Syntactic discriminative language model rerankers for statistical machine translation

This article describes a method that successfully exploits syntactic features for n-best translation candidate reranking using perceptrons. We motivate the utility of syntax by demonstrating the superior performance of parsers over n-gram language models in differentiating between Statistical Machine Translation output and human translations. Our approach uses discriminative language modelling to rerank the n-best translations generated by a statistical machine translation system. The performance is evaluated for Arabic-to-English translation using NIST’s MT-Eval benchmarks. While deep features extracted from parse trees do not consistently help, we show how features extracted from a shallow Part-of-Speech annotation layer outperform a competitive baseline and a state-of-the-art comparative reranking approach, leading to significant BLEU improvements on three different test sets

Recalculation of dose for each fraction of treatment on TomoTherapy.

OBJECTIVE: The VoxTox study, linking delivered dose to toxicity requires recalculation of typically 20-37 fractions per patient, for nearly 2000 patients. This requires a non-interactive interface permitting batch calculation with multiple computers. METHODS: Data are extracted from the TomoTherapy(®) archive and processed using the computational task-management system GANGA. Doses are calculated for each fraction of radiotherapy using the daily megavoltage (MV) CT images. The calculated dose cube is saved as a digital imaging and communications in medicine RTDOSE object, which can then be read by utilities that calculate dose-volume histograms or dose surface maps. The rectum is delineated on daily MV images using an implementation of the Chan-Vese algorithm. RESULTS: On a cluster of up to 117 central processing units, dose cubes for all fractions of 151 patients took 12 days to calculate. Outlining the rectum on all slices and fractions on 151 patients took 7 h. We also present results of the Hounsfield unit (HU) calibration of TomoTherapy MV images, measured over an 8-year period, showing that the HU calibration has become less variable over time, with no large changes observed after 2011. CONCLUSION: We have developed a system for automatic dose recalculation of TomoTherapy dose distributions. This does not tie up the clinically needed planning system but can be run on a cluster of independent machines, enabling recalculation of delivered dose without user intervention. ADVANCES IN KNOWLEDGE: The use of a task management system for automation of dose calculation and outlining enables work to be scaled up to the level required for large studies.JES is supported by Cancer Research UK through the Cambridge Cancer Centre. MR, AB and KH are supported by Cancer Research UK through the VoxTox Research Programme. NGB is supported by the NIHR Cambridge Biomedical Research Centre.This is the author accepted manuscript. The final version is available from British Institute of Radiology via http://dx.doi.org/10.1259/bjr.2015077

Screening for coping style increases the power of gene expression studies

Background: Individuals of many vertebrate species show different stress coping styles and these have a striking influence on how gene expression shifts in response to a variety of challenges. Principal Findings: This is clearly illustrated by a study in which common carp displaying behavioural predictors of different coping styles (characterised by a proactive, adrenaline-based or a reactive, cortisol-based response) were subjected to inflammatory challenge and specific gene transcripts measured in individual brains. Proactive and reactive fish differed in baseline gene expression and also showed diametrically opposite responses to the challenge for 80% of the genes investigated. Significance: Incorporating coping style as an explanatory variable can account for some the unexplained variation that is common in gene expression studies, can uncover important effects that would otherwise have passed unnoticed and greatly enhances the interpretive value of gene expression data

Accumulated dose to the rectum, measured using dose-volume histograms and dose-surface maps, is different from planned dose in all patients treated with radiotherapy for prostate cancer.

