Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis.

Introduction: Exome sequencing has a diagnostic yield ranging from 25% to 70% in rare diseases and regularly implicates genes in novel disorders. Retrospective data reanalysis has demonstrated strong efficacy in improving diagnosis, but poses organizational difficulties for clinical laboratories. Patients and methods: We applied a reanalysis strategy based on intensive prospective bibliographic monitoring along with direct application of the GREP command-line tool (to "globally search for a regular expression and print matching lines") in a large ES database. For 18 months, we submitted the same five keywords of interest [(intellectual disability, (neuro)developmental delay, and (neuro)developmental disorder)] to PubMed on a daily basis to identify recently published novel disease-gene associations or new phenotypes in genes already implicated in human pathology. We used the Linux GREP tool and an in-house script to collect all variants of these genes from our 5,459 exome database. Results: After GREP queries and variant filtration, we identified 128 genes of interest and collected 56 candidate variants from 53 individuals. We confirmed causal diagnosis for 19/128 genes (15%) in 21 individuals and identified variants of unknown significance for 19/128 genes (15%) in 23 individuals. Altogether, GREP queries for only 128 genes over a period of 18 months permitted a causal diagnosis to be established in 21/2875 undiagnosed affected probands (0.7%). Conclusion: The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis.

Endotracheal tube biofilm in critically ill patients during the COVID-19 pandemic : description of an underestimated microbiological compartment.

Biofilm (BF) growth is believed to play a major role in the development of ventilator-associated pneumonia (VAP) in the intensive care unit. Despite concerted efforts to understand the potential implication of endotracheal tube (ETT)-BF dispersal, clinically relevant data are lacking to better characterize the impact of its mesostructure and microbiological singularity on the occurrence of VAP. We conducted a multicenter, retrospective observational study during the third wave of the COVID-19 pandemic, between March and May 2021. In total, 64 ETTs collected from 61 patients were included in the present BIOPAVIR study. Confocal microscopy acquisitions revealed two main morphological aspects of ETT-deposited BF: (1) a thin, continuous ribbon-shaped aspect, less likely monobacterial and predominantly associated with Enterobacter spp., Streptococcus pneumoniae or Viridans streptococci, and (2) a thicker, discontinuous, mushroom-shaped appearance, more likely characterized by the association of bacterial and fungal species in respiratory samples. The microbiological characterization of ETT-deposited BF found higher acquired resistance in more than 80% of analyzed BF phenotypes, compared to other colonization sites from the patient's environment. These findings reveal BF as a singular microbiological compartment, and are of added clinical value, with a view to future ETT-deposited BF-based antimicrobial stewardship in critically ill patients. Trial registration NCT04926493. Retrospectively registered 15 June 2021.

Essential oils for managing Pratylenchus penetrans on Easter lilies.

Easter lily bulbs for greenhouse forcing are produced in Del Norte County, California and Curry County, Oregon, USA. Pratylenchus penetrans infestation seriously affects growth of field grown bulbs. During two consecutive years of field trials containing 22 treatments, commercially prepared formulations of essential oils (EOs) were compared to an untreated control and to a standard chemical fumigant treatment (FU) (1,3-dichloropropene and metam sodium) applied preplant followed by phorate (PH) at planting to determine their value in the management of lesion nematode, and in improving plant health. The EO products Duogard, EF400, EF300, and Cinnamite were tested as preplant dips to bulblet planting stock. The treated bulblets were tested either alone, in combination with PH at-planting, at planting following FU or in combination with PH at planting following FU. The organophosphates ethoprop and fosthiazate were also tested either alone, or at a reduced rate in combination with a reduced rate of PH. With respect to bulb circumference, ten treatments consistently outperformed the control. In consecutive years, three treatments had healthier looking roots than the control. At harvest, levels of lesion nematode within roots were consistently lower in nine treatments. EOs were beneficial in mitigating nematode damage.Easter lily bulbs for greenhouse forcing are produced in Del Norte County, California and Curry County, Oregon, USA. Pratylenchus penetrans infestation seriously affects growth of field grown bulbs. During two consecutive years of field trials containing 22 treatments, commercially prepared formulations of essential oils (EOs) were compared to an untreated control and to a standard chemical fumigant treatment (FU) (1,3-dichloropropene and metam sodium) applied preplant followed by phorate (PH) at planting to determine their value in the management of lesion nematode, and in improving plant health. The EO products Duogard, EF400, EF300, and Cinnamite were tested as preplant dips to bulblet planting stock. The treated bulblets were tested either alone, in combination with PH at-planting, at planting following FU or in combination with PH at planting following FU. The organophosphates ethoprop and fosthiazate were also tested either alone, or at a reduced rate in combination with a reduced rate of PH. With respect to bulb circumference, ten treatments consistently outperformed the control. In consecutive years, three treatments had healthier looking roots than the control. At harvest, levels of lesion nematode within roots were consistently lower in nine treatments. EOs were beneficial in mitigating nematode damage.

