Performance and clinical utility of a new supervised machine-learning pipeline in detecting rare ciliopathy patients based on deep phenotyping from electronic health records and semantic similarity

BACKGROUND

Rare diseases affect approximately 400 million people worldwide. Many of them suffer from delayed diagnosis. Among them, NPHP1-related renal ciliopathies need to be diagnosed as early as possible as potential treatments have been recently investigated with promising results. Our objective was to develop a supervised machine learning pipeline for the detection of NPHP1 ciliopathy patients from a large number of nephrology patients using electronic health records (EHRs).

METHODS AND RESULTS

We designed a pipeline combining a phenotyping module re-using unstructured EHR data, a semantic similarity module to address the phenotype dependence, a feature selection step to deal with high dimensionality, an undersampling step to address the class imbalance, and a classification step with multiple train-test split for the small number of rare cases. The pipeline was applied to thirty NPHP1 patients and 7231 controls and achieved good performances (sensitivity 86% with specificity 90%). A qualitative review of the EHRs of 40 misclassified controls showed that 25% had phenotypes belonging to the ciliopathy spectrum, which demonstrates the ability of our system to detect patients with similar conditions.

CONCLUSIONS

Our pipeline reached very encouraging performance scores for pre-diagnosing ciliopathy patients. The identified patients could then undergo genetic testing. The same data-driven approach can be adapted to other rare diseases facing underdiagnosis challenges.

Audiological phenotyping evaluation in KBG syndrome: Description of a multicenter review

OBJECTIVES

Our objective was to reinforce clinical knowledge of hearing impairment in KBG syndrome. KBG syndrome is a rare genetic disorder due to monoallelic pathogenic variations of ANKRD11.The typical phenotype includes facial dysmorphism, costal and spinal malformation and developmental delay. Hearing loss in KBG patients has been reported for many years, but no study has evaluated audiological phenotyping from a clinical and an anatomical point of view.

METHODS

This French multicenter study included 32 KBG patients with retrospective collection of data on audiological features, ear imaging and genetic investigations.

RESULTS

We identified a typical audiological profil in KBG syndrome: conductive (71%), bilateral (81%), mild to moderate (84%) and stable (69%) hearing loss, with some audiological heterogeneity. Among patients with an abnormality on CT imaging (55%), ossicular chain impairment (67%), fixation of the stapes footplate (33%) and inner-ear malformations (33%) were the most common abnormalities.

CONCLUSION

We recommend a complete audiological and radiological evaluation and an ENT-follow up in all patients presenting with KBG Syndrome. Imaging evaluation is necessary to determine the nature of lesions in the middle and inner ear.

Improving Patient Similarity Using Different Modalities of Phenotypes Extracted from Clinical Narratives

In the context of medical concept extraction, it is critical to determine if clinical signs or symptoms mentioned in the text were present or absent, experienced by the patient or their relatives. Previous studies have focused on the NLP aspect but not on how to leverage this supplemental information for clinical applications. In this paper, we aim to use the patient similarity networks framework to aggregate different phenotyping modalities. NLP techniques were applied to extract phenotypes and predict their modalities from 5470 narrative reports of 148 patients with ciliopathies (a group of rare diseases). Patient similarities were computed using each modality separately for aggregation and clustering. We found that aggregating negated phenotypes improved patient similarity, but further aggregating relatives' phenotypes worsened the result. We suggest that different modalities of phenotypes can contribute to patient similarity, but they should be aggregated carefully and with appropriate similarity metrics and aggregation models.

NOTCH2 related disorders: Description and review of the fetal presentation

Signs of skeletal dysplasias are relatively common in fetuses with abnormal ultrasound (US) findings. The diversity of congenital skeletal disorders, the possibility of late-onset severe phenotypes and overlapping syndromes can be a challenge in the way of diagnosis, even if prenatal high-throuput sequencing allows for a better diagnosis, prognosis and genetic counseling. Hajdu-Cheney spectrum pathologies are rarely described in prenatal, and the signs associated remain poorly known, and do not include specific postnatal signs as acro-osteolysis and premature osteoporosis. We hereby report a couple for whom a medical termination of pregnancy was performed because a severe polymalformative syndrome associating severely short limbs with bowed long bones, severe cardiopathy, hyperechogenic kidneys and dysmorphism. After fetopathological and radiological examinations, Exome Sequencing (ES) was performed and revealed a de novo truncating mutation in the last exon of NOTCH2, responsible for Hajdu-Cheney or Serpentine Fibula Polycystic Kidney syndromes.

Does visual acuity predict visual preference in progressive addition lenses?

