An algorithm to identify patients aged 0-3 with rare genetic disorders

BACKGROUND

With over 7000 Mendelian disorders, identifying children with a specific rare genetic disorder diagnosis through structured electronic medical record data is challenging given incompleteness of records, inaccurate medical diagnosis coding, as well as heterogeneity in clinical symptoms and procedures for specific disorders. We sought to develop a digital phenotyping algorithm (PheIndex) using electronic medical records to identify children aged 0-3 diagnosed with genetic disorders or who present with illness with an increased risk for genetic disorders.

RESULTS

Through expert opinion, we established 13 criteria for the algorithm and derived a score and a classification. The performance of each criterion and the classification were validated by chart review. PheIndex identified 1,088 children out of 93,154 live births who may be at an increased risk for genetic disorders. Chart review demonstrated that the algorithm achieved 90% sensitivity, 97% specificity, and 94% accuracy.

CONCLUSIONS

The PheIndex algorithm can help identify when a rare genetic disorder may be present, alerting providers to consider ordering a diagnostic genetic test and/or referring a patient to a medical geneticist.

A composite biomarker of neutrophil-lymphocyte ratio and hemoglobin level correlates with clinical response to PD-1 and PD-L1 inhibitors in advanced non-small cell lung cancers

BACKGROUND

Immune checkpoint inhibitors (ICIs) have been incorporated into various clinical oncology guidelines for systemic treatment of advanced non-small cell lung cancers (aNSCLC). However, less than 50% (and 20%) of the patients responded to the therapy as a first (or second) line of therapy. PD-L1 immunohistochemistry (IHC) is an extensively studied biomarker of response to ICI, but results from this test have equivocal predictive power. In order to identify other biomarkers that support clinical decision-making around whether to treat with ICIs or not, we performed a retrospective study of patients with aNSCLC who underwent ICI-based therapy in the Mount Sinai Health System between 2014 and 2019.

METHODS

We analyzed data from standard laboratory tests performed in patients as a part of the routine clinical workup during treatment, including complete blood counts (CBC) and a comprehensive metabolic panel (CMP), to correlate test results with clinical response and survival.

RESULTS

Of 11,138 NSCLC patients identified, 249 had been treated with ICIs. We found associations between high neutrophil-to-lymphocyte ratio (NLR ≥ 5) and poor survival in ICI-treated NSCLC. We further observed that sustained high NLR after initiation of treatment had a more profound impact on survival than baseline NLR, regardless of PD-L1 status. Hazard ratios when comparing patients with NLR ≥ 5 vs. NLR < 5 are 1.7 (p = 0.02), 3.4 (p = 4.2 × 10^- 8), and 3.9 (p = 1.4 × 10^- 6) at baseline, 2-8 weeks, and 8-14 weeks after treatment start, respectively. Mild anemia, defined as hemoglobin (HGB) less than 12 g/dL was correlated with survival independently of NLR. Finally, we developed a composite NLR and HGB biomarker. Patients with pretreatment NLR ≥ 5 and HGB < 12 g/dL had a median overall survival (OS) of 8.0 months (95% CI 4.5-11.5) compared to the rest of the cohort with a median OS not reached (95% CI 15.9-NE, p = 1.8 × 10^- 5), and a hazard ratio of 2.6 (95% CI 1.7-4.1, p = 3.5 × 10^- 5).

CONCLUSIONS

We developed a novel composite biomarker for ICI-based therapy in NSCLC based on routine CBC tests, which may provide meaningful clinical utility to guide treatment decision. The results suggest that treatment of anemia to elevate HGB before initiation of ICI therapy may improve patient outcomes or the use of alternative non-chemotherapy containing regimens.