Effect of cooking method, distiller's grains, and vitamin E supplementation on the vitamin content of value cuts from beef steers fed wet distiller's grains and solubles and supplemental vitamin E.

Vitamin E, thiamin, riboflavin, niacin, vitamin B(6), and vitamin B(12) concentrations of flat iron steaks and petite tenders from steers fed finishing rations containing 0% and 40% corn wet distiller's grains and solubles (WDGS) with and without supplemental vitamin E were determined. Feeding treatment groups were: 0% WDGS with basal vitamin E, 0% WDGS with supplemental vitamin E (500 IU daily), 40% WDGS with basal vitamin E, and 40% WDGS and supplemental vitamin E. Cattle can be fed 40% WDGS diets more economically than corn diets. The incorporation of 40% WDGS, with and without vitamin E, was hypothesized to have little effect on the vitamin concentrations of these value meat cuts. Flat iron steaks and petite tenders were broiled and/or grilled to 70 degrees C internal temperature. Mean cooking yields ranged from 68.7% to 78.2%. The majority of the vitamin concentrations of broiled and of grilled meat were significantly different (P < 0.05) from that of raw meat. Vitamin E concentrations of raw and cooked meat from steers that received supplemental vitamin E were significantly higher (P < 0.05) than those fed basal vitamin E. Significant differences in thiamin, riboflavin, vitamin B(6), and vitamin B(12) concentrations in raw flat iron steaks and in vitamin B(6) in raw petite tenders were observed by WDGS. Thiamin, vitamin B(6), and vitamin B(12) concentrations of broiled flat iron steaks were significantly different (P < 0.05) than grilled. A few differences in vitamin concentrations of the flat iron steaks and petite tenders were observed by WDGS, vitamin E supplementation, and cooking treatments, but most of the vitamin concentrations were statistically similar.

Management Options for Pratylenchus penetrans in Easter Lily.

Alternatives to reduce or modify nematicide use for minimizing groundwater contamination in Easter lily were explored in two field trials. Alternatives to standard 1,3-dichloropropene (1,3-D) plus phorate injection in the first trial were: (i) delaying applications until after winter rains, (ii) removing roots from planting stock, (iii) 1,3-D via drip irrigation, (iv) a chitin-urea soil amendment, (v) the registered insecticide disulfoton, and (vi) several nonregistered nematicides. None of the treatments equaled the standard treatment. In the second trial, potential benefits of adding a systemic nematicide, oxamyl (OX), or a fungicide, metalaxyl (MX), to the standard treatment were explored. Preplant drip irrigation applications of metam sodium (MS), sodium tetrathiocarbonate (ST), and emulsifiable 1,3-D were evaluated alone and in combination with postplant applications of OX and MX. Several drip-applied treatments performed comparably to the standard treatment with respect to the most important criteria of crop quality, bulb circumference. Metam-sodium in combination with either or both OX and MX, 1,3-D plus OX and MX, and ST plus OX and MX provided the best results.

[Clinical and biological surveillance of envenomed patients]. / Surveillance clinique et biologique des patients envenimés.

Faced with an envenomation, the problem is to take sufficiently rapidly the decision to administer the only effective treatment--immunotherapy--, to know which antivenom to choose and how long to administrate it. If the snake is not identified, symptoms and initial development give information on the type of venom. It is convenient to classify the symptoms according to four clinical types: i) the cobra syndrome with a potentially fatal evolution within two to ten hours and which resembles an Elapid bite, ii) the viper syndrome associating bleeding and inflammation, which can be due either to a viper, pit viper or, in Australia, to Elapids, iii) disturbance of blood circulating functions and iv) disturbance of other live functions. Between the third to the half of snakebite victims present no envenomation. Severe envenomations must be monitored in an intensive care unit, with experience in emergency management and monitoring of patients with major life-threatening conditions. Throughout the world, snakebites induce more than 100,000 deaths every year. Schematically, the emergency may be considered in terms of seconds for blood circulation disorders, minutes for respiratory paralysis, and hours for the coagulopathy.