PURPOSE

We aimed to determine if visual acuity (VA) could differentiate the quality of vision with two ophthalmic lenses with unwanted astigmatism.

METHODS

Twenty presbyopic subjects (48 to 62 years old; VA better than 0.0 logMAR) graded the magnitude of their preference between two progressive addition lenses (plano addition 2.00D) and their visual acuities were measured with both lenses at various eccentricities from -12 to +12 mm from the near vision point every 3 mm in controlled conditions.

RESULTS

The Lens with the least peripheral astigmatism was preferred by 75% of the subjects. VA measured at the near vision point was statistically worse (p<0.01) with this lens whereas the contrary was observed in the periphery (± 12 and -9 mm of eccentricity). The Friedman test shows that the eccentricity (p<0.001) has a significant effect on visual acuity. However, the lens did not show any significant effect (p=0.76). The choice of the favorite lens was predicted for only 35% when considering central VA (up to 6mm) and 80% of the subjects when considering peripheral VA (9 to 12mm). However, the magnitude of the difference could be predicted by peripheral VA in only 60% of the subjects.

CONCLUSION

High contrast Visual acuity was clearly able to differentiate the 2 lens designs tested in our experiment. However, even under the controlled conditions of this study, it was not possible to predict the quality of vision, as measured by a subjective appreciation, through progressive addition lenses at various eccentricities from the near vision with an addition of 2.0D.

Consideration of oral health in rare disease expertise centres: a retrospective study on 39 rare diseases using text mining extraction method

Background

Around 8000 rare diseases are currently defined. In the context of individual vulnerability and more specifically the one induced by rare diseases, ensuring oral health is a particularly important issue. The objective of the study is to evaluate the pattern of oral health care course for patients with any rare genetic disease. Description of oral phenotypic signs—which predict a theoretical dental health care course—and effective orientation into an oral healthcare were evaluated.

Materials and methods

We set up a retrospective cohort study to describe the consideration of patient oral health and potential orientation to an oral health care course who have at least been seen once between 1 January 2017 and 1 January 2020 in Necker Enfants Malades Hospital. We recruited patients from this study using the data warehouse, Dr Warehouse® (DrWH), from Necker-Enfants Malades Hospital.

Results

The study sample included 39 rare diseases, 2712 patients, with 54.7% girls and 45.3% boys. In the sample studied, 27.9% of patients had an acquisition delay or a pervasive developmental disorder. Among the patient files studied, oral and dental phenotypic signs were described for 18.40% of the patients, and an orientation in an oral healthcare was made in 15.60% of patients. The overall "network" effect was significantly associated with description of phenotypic signs (corrected p = 1.44e−77) and orientation to an oral healthcare (corrected p = 23.58e−44). Taking the Defiscience network (rare diseases of cerebral development and intellectual disability) as a reference for the odd ratio analysis, OSCAR, TETECOU, FILNEMUS, FIMARAD, MHEMO networks stand out from the other networks for their significantly higher consideration of oral phenotypic signs and orientation in an oral healthcare.

Conclusion

To our knowledge, no study has explored the management of oral health in so many rare diseases. The expected benefits of this study are, among others, a better understanding, and a better knowledge of the oral care, or at least of the consideration of oral care, in patients with rare diseases. Moreover, with the will to improve the knowledge on genetic diseases, oral heath must have a major place in the deep patient phenotyping. Therefore, interdisciplinary consultations with health professionals from different fields are crucial.

Using Deep Learning to Improve Phenotyping from Clinical Reports

With the development of clinical databases and the ubiquity of EHRs, physicians and researchers alike have access to an unprecedented amount of data. Complexity of the available data has also increased since clinical reports are also included and require frameworks with natural language processing capabilities in order to process them and extract information not found in other types of documents. In the following work we implement a data processing pipeline performing phenotyping, disambiguation, negation and subject prediction on such reports. We compare it to an existing solution routinely used in a children's hospital with special focus on genetic diseases. We show that by replacing components based on rules and pattern matching with components leveraging deep learning models and fine-tuned word embeddings we obtain performance improvements of 7%, 10% and 27% in terms of F1 measure for each task. The solution we devised will help build more reliable decision support systems.

Enriching UMLS-Based Phenotyping of Rare Diseases Using Deep-Learning: Evaluation on Jeune Syndrome

The wide adoption of Electronic Health Records (EHR) in hospitals provides unique opportunities for high throughput phenotyping of patients. The phenotype extraction from narrative reports can be performed by using either dictionary-based or data-driven methods. We developed a hybrid pipeline using deep learning to enrich the UMLS Metathesaurus for automatic detection of phenotypes from EHRs. The pipeline was evaluated on a French database of patients with a rare disease characterized by skeletal abnormalities, Jeune syndrome. The results showed a 2.5-fold improvement regarding the number of detected skeletal abnormalities compared to the baseline extraction using the standard release of UMLS. Our method can help enrich the coverage of the UMLS and improve phenotyping, especially for languages other than English.