Double-Tip Artefact Removal from Atomic Force Microscopy Images

The Atomic Force Microscope (AFM) allows the measurement of interactions at interfaces with nanoscale resolution. Imperfections in the shape of the tip often lead to the presence of imaging artefacts such as the blurring and repetition of objects within images. Generally, these artefacts can only be avoided by discarding data and replacing the probe. Under certain circumstances (e.g., rare, high value samples, or extensive chemical/physical tip modification) such an approach is not feasible. Here, we apply a novel deblurring technique, using a Bayesian framework, to yield a reliable estimation of the real surface topography without any prior knowledge of the tip geometry (blind reconstruction). A key contribution is to leverage the significant recently successful body of work in natural image deblurring to solve this problem. We focus specifically on the 'double-tip' effect, where two asperities 1 are present on the tip, each contributing to the image formation mechanism. Finally, we demonstrate that the proposed technique successfully removes the 'double-tip' effect from high resolution AFM images which demonstrate this artefact whilst preserving feature resolution.

Algorithms for the digital restoration of torn films

This paper presents algorithms for the digital restoration of films damaged by tear. As well as causing local image data loss, a tear results in a noticeable relative shift in the frame between the regions at either side of the tear boundary. This paper describes a method for delineating the tear boundary and for correcting the displacement. This is achieved using a graph-cut segmentation framework that can be either automatic or interactive when automatic segmentation is not possible. Using temporal intensity differences to form the boundary conditions for the segmentation facilitates the robust division of the frame. The resulting segmentation map is used to calculate and correct the relative displacement using a global-motion estimation approach based on motion histograms. A high-quality restoration is obtained when a suitable missing-data treatment algorithm is used to recover any missing pixel intensities.

Relationship between knee extension force and stand-up performance in community-dwelling elderly women

OBJECTIVE

To describe the relationship between knee extension force and stand-up performance.

DESIGN

Prospective, cross-sectional, descriptive, and correlational.

SETTING

Community.

PARTICIPANTS

Fifty-five community-dwelling women 60 or more years old.

INTERVENTIONS

Information pertaining to stand-up performance was gathered via structured questions. The time to complete 1 sit-to-stand from a bench of known height (16in) was obtained in conjunction with subjects' ratings of perceived exertion (RPEs) relative to the task. Bilateral lower extremity knee extension strength was measured with a hand-held dynamometer and normalized against body weight.

MAIN OUTCOME MEASURES

Total knee extension forces (raw and body-weight normalized values) generated by each subject were correlated with 3 measures of stand-up performance.

RESULTS

Low to moderate correlations (r = -.323 to -.526) were found between knee extension forces and the stand-up performance measures of bench stand time and stand-up difficulties. Normalized knee extension force had a higher correlation than raw knee extension force with stand-up difficulties and RPE. Correlations were higher when the curvilinear nature of the relationship was taken into account. The highest correlation was between normalized knee extension force and the RPE associated with the bench stand task (r = -.767).

CONCLUSION

Knee extension force offers an important but incomplete explanation of stand-up performance from low surfaces by elderly women. Interventions leading to increased knee extension force may improve stand-up performance.

Development of a bioassay for phytochemicals using Daphnia pulex

The freshwater cladoceran Daphnia pulex was explored as an alternative to Artemia salina for the biological screening of phytochemicals. This paper reports on the results of screening 27 compounds, and comparisons are made with screens using Artemia salina. The effect of miniaturisation of the assay system was investigated. Petri-dish based tests were performed for the 27 compounds using 10 daphnids at each of 5 concentrations (1 - 1000 mg l(-1)). Potassium dichromate was used as a control and the number immobile after 24 hours were counted. Results were expressed as EC(50) values. The active compounds (EC(50) < 25 mg l(-1)) comprised mainly adrenoceptor agonist alkaloids, while the cytotoxins vincristine and colchicine, and several antibiotics were relatively non-toxic towards Daphnia. The method was validated by comparative bioassay of A. belladonna fractions. Overall, this screen compared favourably with those based on Artemia. Daphnia were sensitive to a wide range of biologically active molecules including CNS-stimulants, anti-malarials, narcotics and anti-spasmodics, and the sensitivity was broader than previously seen with Artemia. The screen is perhaps limited by the lack of sensitivity to cytotoxins, but this might be overcome by altering the test criteria.