OBJECTIVE: We sought to calculate accumulated dose (DA) to the rectum in patients treated with radiotherapy for prostate cancer. We were particularly interested in whether dose-surface maps (DSMs) provide additional information to dose-volume histograms (DVHs). METHODS: Manual rectal contours were obtained for kilovoltage and daily megavoltage CT scans for 10 participants from the VoxTox study (380 scans). Daily delivered dose recalculation was performed using a ray-tracing algorithm. Delivered DVHs were summated to create accumulated DVHs. The rectum was considered as a cylinder, cut and unfolded to produce daily delivered DSMs; these were summated to produce accumulated DSMs. RESULTS: Accumulated dose-volumes were different from planned in all participants. For one participant, all DA levels were higher and all volumes were larger than planned. For four participants, all DA levels were lower and all volumes were smaller than planned. For each of these four participants, ≥1% of pixels on the accumulated DSM received ≥5 Gy more than had been planned. CONCLUSION: Differences between accumulated and planned dose-volumes were seen in all participants. DSMs were able to identify differences between DA and planned dose that could not be appreciated from the DVHs. Further work is needed to extract the dose data embedded in the DSMs. These will be correlated with toxicity as part of the VoxTox Programme. ADVANCES IN KNOWLEDGE: DSMs are able to identify differences between DA and planned dose that cannot be appreciated from DVHs alone and should be incorporated into future studies investigating links between DA and toxicity.JES is supported by Cancer Research UK through the Cambridge Cancer Centre. NGB is supported by the NIHR Cambridge Biomedical Research Centre. KH, MR and AMB are supported by the VoxTox Research Programme, which is funded by Cancer Research UK.This is the final version of the article. It first appeared from the British Institute of Radiology via http://dx.doi.org/10.1259/bjr.2015024

Borrelia recurrentis employs a novel multifunctional surface protein with anti-complement, anti-opsonic and invasive potential to escape innate immunity

Borrelia recurrentis, the etiologic agent of louse-borne relapsing fever in humans, has evolved strategies, including antigenic variation, to evade immune defence, thereby causing severe diseases with high mortality rates. Here we identify for the first time a multifunctional surface lipoprotein of B. recurrentis, termed HcpA, and demonstrate that it binds human complement regulators, Factor H, CFHR-1, and simultaneously, the host protease plasminogen. Cell surface bound factor H was found to retain its activity and to confer resistance to complement attack. Moreover, ectopic expression of HcpA in a B. burgdorferi B313 strain, deficient in Factor H binding proteins, protected the transformed spirochetes from complement-mediated killing. Furthermore, HcpA-bound plasminogen/plasmin endows B. recurrentis with the potential to resist opsonization and to degrade extracellular matrix components. Together, the present study underscores the high virulence potential of B. recurrentis. The elucidation of the molecular basis underlying the versatile strategies of B. recurrentis to escape innate immunity and to persist in human tissues, including the brain, may help to understand the pathological processes underlying louse-borne relapsing fever

Quantifying the Detrimental Impacts of Land-Use and Management Change on European Forest Bird Populations

The ecological impacts of changing forest management practices in Europe are poorly understood despite European forests being highly managed. Furthermore, the effects of potential drivers of forest biodiversity decline are rarely considered in concert, thus limiting effective conservation or sustainable forest management. We present a trait-based framework that we use to assess the detrimental impact of multiple land-use and management changes in forests on bird populations across Europe. Major changes to forest habitats occurring in recent decades, and their impact on resource availability for birds were identified. Risk associated with these changes for 52 species of forest birds, defined as the proportion of each species' key resources detrimentally affected through changes in abundance and/or availability, was quantified and compared to their pan-European population growth rates between 1980 and 2009. Relationships between risk and population growth were found to be significantly negative, indicating that resource loss in European forests is an important driver of decline for both resident and migrant birds. Our results demonstrate that coarse quantification of resource use and ecological change can be valuable in understanding causes of biodiversity decline, and thus in informing conservation strategy and policy. Such an approach has good potential to be extended for predictive use in assessing the impact of possible future changes to forest management and to develop more precise indicators of forest health

Referral of patients with depression to mental health care by Dutch general practitioners: an observational study