Patient-Patient Similarity-Based Screening of a Clinical Data Warehouse to Support Ciliopathy Diagnosis

A timely diagnosis is a key challenge for many rare diseases. As an expanding group of rare and severe monogenic disorders with a broad spectrum of clinical manifestations, ciliopathies, notably renal ciliopathies, suffer from important underdiagnosis issues. Our objective is to develop an approach for screening large-scale clinical data warehouses and detecting patients with similar clinical manifestations to those from diagnosed ciliopathy patients. We expect that the top-ranked similar patients will benefit from genetic testing for an early diagnosis. The dependence and relatedness between phenotypes were taken into account in our similarity model through medical concept embedding. The relevance of each phenotype to each patient was also considered by adjusted aggregation of phenotype similarity into patient similarity. A ranking model based on the best-subtype-average similarity was proposed to address the phenotypic overlapping and heterogeneity of ciliopathies. Our results showed that using less than one-tenth of learning sources, our language and center specific embedding provided comparable or better performances than other existing medical concept embeddings. Combined with the best-subtype-average ranking model, our patient-patient similarity-based screening approach was demonstrated effective in two large scale unbalanced datasets containing approximately 10,000 and 60,000 controls with kidney manifestations in the clinical data warehouse (about 2 and 0.4% of prevalence, respectively). Our approach will offer the opportunity to identify candidate patients who could go through genetic testing for ciliopathy. Earlier diagnosis, before irreversible end-stage kidney disease, will enable these patients to benefit from appropriate follow-up and novel treatments that could alleviate kidney dysfunction.

Flow Marks in Injection Molding of PP

Flow marks in injection moulding is quite often encountered on different type of polymers. This defects is known as successive and periodic bright and dull bands oriented perpendicular to the flow direction. Their appearances meanly depend on processing and observation conditions. This study was lead on two industrial polypropylene polymers with a simplified polished rectangular mould geometry. We show that this defect appears during the filling stage and comes from a local change of morphological and molecular orientation along the filling direction on the surface. An instability of the flow front due to a limited sliding at the contact combined to the strong changed of molecular orientation before and after the stagnation point are invoked to explain this instability.

Injection Molding of Reinforced Thermosets

The orientation of glass fibers (initial length 20 mm) and the mold filling of reinforced unsaturated polyester compounds have been studied. Observations of the fiber orientation have been made in three molds where shear and elongational flows occur in variable ways. A part of the fibers are split and broken into filaments. Reinforcement can be more or less buckled. A thin skin layer without fibers is observed. The great thickness of a core region with an orientation perpendicular to the flow direction shows the importance of negative elongational flows. Efficiency of positive elongational flows to suppress buckling and to give a well flow aligned orientation is also observed. On the contrary the efficiency of shear flows is limited compared to elongational flows. The incidence of injection conditions on the pressure inside a rectangular plaque has been studied both experimentally and theoretically. Experimental difficulties due to the material heterogeneity leads to measure viscosity data of the uncured material on a special capillary rheometer and rheological kinetic data on a simplified compound. Numerical results are in good agreement with experimental measurements. For instance the effect of crosslinking which leads to a pressure rise at low flow rate or high mold temperature is well predicted.

Confirmation of the systematic presence of tin particles in fallopian tubes or uterine horns of Essure implant explanted patients: A study of 18 cases with the same pathological process

OBJECTIVE

To examine associations between local and systemic symptoms and the wear of the tin weld of Essure implants.

DESIGN

study of a series of cases.

SETTINGS

Two French hospitals.

PARTICIPANTS

Eighteen patients explanted by hysterectomy and salpingectomy for removal of their Essure implants between September 2019 and July 2020, have had a common anatomopathological process.

MAIN OUTCOME MEASURES

anatomopathological examination by optical microscopy and mineralogical analysis of the fallopian tube or uterine horn with scanning electron microscopy coupled with energy dispersive X-ray (SEM-EDX). Evaluation of local and systemic symptoms with a questionnaire. Examination of blood metal assays (nickel, chromium, and tin).