Phenylalkylamine abuse among opiate addicts attending a methadone treatment programme in the Republic of Ireland

Since the early 1990s ring-substituted derivatives of amphetamine have been abused widely in the Republic of Ireland. The main ring-substituted amphetamines being abused include methylenedioxyamphetamine (MDA), methylenedioxymethamphetamine (MDMA) and methylenedioxyethamphetamine (MDEA). A newer illicit synthetic analogue, which has been seized to a lesser extent by Irish police, is N-methyl-1-(3,4-methylenedioxyphenyl)-2-butanamine (MBDB). The work presented here involved the determination of the type of ring-substituted amphetamines being abused by a group of recovering opiate abusers participating in a methadone maintenance programme in a Dublin Drug Rehabilitation Centre. Urine samples which tested positive for amphetamines and ring-substituted amphetamines via EMIT immunoassay were subjected to further analysis using GC-MS with MBTFA flash derivatization. It was found that the methylenedioxypropanamines were being abused, as was amphetamine itself. However, no abuse of methylenedioxybutanamines or thioamphetamines was observed.

A broad range of forces is encompassed by the maximum manual muscle test grade of five

This retrospective study summarizes the range of knee extension forces associated with the manual muscle test grade of 5. The range of the forces (>560 Newtons) was large and encompassing of more than 86% of measurable forces. These findings help to explain the insensitivity of manual muscle testing and why it has such a profound ceiling effect.

Impact of pasture type on methane production by lactating beef cows

In order to determine the quantity of methane (CH4) produced by lactating beef cows on pasture, 16 Hereford–Simmental first-calf heifers with a mean weight of 511.2 ± 5.8 kg were randomly selected from a larger group of cows (n = 60) on a grazing management experiment and used to evaluate the effects of pasture type on ruminal CH4 production using the sulfur hexafluoride (SF6) tracer-gas technique. Pasture treatments consisted of two pasture types, alfalfa-grass [78% alfalfa (Medicago sativa L.) – 22% meadow bromegrass (Bromus biebersteinii Roem and Schult.)] or 100% meadow bromegrass at each of two fertility levels (either unfertilized or soil test recommended fertilizer levels) with two replications of each pasture treatment (8 pastures). Cows were managed using a "put and take" stocking system to leave equal residual herbage mass on all treatments following the grazing period in each paddock. During the 69-d grazing season, two cows from each pasture were sampled to determine daily forage intake and CH4 production on four occasions. The chemical composition of diets differed between pasture types and sampling periods. Dry matter intake was greater for cows grazing alfalfa–grass pastures than for cows grazing grass-only pastures (11.4 vs. 9.7 kg DM d−1. P < 0.018). However, methane production was greater for cows grazing alfalfa–grass pastures than for cows grazing grass-only pastures (373.8 vs. 411.0 L CH4 d−1. P < 0.008). Consequently, energy lost through eructation of CH4 was less for cows grazing alfalfa–grass pastures than it was for cows grazing grass-only pastures (7.1 vs. 9.5% of GEI; P < 0.001). Key words: Methane, cattle, environment, digestion efficiency, pasture, forage

Hepatic enzyme abnormalities in children on triple therapy for tuberculosis

Standard chemotherapy for tuberculosis (TB) in children uses hepatotoxic drugs. Published data and guidelines on monitoring of liver function during TB treatment are often contradictory and not directly relevant to the pediatric population. We carefully monitored 43 children (age 6.6 years, 0.7-15.1 [median, range]; 49% male; 72% Caucasian) being treated for TB infection (n = 8) or disease (n = 35) with triple therapy, using pyrazinamide, rifampicin, and isoniazid in standard recommended doses. Children on other hepatotoxic drugs were excluded. Measurements of liver function tests (LFT) included aspartate transaminase (AST), alanine transaminase (ALT), and bilirubin, and they were checked before and a median of 5 times (1-23) during treatment. Only one child had mildly abnormal LFTs pretreatment. Thirteen children (n = 13, [30%]; age 7.6 years, 1.8-10.9; 54% male; 77% Caucasian) developed abnormal LFTs (> mean + 2 SD) and of these 10 had TB disease. Eight of the 13 had mildly elevated enzymes (< twice upper limit of normal) while in five, all with disease, the enzymes were more markedly raised. In the group with normal LFTs (n = 30, [70%]; age 6.6 years 0.7-15.1; 47% male; 70% Caucasian) 25 had disease (83%). Liver enzyme elevation occurred early (1.65 weeks, 0.6-16.6). Only two children had symptoms (one jaundice, one pruritus) with treatment being stopped temporarily only in the jaundiced child. Otherwise, LFTs normalized without interrupting treatment. We conclude that elevated liver enzymes are not uncommon in children receiving triple therapy for TB, generally occurring early in treatment. Symptoms are rare. Current British Thoracic Society and American Thoracic Society guidelines (that if LFTs are normal prior to treatment then further monitoring should only be performed if clinically indicated) seem adequate for children.

