Passage Re-Ranking in Live QA NLP Pipelines with BERT

Passage ranking and document ranking are two common tasks in NLP. Many state of the art pipelines use BM25 to retrieve passages. The top results of this ranking are then re-ranked using a BERT transformer trained on the MS MARCO Passage data set. This system and variations have proved highly effective. In addition, questions and answers using BERT are also well explored topics. However, these systems are fundamentally limited by speed and resource consumption requirements. Given an arbitrary corpus and a collection of pre-trained models, we would like to prove that it is possible to create a live Question Answering machine without fine tuning for a particular topic. In particular, we employ a BERT re-ranker to find the first acceptable fit to pass to our QA transformer. This approach is fundamentally different from past research in that it is focused on first fit and not best fit. The goal of this research is to allow anyone to employ off the shelf components to create an effective, interactive question answering system

Surgical management of low grade isthmic spondylolisthesis; a randomized controlled study of the surgical fixation with and without reduction

<p>Abstract</p> <p>Background</p> <p>spondylolisthesis is a condition in which a vertebra slips out of the proper position onto the bone below it as a result of pars interarticularis defect. The slipped segment produces abnormal positioning of the vertebrae in relation to each other along the spinal column and causes mechanical back pain and neural breach.</p> <p>Materials and methods</p> <p>A randomized and double blinded study consisted of 41 patients aged 36-69 years (18 females and 28 males) treated for symptomatic spondylolisthesis between December,2006 and December, 2009. All patients were randomly distributed into two groups I and II. Twenty patients were in Group I; they underwent reduction of the slipped vertebrae by using Reduction-Screw Technique and posterior lumbar interbody fixation (PLIF). Group II consisted of twenty one patients who underwent only surgical fixation (PLIF) without reduction. All patients in this study had same pre and post operative management.</p> <p>Results</p> <p>only one case had broken rod in group I that required revision. Superficial wound infection was experienced in two patients and one patient, from group II, developed wound hematoma. The outcome in both groups was variable on the short term but was almost the same on the long term follow up.</p> <p>Conclusion</p> <p>surgical management of symptomatic low grade spondylolisthesis should include neural decompression and surgical fixation. Reduction of slipped vertebral bodies is unnecessary as the ultimate outcome will be likely similar.</p

Reusable photocatalytic optical fibers for underground, deep-sea, and turbid water remediation

An approach for underground, deep, and turbid water remediation is presented based on optical fibers with a photocatalytic coating. Thus, photocatalytic TiO2 P25 nanoparticles immobilized in a poly(vinylidene difluoride) (PVDF) matrix are coated on polymeric optical fibers (POFs) and the photocatalytic performance of the system is assessed under artificial sunlight. To the best of our knowledge, poly(methyl methacrylate)-POF coated with TiO2/PVDF and the reusability of any type of POF for photocatalytic applications are not previously reported. The photocatalytic efficiency of the hybrid material in the degradation of ciprofloxacin (CIP) and its reusability are evaluated here. It is shown that 50 w/w% of TiO2 P25 achieves a degradation of 95% after 72 h under artificial sunlight and a reusability of three times leads to a loss of activity inferior to 11%. The efficient removal of ciprofloxacin and the stability of the POF coated with TiO2 P25 successfully demonstrate its suitability in the degradation of pollutants with potential application in regions with low light illumination, as in underground and deep water.Peer ReviewedPostprint (published version

Nickel on nitrogen doped carbon pellets for continuous flow hydrogenation of biomass derived compounds in water