RESULTS

anatomopathological examination highlights foreign body granulomas, fibrosis, adenomyosis, nonspecific inflammation, cysts and myomas in the Fallopian tubes, uterine horns, or both and mentions the presence of foreign bodies in seven cases. SEM-EDX analyses showed, systematically, the presence of tin particles integrated in the wall near the weld, generally in clusters, and with a size ranging from about one micron to several dozen microns. The questionnaire shows that the most frequent local symptoms were pelvic pain, urinary disorders, bleeding, and pains during intercourse. The most common systemic symptoms were: asthenia, visual disturbances, amnesia, giddiness, dorsal pains, headaches, and joint pains. The majority of local and systemic symptoms decreased after explantation, but sometimes incompletely. Before explantation, high levels of nickel, tin and chromium were observed in 11/17, 1/7 and 2/17 patients. After explantation, tin levels were high in 3/11 patients.

CONCLUSIONS

our new anatomopathological process systematically demonstrates the presence of tin particles in tissue near the weld. These particles could be responsible for granulomatous inflammations as well as local symptoms. Many of the systemic symptoms are consistent with chronic organotin poisoning but further studies are needed to find out whether tin from the solder can be converted to organotin in the patients' bodies.

Subjective Evaluation of Defocus and Astigmatism Combinations Using Image Simulation in Presbyopes

SIGNIFICANCE

Image simulation is a useful and efficient tool to explore the impact of defocus and astigmatism combinations on visual acuity and image quality score when accommodation is taken into account.

PURPOSE

The goal of this experiment was to determine if a simulation is able to predict visual acuity and image quality score (IQS) with defocus and astigmatism combinations in presbyopes.

METHODS

We measured visual acuity and IQS in five defocus and astigmatism combinations in either real or simulated conditions. In real conditions, the subjects viewed a stimulus through an ophthalmic lens or a deformable mirror. In simulated conditions, subjects viewed images of the same stimulus with simulated blur. The amounts of defocus and astigmatism combinations of a progressive addition lens in near vision were generated through a static correction of the subject's aberrations. We simulated three levels of accommodation: subject could not accommodate (FOC0), subject could accommodate to the less hyperopic focal point (FOC1), or subject could accommodate to the circle of least confusion (FOC2).

RESULTS

Visual acuity or IQS did not differ between mirror and progressive addition lens conditions. Visual acuity measured in real blur conditions differed significantly from that in FOC0 simulated blur condition but were similar to that in FOC1 and FOC2 simulated blur conditions. Image quality score obtained in real conditions were between scores measured with the FOC0 and FOC1 simulated conditions, suggesting that the subjects were able to produce a low level of accommodation.

CONCLUSIONS

Accommodation may play a role when comparing optical and simulated defocus and astigmatism combinations. Presbyopic subjects are able to produce a low level of accommodation that may counterbalance a part of the deleterious effect of the astigmatism on image quality. Simulation remains a useful tool if the correct accommodation state is taken into account.

Hyperoxia is associated with adverse outcomes in the cardiac intensive care unit: insights from the Medical Information Mart for Intensive Care (MIMI-III) database

Background

Hyperoxia produces reactive oxygen species, apoptosis, and vasoconstriction, and is associated with adverse outcomes in patients with heart failure and cardiac arrest. Our aim was to evaluate the association between hyperoxia and mortality in patients (pts) receiving positive pressure ventilation (PPV) in the cardiac intensive care unit (CICU).

Methods

Patients admitted to our medical center CICU who received any PPV (invasive or non-invasive) from 2001 through 2012 were included. Hyperoxia was defined as time-weighted mean of PaO2 &gt;120mmHg and non-hyperoxia as PaO2 ≤120mmHg during CICU admission. Primary outcome was in-hospital mortality. Multivariable logistic regression was used to assess the association between hyperoxia and in-hospital mortality adjusted for age, female sex, Oxford Acute Severity of Illness Score, creatinine, lactate, pH, PaO2/FiO2 ratio, PCO2, PEEP, and estimated time spent on PEEP.

Results

Among 1493 patients, hyperoxia (median PaO2 147mmHg) during the CICU admission was observed in 702 (47.0%) pts. In-hospital mortality was 29.7% in the non-hyperoxia group and 33.9% in the hyperoxia group ((log rank test, p=0.0282, see figure). Using multivariable logistic regression, hyperoxia was independently associated with in-hospital mortality (OR 1.507, 95% CI 1.311–2.001, p=0.00508). Post-hoc analysis with PaO2 as a continuous variable was consistent with the primary analysis (OR 1.053 per 10mmHg increase in PaO2, 95% CI 1.024–1.082, p=0.0002).

Conclusions

In a large CICU cohort, hyperoxia was associated with increased mortality. Trials of titration of supplemental oxygen across the full spectrum of critically ill cardiac patients are warranted.