Methane production by steers on pasture

In order to determine the quantity of methane (CH4) produced by steers on pasture, 16 steers with a mean weight of 356 ± 25 kg were randomly selected from a larger group of cattle (n = 48) to evaluate the effects of grazing management and monensin controlled release capsule (CRC) administration on ruminal CH4 production using the sulphur hexafluoride (SF6) tracer-gas technique. Pasture management treatments consisted of two grazing systems (continuous stocking or 10-paddock rotational stocking) at each of two stocking rates (low, 1.1 steer ha−1 or high, 2.2 steers ha−1) with two replications of each pasture treatment. Half of the animals on each pasture treatment were administered a monensin CRC delivering 270 mg d−1, and untreated animals served as controls. During the 140-d grazing season, one steer from each treatment-replicate combination was sampled to determine daily intake and CH4 production on four occasions. The chemical composition of diets differed between grazing management treatments and sampling periods. Voluntary intake and CH4 production, adjusted for differences in body weight, were unaffected by grazing management, sampling period or by monensin CRC administration and averaged 0.69 ± 0.1 L kg BW−1 d−1 across all grazing management treatments. The energy lost through eructation of CH4 averaged 4.5 ± 1.4% of gross energy intake. Key words: Methane, cattle, environment, digestion efficiency, pasture, forage

Comparison of resistance of fungal spores to gamma and electron beam radiation

The irradiation sensitivity of fungal spores to either gamma or electron beam irradiation was evaluated in distilled water. The D10 (the dose required to reduce the initial population by 90%) gamma values ranged from 0.236 to 0.416 kGy and from 0.209 to 0.319 kGy for Penicillium and Aspergillus species, respectively. The D10 electron beam values ranged from 0.194 to 0.341 and from 0.198 to 0.243 kGy for Penicillium and Aspergillus species, respectively. Of the aspergilli species evaluated, only half exhibited significantly (P < 0.05) greater sensitivity to the electron beam treatment compared to gamma irradiation. Four of the six penicillia species evaluated also exhibited significantly (P < 0.05) higher sensitivities to electron beam treatment.

The effects of aerobic and anaerobic exercise conditioning on resting metabolic rate and the thermic effect of a meal

This study examined resting metabolic rate (RMR) and thermic effect of a meal (TEM) among athletes who had participated in long-term anaerobic or aerobic exercise. Nine collegiate wrestlers were matched for age, weight, and fat-free weight with 9 collegiate swimmers. Preliminary testing included maximal oxygen consumption, maximal anaerobic capacity (MAnC) for both the arms and the legs, and percent body fat. On two separate occasions, RMR and TEM were measured using indirect calorimetry. VO2max was significantly higher in the swimmers while MAnC was significantly higher in the wrestlers for both the arms and the legs. RMR adjusted for fat-free weight was not significantly different between groups. The differences in total and percentage of TEM between the groups were not statistically significant, and there were no differences in baseline thyroid hormones. These data suggest that despite significant differences in VO2max and WAnT values following long-term aerobic and anaerobic exercise training, resting energy expenditure does not differ between these college athletes.

