model also estimated the sensibility of PGL-1 positivity and positive predictive value. Results Contacts who were anti PGL-1 positive at baseline were 3 times as likely to develop leprosy; the proportion of cases of leprosy that were PGL-1 positive at baseline varied but was always under 50%. Conclusions Although there is a clear and consistent association between positivity to anti PGL-1 and development of leprosy in healthy contacts, selection of contacts for prophylaxis based on anti PGL1 response would miss more than half future leprosy cases. Should chemoprophylaxis of controls be incorporated into leprosy control programmes, PGL1 appears not to be a useful test in the decision of which contacts should receive chemoprophylaxis.