Funding Acknowledgement

Type of funding source: None

Health consequences of cocaine use in France: data from the French Addictovigilance Network

As the number and severity of complications related to cocaine use reported to the French Addictovigilance Network have increased, the French health authorities requested a national epidemiologic study of the data collected by this network from 2010 to 2016. For this purpose, the spontaneous reports (SRs) linked to cocaine notified by health professionals were analyzed as well as the data from the pharmacoepidemiological surveys OPPIDUM (observation of illegal drugs and misuse of psychotropic medications) and DRAMES (deaths related to the abuse of licit and illicit psychoactive substances). In total, 1 265 SRs were analyzed (510% increase from 2010 to 2016). Users were mainly men (952/1 261; 75%), with a median age of 35.0 years [IQ_25-75 : 28-42]. Cocaine was consumed through the intranasal route by 52% of users (416/797), followed by intravenous administration (32%, 253/797) and inhalation (24%, 190/797). The use of cocaine powder and crack cocaine was reported in 70% (475/674) and 23% (154/674) of SRs, respectively. Cocaine was consumed with other psychoactive substances and alcohol in 47% (603/1265) and 60% (387/649) of cases, respectively. The main cocaine-related complications were psychiatric complications (29%), neurologic complications (24%) and cardiovascular complications (23%). Analysis of the OPPIDUM survey data showed that in 2016, 15.9 and 2.4% of the included subjects consumed cocaine or crack cocaine the week preceding the survey, the highest rate for the 2006-2016 period. The DRAMES survey indicated that cocaine-related deaths increased by threefold from 2014 to 2016. These data confirm that cocaine use in France is worrying with an increase in the number of severe complications and deaths.

Somatic profile in lung cancers is associated to reproductive factors in never-smokers women: Results from the IFCT-1002 BioCAST study

BACKGROUND

Lung cancer in women is on the rise, with a higher proportion occurring in lifelong never-smokers. Lung cancer in never-smokers (LCINS) exhibits a high frequency of driver oncogene alterations. In this study, we aimed to investigate whether exposure to reproductive factors in women with LCINS may modulate the molecular pattern.

METHODS

All newly diagnosed LCINSs were included in a prospective, observational study (IFCT-1002 BioCAST). Each patient responded to a questionnaire including reproductive factors. Biomarker test results were also collected.

RESULTS

Two hundred and sixty women were included in this analysis, and 166 alterations were characterized. EGFR mutation frequency proved greater among patients with late menarche (74% in age>14 vs. 40% and 41% for 12-14 and ≤12 years, respectively; P=0.020) and tended to decrease with increasingly late age at menopause. In multivariate analysis, EGFR mutation frequency increased by 23% per increment of 1 year of age at menarche (P=0.048), and by 9% for each year at age at first birth (P=0.035). ALK alteration frequency was greater in women with high parity (50% in≥5 vs. 12% and 7% for 1-4 and nulliparity, respectively; P=0.021).

CONCLUSION

In a cohort of women LCINSs, female hormonal factors appear to impact molecular pattern.

91 To What Extent are Patients’ Future Care Preferences Shared Between Secondary and Primary Care? A Retrospective Chart Review

Introduction

When a doctor is informed of a patient’s future care preferences if they were to lose capacity, there is an ethical and legal obligation to share this information with the treating medical team. In frail older patients, conversations about treatment preferences often occur during hospital admission. We sought to assess the communication of these preferences to the patient’s GP.

Methods

Retrospective chart review of consecutive discharges from acute geriatric wards across seven hospitals. Records were excluded if the patient was admitted for less than 48 hours, was under orthogeriatric care, or died in hospital.

Results

339 notes were included, 41-50 from each hospital. GPs were informed of the resuscitation status of 28% of all patients. 52% of patients had an inpatient DNACPR, the GP was informed of 54% of these. 36% of patients had an inpatient ceiling of treatment documented, of which GPs were informed of 19%. 53% of hospital DNACPRs were converted into community DNACPRs on discharge: GPs were informed of only 24% of new community DNACRPs. 47% of patients discharged with a new community DNACPR lacked capacity to be involved in that decision; for just 6% of these was the GP asked to review the DNACPR order in the community. Inpatient Advance Care Planning (ACP) discussions were held for 9% of patients, of which the GP was informed in 59% of cases. 49% of ACP conversations involved the next-of-kin but not the patient. Among patients who had a new DNACPR decision made during their admission (n=124), there was documentary evidence in only 25% that the patient or next-of-kin was informed whether this was time-limited or indefinite.

Conclusions

Communication from hospitals to GPs about resuscitation, ceiling of care and ACP discussions is very limited. For patients who have expressed ongoing future care preferences, there is a legal obligation to share this information with the treating medical team, which on discharge is the GP.