Two seasons of weight cycling does not lower resting metabolic rate in college wrestlers

Over the course of 2 yr, we prospectively studied the effect on resting metabolic rate (RMR) of multiple cycles of weight loss followed by regain in six weight cycling collegiate wrestlers (WC) (mean age = 19.0 yr) compared with 12 weight stable, physically active, nonwrestling controls (C) (mean age = 20.9 yr), whose body composition was similar to the wrestlers. Furthermore, during the second year of the investigation, a group of six nonweight cycling collegiate wrestlers (NWC) (mean age = 18.8 yr) were included in the analyses. The WC had previously undergone at least three seasons of weight cycling and continued this pattern during each year of the study. For the WC, RMR was determined by indirect calorimetry before and after a 6-month season of weight cycling for each of two consecutive years. A similar time frame was followed for measurement of RMR in the C, while for the NWC, pre- and postseason RMRs were measured only during the second year. During the 2 yr, the WC had significantly higher (P < 0.05) pre- and postseason measures of RMR compared with the C. A separate analysis comparing all three groups during the second year showed that RMR was not different for WC and NWC, and that RMR was higher for both wrestling groups compared with C. In this prospective study, weight cycling did not increase the thermogenic efficiency of collegiate wrestlers compared with either nonweight cycling wrestlers or weight stable controls, who were not wrestlers.

Resting metabolic rate in weight-cycling collegiate wrestlers compared with physically active, noncycling control subjects

To determine the effect of multiple cycles of weight loss and regain on resting metabolic rate (RMR), we compared RMR between 12 weight-cycling collegiate wrestlers (means age 19.4 y) with a minimum of three previous seasons of weight cycling and 13 weight-stable nonwrestlers of similar weight and body composition (means age 20.6 y). RMR was measured before, during, and after a 6-mo wrestling season. Wrestlers exhibited a significantly higher baseline RMR compared with the control subjects (p less than 0.05). During the season when wrestlers had lost weight for competition, RMR was reduced (p less than 0.05) but was not significantly lower than that of the weight-stable control subjects. After a season of weight cycling and the final weight regain, the wrestler's postseason RMR was similar to preseason values and higher than the postseason RMR of the control subjects (p less than 0.05). Participation in numerous cycles of weight loss and regain did not lower RMR in these competitive athletes, as has been previously suggested.

The thebaine content of ornamental poppies belonging to the papaver section oxytona

Encouraging yields of thebaine have been obtained from Papaver bracteatum grown in Ireland. However climatic conditions adversely affect flower (and subsequent capsule production). Twelve vigorously flowering ornamental cultivars labelled P. orientale or "oriental poppy" were screened for the presence of thebaine. Five of the cultivars had no detectable thebaine. The thebaine content of the remaining 7 cultivars was determined. The capsules of the cultivar "Goliath" had a thebaine content of 3.0%. The identity of the thebaine was confirmed by isolation and examination of spectral evidence. In addition the two known N-oxides of thebaine were isolated and characterised from cv. Goliath. The combination of this chemical evidence and stomatal pore length measurements indicate that the plant labelled P. orientale cv. Goliath is closely related to P. bracteatum Lindl . This cultivar shows promise as a source of thebaine and has a potential in the hybridisation of genuine P. bracteatum to improve its flowering characteristics in mild climates.

The identification of drugs of abuse in the Republic of Ireland during the years 1968-1978

A survey of the composition of 4,933 exhibits submitted for laboratory analysis by the Drug Squad of the Irish police during the years 1968-1978 indicated an increase in the level of non-medical drug consumption in the Republic of Ireland. Cannabis was the most widely encountered drug. Barbiturates constituted a considerable proportion. Amphetamines were rarely found; this was attributed to the unique legislation controlling the storage and sale of amphetamines. Various substances were sold as drugs of abuse. For example, Datura was sold as cannabis which caused a considerable concern because of its toxicity. The recognition of a drug-related problem of some significance in Ireland during 1968 led to the formation of a drug squad in the Irish police. Since that time a total of 4,933 exhibits arising from arrests and drug seizures have been submitted for laboratory analyses. These exhibits ranged from "normal" pharmaceutical formulations (tablets, ampoules, etc.) to unknown powders and a large number of more unusual items (table 1). The drugs were identified using an appropriate combination of microscopic, chromatographic and spectroscopic techniques (1, 2).