Hydrogenation reactions in water at elevated temperatures are challenging for heterogeneous catalyst. Thus, we present a simple, cheap, scalable, and sustainable approach for synthesizing an efficient and water-tolerant Ni catalyst supported on highly porous nitrogen-doped carbon (NDC) in pellet shape. The performance of this catalyst was evaluated in the aqueous-phase hydrogenation of lignocellulosic biomass-derived compounds, i.e., glucose (Glu), xylose (Xyl) and vanillin (V), using a continuous-flow system. The prepared 35 wt.- Ni on NDC catalyst exhibited a high catalytic performance in all three different aqueous-phase hydrogenation reactions, i.e., conversion of Glu, Xyl and V was 96.3 mol, 85 mol and 100 mol and yield of sorbitol (Sor), xylitol (Xyt) and 2-methoxy-4-methylphenol (MMP) was 82 mol, 62 mol and 100 mol, respectively. This high activity was attributed to heterojunction effects stabilizing and adjusting the homogenously dispersed Ni nanoparticles on the surface of NDC. Changing the electron density in the Nickel nanoparticle allows high performance of the catalyst under long time of stream (7 to 30 h) with minimized Ni leaching

Assessing the impact of biomedical research in academic institutions of disparate sizes

Abstract Background The evaluation of academic research performance is nowadays a priority issue. Bibliometric indicators such as the number of publications, total citation counts and h-index are an indispensable tool in this task but their inherent association with the size of the research output may result in rewarding high production when evaluating institutions of disparate sizes. The aim of this study is to propose an indicator that may facilitate the comparison of institutions of disparate sizes. Methods The Modified Impact Index (MII) was defined as the ratio of the observed h-index (h) of an institution over the h-index anticipated for that institution on average, given the number of publications (N) it produces i.e. (α and β denote the intercept and the slope, respectively, of the line describing the dependence of the h-index on the number of publications in log10 scale). MII values higher than 1 indicate that an institution performs better than the average, in terms of its h-index. Data on scientific papers published during 2002–2006 and within 36 medical fields for 219 Academic Medical Institutions from 16 European countries were used to estimate α and β and to calculate the MII of their total and field-specific production. Results From our biomedical research data, the slope β governing the dependence of h-index on the number of publications in biomedical research was found to be similar to that estimated in other disciplines (≈0.4). The MII was positively associated with the average number of citations/publication (r = 0.653, p Conclusion The MII should complement the use of h-index when comparing the research output of institutions of disparate sizes. It has a conceptual interpretation and, with the data provided here, can be computed for the total research output as well as for field-specific publication sets of institutions in biomedicine.</p

Epidemiological trends in nosocomial candidemia in intensive care

BACKGROUND: Infection represents a frequent complication among patients in Intensive Care Units (ICUs) and mortality is high. In particular, the incidence of fungal infections, especially due to Candida spp., has been increasing during the last years. METHODS: In a retrospective study we studied the etiology of candidemia in critically ill patients over a five-year period (1999–2003) in the ICU of the San Martino University Hospital in Genoa, Italy. RESULTS: In total, 182 episodes of candidaemia were identified, with an average incidence of 2.22 episodes/10 000 patient-days/year (range 1.25–3.06 episodes). Incidence of candidemia increased during the study period from 1.25 in 1999 to 3.06/10 000 patient-days/year in 2003. Overall, 40% of the fungemia episodes (74/182) were due to C.albicans, followed by C. parapsilosis(23%), C.glabrata (15%), C.tropicalis (9%) and other species (13%). Candidemia due to non-albicans species increased and this was apparently correlated with an increasing use of azoles for prophylaxis or empirical treatment. CONCLUSION: The study demonstrates a shift in the species of Candida causing fungemia in a medical and surgical ICU population during a 5 year period. The knowledge of the local epidemiological trends in Candida species isolated in blood cultures is important to guide therapeutic choices