There is poor documentary evidence of discussions with patients about whether DNACPR decisions are time-limited or indefinite. Furthermore, many hospitalised frail patients lack capacity to make DNACPR decisions but they may subsequently regain capacity, particularly those with delirium. Despite this, GPs are rarely asked to review new community DNACPRs, including those made for patients without capacity.

Investigation of the antibacterial activity of Ag-NPs conjugated with a specific antibody against Staphylococcus aureus after photoactivation

AIM

This work reports a new method for the use of lasers for the selective killing of bacteria targeted using light-absorbing Silver nanoparticles (Ag-NPs) conjugated with a specific antibody against the Gram-positive bacterium Staphylococcus aureus (S. aureus).

METHODS AND RESULTS

Ag-NPs were synthesized using a chemical reduction method and characterized with respect to their surface plasmon resonance, surface morphology via transmission electron microscopy (TEM) and dynamic light scattering (DLS). The bacterial surface was targeted using 20 nm Ag-NPs conjugated with an anti-protein A antibody. Labelled bacteria were irradiated with blue visible laser at 2·04 W/cm² . The antibacterial activity of functionalized Ag-NPs was investigated by fluorescence microscopy after irradiation, and morphological changes in S. aureus after laser treatment were assessed using scanning electron microscopy (SEM). The laser-irradiated, functionalized Ag-NPs exhibited significant bactericidal activity, and laser-induced bacterial damage was observed after 10 min of laser irradiation against S. aureus. The fluorescence microscopic analysis results supported that bacterial cell death occurred in the presence of the functionalized Ag-NPs.

CONCLUSIONS

The results of this study suggest that a novel method for the preparation of functionalized nanoparticles has potential as a potent antibacterial agent for the selective killing of resistant disease-causing bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that Ag-NPs functionalized with a specific antibody, could be used in combination with laser radiation as a novel treatment to target resistant bacterial and fungal pathogens with minimal impact on normal microflora.

Gemcitabine-induced pseudocellulitis: a case report and review of the literature

Gemcitabine is a chemotherapeutic agent used in a wide variety of solid tumours. Known side effects include a dose-limiting myelosuppressive toxicity, mild rash, and radiation-dependent dermatitis. Rarely, localized inflammation in the form of pseudocellulitis has also been observed. We present the case of a 77-year-old woman with a history of a Whipple procedure for pancreatic adenocarcinoma who presented to the emergency department after the start of gemcitabine therapy with increased erythema, swelling, and tenderness in her lower legs. Relevant past medical history included peripheral vascular disease, dyslipidemia, and hypertension. A diagnosis of gemcitabine-induced pseudocellulitis aggravated by venous stasis was confirmed after an extensive workup. This case report and the literature review describe this rare reaction, highlighting the need for increased recognition to avoid unnecessary therapeutic intervention.

Polyoxazolines based mixed micelles as PEG free formulations for an effective quercetin antioxidant topical delivery

This study aims to prove the value of the polyoxazolines polymer family as surfactant in formulations for topical application and as an alternative to PEG overuse. The amphiphilic polyoxazolines (POx) were demonstrated to have less impact on cell viability of mice fibroblasts (NIH3T3) than their PEG counterparts. Mixed micelles, made of POx and phosphatidylcholine, were manufactured using thin film and high pressure homogenizer process. The mixed micelles were optimized to produce nanosized vesicles of about 20 nm with a spherical shape and stable over 28 days. The natural lipophilic antioxidant, quercetin, was successfully encapsulated (encapsulation efficiency 94 ± 4% and drug loading 3.6 ± 0.2%) in the mixed micelles with no morphological variation. Once loaded in the formulation, the quercetin impact on cell viability of NIH3T3 was decreased while its antioxidant activity remained unchanged. This work highlights the capacity of amphiphilic POx to create, in association with phospholipids, stable nanoformulations which show promise for topical delivery of antioxidant and ensure skin protection against oxidative stress.

Impact of single-nucleotide polymorphisms in DNA repair pathway genes on response to chemoradiotherapy in rectal cancer patients: Results from ACCORD-12/PRODIGE-2 phase III trial