<p>Abstract</p> <p>Background</p> <p>Depression is a common illness, often treated in primary care. Guidelines provide recommendations for referral to mental health care. Several studies investigated determinants of referral, none investigated guideline criteria as possible determinants.</p> <p>We wanted to evaluate general practitioner's referral of depressed patients to mental health care and to what extent this is in agreement with (Dutch) guideline recommendations.</p> <p>Methods</p> <p>We used data of primary care respondents from the Netherlands Study of Depression and Anxiety with major depressive disorder in the past year (n = 478). We excluded respondents with missing data (n = 134). Referral data was collected from electronic patient files between 1 year before and after baseline and self report at baseline and 1-year follow-up. Logistic regression was used to describe association between guideline referral criteria (e.g. perceived need for psychotherapy, suicide risk, severe/chronic depression, antidepressant therapy failure) and referral.</p> <p>Results</p> <p>A high 58% of depressed patients were referred. Younger patients, those with suicidal tendency, chronic depression or perceived need for psychotherapy were referred more often. Patients who had used ≥2 antidepressants or with chronic depression were more often referred to secondary care. Referred respondents met on average more guideline criteria for referral. However, only 8-11% of variance was explained.</p> <p>Conclusion</p> <p>The majority of depressed patients were referred to mental health care. General practitioners take guideline criteria into account in decision making for referral of depressed patients to mental health care. However, other factors play a part, considering the small percentage of variance explained. Further research is necessary to investigate this.</p

Human bite injuries in the oro-facial region at the Muhimbili National Hospital, Tanzania

<p>Abstract</p> <p>Background</p> <p>Human bites in the maxillofacial region compromise function and aesthetics, resulting in social and psychological effects. There is paucity of information regarding human bite injuries in Tanzania. The aim of the study was to assess the occurrence, treatment modalities and prognosis of human bite injuries in the oro-facial region at the Muhimbili National Hospital Dar es Salaam, Tanzania.</p> <p>Methods</p> <p>In a prospective study the details of patients with human bite injuries in the oro-facial region who attended at the Department of Oral and Maxillofacial Surgery of the Muhimbili National Hospital between January 2001 and December 2005 were recorded. Data included information on age, sex, site, duration of the injury at the time of reporting to hospital, reasons, details of treatment offered and outcome after treatment.</p> <p>Results</p> <p>A total of 33 patients, 13 males and 20 females aged between 12 and 49 years with human bite injuries in the oro-facial region were treated. Thirty patients presented with clean uninfected wounds while 3 had infected wounds. The most (45.5%) frequently affected site was the lower lip. Treatment offered included thorough surgical cleansing with adequate surgical debridement and primary suturing. Tetanus prophylaxis and a course of broad-spectrum antibiotics were given to all the patients. In 90% of the 30 patients who were treated by suturing, the healing was uneventful with only 10% experiencing wound infection or necrosis. Three patients who presented with wounds that had signs of infection were treated by surgical cleansing with debridement, antibiotics and daily dressing followed by delayed primary suturing.</p> <p>Conclusion</p> <p>Most of the human bite injuries in the oro-facial region were due to social conflicts. Although generally considered to be dirty or contaminated they could be successfully treated by surgical cleansing and primary suture with a favourable outcome. Management of such injuries often need multidisciplinary approach.</p

Predicting first-episode psychosis patients who will never relapse over 10 years.

BACKGROUND: Although relapse in psychosis is common, a small proportion of patients will not relapse in the long term. We examined the proportion and predictors of patients who never relapsed in the 10 years following complete resolution of positive symptoms from their first psychotic episode. METHOD: Patients who previously enrolled in a 12-month randomized controlled trial on medication discontinuation and relapse following first-episode psychosis (FEP) were followed up after 10 years. Relapse of positive symptoms was operationalized as a change from a Clinical Global Impression scale positive score of <3 for at least 3 consecutive months to a score of ⩾3 (mild or more severe). Baseline predictors included basic demographics, premorbid functioning, symptoms, functioning, and neurocognitive functioning. RESULTS: Out of 178 first-episode patients, 37 (21%) never relapsed during the 10-year period. Univariate predictors (p ⩽ 0.1) of patients who never relapsed included a duration of untreated psychosis (DUP) ⩽30 days, diagnosed with non-schizophrenia spectrum disorders, having less severe negative symptoms, and performing better in logical memory immediate recall and verbal fluency tests. A multivariate logistic regression analysis further suggested that the absence of any relapsing episodes was significantly related to better short-term verbal memory, shorter DUP, and non-schizophrenia spectrum disorders. CONCLUSIONS: Treatment delay and neurocognitive function are potentially modifiable predictors of good long-term prognosis in FEP. These predictors are informative as they can be incorporated into an optimum risk prediction model in the future, which would help with clinical decision making regarding maintenance treatment in FEP