SNP genotyping to screen for a common deletion in CHARGE Syndrome

BACKGROUND: CHARGE syndrome is a complex of birth defects including coloboma, choanal atresia, ear malformations and deafness, cardiac defects, and growth delay. We have previously hypothesized that CHARGE syndrome could be caused by unidentified genomic microdeletion, but no such deletion was detected using short tandem repeat (STR) markers spaced an average of 5 cM apart. Recently, microdeletion at 8q12 locus was reported in two patients with CHARGE, although point mutation in CHD7 on chromosome 8 was the underlying etiology in most of the affected patients. METHODS: We have extended our previous study by employing a much higher density of SNP markers (3258) with an average spacing of approximately 800 kb. These SNP markers are diallelic and, therefore, have much different properties for detection of deletions than STRs. RESULTS: A global error rate estimate was produced based on Mendelian inconsistency. One marker, rs431722 exceeded the expected frequency of inconsistencies, but no deletion could be demonstrated after retesting the 4 inconsistent pedigrees with local flanking markers or by FISH with the corresponding BAC clone. Expected deletion detection (EDD) was used to assess the coverage of specific intervals over the genome by deriving the probability of detecting a common loss of heterozygosity event over each genomic interval. This analysis estimated the fraction of unobserved deletions, taking into account the allele frequencies at the SNPs, the known marker spacing and sample size. CONCLUSIONS: The results of our genotyping indicate that more than 35% of the genome is included in regions with very low probability of a deletion of at least 2 Mb

Bilateral effects of unilateral cerebellar lesions as detected by voxel based morphometry and diffusion imaging

Over the last decades, the importance of cerebellar processing for cortical functions has been acknowledged and consensus was reached on the strict functional and structural cortico-cerebellar interrelations. From an anatomical point of view strictly contralateral interconnections link the cerebellum to the cerebral cortex mainly through the middle and superior cerebellar peduncle. Diffusion MRI (dMRI) based tractography has already been applied to address cortico-cerebellar-cortical loops in healthy subjects and to detect diffusivity alteration patterns in patients with neurodegenerative pathologies of the cerebellum. In the present study we used dMRI-based tractography to determine the degree and pattern of pathological changes of cerebellar white matter microstructure in patients with focal cerebellar lesions. Diffusion imaging and high-resolution volumes were obtained in patients with left cerebellar lesions and in normal controls. Middle cerebellar peduncles and superior cerebellar peduncles were reconstructed by multi fiber diffusion tractography. From each tract, measures of microscopic damage were assessed, and despite the presence of unilateral lesions, bilateral diffusivity differences in white matter tracts were found comparing patients with normal controls. Consistently, bilateral alterations were also evidenced in specific brain regions linked to the cerebellum and involved in higher-level functions. This could be in line with the evidence that in the presence of unilateral cerebellar lesions, different cognitive functions can be affected and they are not strictly linked to the side of the cerebellar lesion

Increased Mast Cell Density and Airway Responses to Allergic and Non-Allergic Stimuli in a Sheep Model of Chronic Asthma

BACKGROUND: Increased mast cell (MC) density and changes in their distribution in airway tissues is thought to contribute significantly to the pathophysiology of asthma. However, the time sequence for these changes and how they impact small airway function in asthma is not fully understood. The aim of the current study was to characterise temporal changes in airway MC density and correlate these changes with functional airway responses in sheep chronically challenged with house dust mite (HDM) allergen. METHODOLOGY/PRINCIPAL FINDINGS: MC density was examined on lung tissue from four spatially separate lung segments of allergic sheep which received weekly challenges with HDM allergen for 0, 8, 16 or 24 weeks. Lung tissue was collected from each segment 7 days following the final challenge. The density of tryptase-positive and chymase-positive MCs (MC(T) and MC(TC) respectively) was assessed by morphometric analysis of airway sections immunohistochemically stained with antibodies against MC tryptase and chymase. MC(T) and MC(TC) density was increased in small bronchi following 24 weeks of HDM challenges compared with controls (P<0.05). The MC(TC)/MC(T) ratio was significantly increased in HDM challenged sheep compared to controls (P<0.05). MC(T) and MC(TC) density was inversely correlated with allergen-induced increases in peripheral airway resistance after 24 weeks of allergen exposure (P<0.05). MC(T) density was also negatively correlated with airway responsiveness after 24 challenges (P<0.01). CONCLUSIONS: MC(T) and MC(TC) density in the small airways correlates with better lung function in this sheep model of chronic asthma. Whether this finding indicates that under some conditions mast cells have protective activities in asthma, or that other explanations are to be considered requires further investigation