We examined whether 66 germline single-nucleotide polymorphisms (SNPs) in 10 candidate genes would predict clinical outcome in 316 patients with resectable locally advanced rectal cancer (LARC) enrolled in the ACCORD-12 phase III trial who were randomly treated with preoperative radiotherapy plus capecitabine (CAP45; n = 155) or dose-intensified radiotherapy plus capecitabine and oxaliplatin (CAPOX50; n = 161). The primary endpoint was tumor response according to the Dworak score. Multivariate logistic regression models adjusted on treatment arm and T stage determined the SNPs prognostic and predictive values for tumor response. In univariate analysis, five SNPs in ERCC2, XPA, MTHFR and ERCC1 were associated with the Dworak score in the CAPOX50 arm. In the overall population, interaction with treatment arm was significant for ERCC2 rs1799787 (p_interaction = 0.05) and XPA rs3176683 (p_interaction = 0.008), suggesting a predictive effect for response to oxaliplatin-based chemoradiotherapy (CRT). All but XPA rs3176683 had a prognostic effect on tumor response. In a multivariate model, interaction remained significant for XPA rs3176683 ([OR 7.33, 95% CI 1.40-38.23], p_interaction = 0.018) and the prognostic effect significant for ERCC2 rs1799787 ([OR 0.55, 95%CI 0.32-0.93], p = 0.027) and ERCC1 rs10412761 ([OR 0.57, 95%CI 0.34-0.98], p = 0.042). Patients with the T/G haplotype of rs1799787 and rs10412761 had a 60% decrease in odds of response (p < 0.001). None of the five SNPs were associated with toxicity, overall and disease-free survival. These data suggest that genetic variation in DNA repair genes influences response to preoperative CRT in LARC and identify patients who benefit from the addition of oxaliplatin to CRT.

What is a clinically meaningful survival benefit in refractory metastatic colorectal cancer?

Assessment of the clinical benefit of cancer treatments can be highly subjective, influenced by both perspective and context. Such assessments are required in regulatory and policy decision-making, but consistency between jurisdictions is often lacking. Clear and consistent standards for determining when a treatment offers a meaningful benefit, relative to the current standard of care, can help to address issues of equity and transparency in health technology assessment. For metastatic colorectal cancer (mcrc), no standardized Canadian definition of clinically meaningful benefit has yet been proposed. Colorectal Cancer Canada therefore convened a group of medical oncologists expert in colorectal cancer to review the literature about clinical significance. The resulting consensus is intended to apply to any therapeutic agent being considered in the setting of chemotherapy-refractory mcrc. It was agreed that overall survival is the appropriate measure of clinical efficacy in chemorefractory mcrc. As quantitative targets for efficacy, an improvement of 2 months or more in median overall survival or a hazard ratio for survival of 0.75 or lower (or both) are proposed as the threshold for clinically meaningful benefit. That threshold could be influenced by a treatment's effect on quality of life. Treatment toxicity is also relevant to the assessment of clinical benefit in this setting, specifically when significant differences in treatment tolerability are evident.

Haploidentical Hematopoietic Stem Cell Transplantation with Post-Transplant Cyclophosphamide for Primary Immunodeficiencies and Inherited Disorders in Children

Allogeneic hematopoietic stem cell transplantation (HSCT) is a potentially curative treatment for some inherited disorders, including selected primary immunodeficiencies (PIDs). In the absence of a well-matched donor, HSCT from a haploidentical family donor (HIFD) may be considered. In adult recipients high-dose post-transplant cyclophosphamide (PTCY) is increasingly used to mitigate the risks of graft failure and graft-versus-host disease (GVHD). However, data on the use of PTCY in children (and especially those with inherited disorders) are scarce. We reviewed the outcomes of 27 children transplanted with an HIFD and PTCY for a PID (n = 22) or osteopetrosis (n = 5) in a single center. The median age was 1.5 years (range, .2 to 17). HSCT with PTCY was a primary procedure (n = 21) or a rescue procedure after graft failure (n = 6). The conditioning regimen was myeloablative in most primary HSCTs and nonmyeloablative in rescue procedures. After a median follow-up of 25.6 months, 24 of 27 patients had engrafted. Twenty-one patients are alive and have been cured of the underlying disease. The 2-year overall survival rate was 77.7%. The cumulative incidences of acute GVHD grade ≥ II, chronic GVHD, and autoimmune disease were 45.8%, 24.2%, and 29.6%, respectively. There were 2 cases of grade III acute GVHD and no extensive cGVHD. The cumulative incidences of blood viral replication and life-threatening viral events were 58% and 15.6%, respectively. There was evidence of early T cell immune reconstitution. In the absence of an HLA-identical donor, HIFD HSCT with PTCY is a viable option for patients with life-threatening inherited disorders.

Simulations of Heat Transfer in Thermoplastic Injection Molds Manufactured by Additive Techniques

The cost and quality of complex thermoplastic parts manufactured by injection are traditionally limited by the design constraints on the mold cooling system. A possible way to overcome this problem is to produce the mold by additive manufacturing, which makes it possible to freely design the shape and position of the cooling channels. Such molds can have hollow spaces in order to reduce the manufacturing time by Selective Laser Melting and the use of costly materials. The complex geometry resulting from optimized cooling channels and hollow regions makes the prediction of the cooling system performance difficult. This work aims to devise a numerical methodology for the simulation of heat transfer phenomena between the polymer, the mold and the cooling channels. An Immersed Volume approach is chosen, where the different parts of the domain (i.e. the polymer, the cooling channels, the hollow regions and the mold) are represented implicitly and the thermo-mechanical properties of the materials vary smoothly at the interface between the parts. The energy and momentum equations are solved by a stabilized Finite Element method. In order to accurately resolve the large variations of material properties and the steep temperature gradients at interfaces, state-of-the art anisotropic mesh refinement techniques are employed. In a first step, we perform thermal calculations only. We then consider the proper thermo-mechanical coupling in the packing stage, as well as the ejection stage and the thermal contact resistance between the polymer part and the mold, in order to weight their influence on the part and the mold temperatures. The modeling strategy is first validated on a simple geometry of a center-gated disk and compared with experimental measurements. The agreement between the experimental results and the simulation is good. Simulations are then performed on an industrial case which illustrates the ability of the method to deal with complex geometries.

Canadian perspectives: update on inhibition of ALK-positive tumours in advanced non-small-cell lung cancer

Background

Inhibition of the anaplastic lymphoma kinase (alk) oncogenic driver in advanced non-small-cell lung carcinoma (nsclc) improves survival. In 2015, Canadian thoracic oncology specialists published a consensus guideline about the identification and treatment of ALK-positive patients, recommending use of the alk inhibitor crizotinib in the first line. New scientific literature warrants a consensus update.

Methods

Clinical trials of alk inhibitor were reviewed to assess benefits, risks, and implications relative to current Canadian guidance in patients with ALK-positive nsclc.

Results

Randomized phase iii trials have demonstrated clinical benefit for single-agent alectinib and ceritinib used in treatment-naïve patients and as second-line therapy after crizotinib. Phase ii trials have demonstrated activity for single-agent brigatinib and lorlatinib in further lines of therapy. Improved responses in brain metastases were observed for all second- and next/third-generation alk tyrosine kinase inhibitors in patients progressing on crizotinib. Canadian recommendations are therefore revised as follows:■ Patients with advanced nonsquamous nsclc have to be tested for the presence of an ALK rearrangement.■ Treatment-naïve patients with ALK-positive disease should initially be offered single-agent alectinib or ceritinib, or both sequentially.■ Crizotinib-refractory patients should be treated with single-agent alectinib or ceritinib, or both sequentially.■ Further treatments could include single-agent brigatinib or lorlatinib, or both sequentially.■ Patients progressing on alk tyrosine kinase inhibitors should be considered for pemetrexed-based chemotherapy.■ Other systemic therapies should be exhausted before immunotherapy is considered.

Summary

Multiple lines of alk inhibition are now recommended for patients with advanced nsclc with an ALK rearrangement.

Analysis of the No-Flow Criterion Based on Accurate Crystallization Data for the Simulation of Injection Molding of Semi-Crystalline Thermoplastics

It is well known in practice that the shape and dimensions of injected parts are highly dependent on the packing-holding stage. A major problem in semi-crystalline polymers is the prediction of the solidified layer, whose thickness has an important effect on shrinkage and warpage. We propose a pragmatic approach based on the concept of no-flow temperature. This temperature should be related to crystallization temperature, but the choice is not easy because it depends on cooling rate and pressure which are functions of time and position. The objective of the work is to evaluate the sensitivity of an injection molding computation to the no-flow temperature and to evaluate the relevance of its choice. The crystallization temperature of an isotactic polypropylene is determined as a function of cooling rate and pressure in laboratory experiments. The pressure dependence is measured using the original Cristapress cell. As a case study, we simulate the filling and post-filling of a plate mold using Rem3D, a 3D code for injection molding. Three no-flow temperatures and two sets of parameters for temperature dependence of viscosity are tested. Their respective influences on the pressure evolution are shown, and the crystallization temperature calculated a posteriori using the experimental material data is compared to the “arbitrary” no-flow temperature.

Contact killing and antimicrobial properties of copper

With the emergence of antibiotic resistance, the interest for antimicrobial agents has recently increased again in public health. Copper was recognized in 2008 by the United States Environmental Protection Agency (EPA) as the first metallic antimicrobial agent. This led to many investigations of the various properties of copper as an antibacterial, antifungal and antiviral agent. This review summarizes the latest findings about 'contact killing', the mechanism of action of copper nanoparticles and the different ways micro-organisms develop resistance to copper.