Carotenoid content, physicochemical, and sensory qualities of deep-fried carrot chips as affected by dehydration/rehydration, antioxidant, and fermentation.

Carrot slices were subjected to one of the following experiments prior to deep-frying: (A) dehydration/rehydration, (B) soaking in different antioxidants, and (C) fermentation with/without blanching. There were no significant differences (P > or = 0.05) in carotenoid contents among carrot chips treated with/without dehydration. Soaking in sodium metabisulfite resulted in the highest carotenoid content and lightness (L), redness (a), and yellowness (b) values among the antioxidant treatments. Fermentation without blanching significantly decreased (P < 0.05) carotenoid content, vitamin A activity, and fat content. Dehydration and fermentation with blanching significantly increased (P < 0.05) the lightness (L), redness (a), and yellowness (b) values of the chips. Dehydration/rehydration, but not antioxidant and fermentation, significantly decreased (P < 0.05) the water activity of the chips. The textural values of carrot chips prepared using sodium metabisulfite, without dehydration and without fermentation, were the lowest among other treatments which suggests the crispiest. Carrot chips prepared using sodium metabisulfite, without dehydration and without fermentation, had the highest carotenoid content and retention, and the highest overall acceptability score.

Plasma homocysteine concentrations of Indonesian children with inadequate and adequate vitamin B-6 status.

The objective of the study was to determine the usefulness of utilizing plasma homocysteine concentrations as an indicator of vitamin B-6 status in subjects with inadequate and adequate status as demonstrated by currently accepted indicators. Plasma homocysteine concentrations of 77 third-grade Indonesian children (aged 8-9 y; boys and girls) were measured. About a quarter of these subjects had inadequate vitamin B-6 status as indicated by their plasma pyridoxal-5'-phosphate concentrations, erythrocyte alanine aminotransferase activity coefficients, and reported dietary vitamin B-6 intakes. No significant differences in plasma homocysteine concentrations were observed between subject groups shown to have inadequate and adequate vitamin B-6 status using currently accepted indicators. Plasma homocysteine concentrations of the subjects were not correlated with values for other vitamin B-6 indices. Plasma homocysteine concentration was not an indicator of vitamin B-6 status in these children, as it did not differentiate between children shown otherwise to have inadequate and adequate status of the vitamin.

Vitamin B-6 intakes and plasma B-6 vitamer concentrations of men and women, 19-50 years of age.

The vitamin B-6 intakes and plasma B-6 vitamer levels of healthy nonsupplemented men and women, 19-24 and 25-50 years, were compared. The subjects did not take nutrient supplements or medications or use tobacco products. Subjects were grouped as follows: eight, 19-24 y men; nine, 25-50 y men; 11, 19-24 y women; and 13, 25-50 y women. The estimated vitamin B-6 intakes, obtained via 24-h recalls followed by 2-d food records, of the two groups of men were significantly higher (P < 0.05) than those of the two groups of women. Thirty-five percent of the women reported consuming less than the Estimated Average Requirement for vitamin B-6. The four gender: age groups had similar B-6 vitamer concentrations of plasma pyridoxal-5'-phosphate, 4-pyridoxic acid, pyridoxine, pyridoxamine, and pyridoxamine-5'-phosphate. Males 25-50 y had significantly higher (P < 0.05) plasma pyridoxal concentrations than the two groups of females. All subjects had pyridoxal-5'-phosphate concentrations indicative of vitamin B-6 adequacy. Generally the plasma B-6 vitamer concentrations of these men and women, 19-24 and 25-50 years of age, all having adequate vitamin B-6 status, were similar.

Riboflavin and niacin concentrations of bison cuts.

We analyzed the riboflavin and niacin contents of individual cuts from clod (triceps brachii), ribeye (longissimus thoracis), top round (semimembranosus), and top sirloin (gluteus medius) from 24 fed bison bulls. The bulls came from producers in the United States and Canada and had consumed concentrate diets plus hay free choice for at least 100 d. The mean riboflavin and niacin concentrations of all of the bison cuts combined were .094 and 1.910 mg/100 g wet weight, respectively. The riboflavin and niacin content values did not differ (P < .05) among the cuts of meat. Cuts from individual bulls were significantly different (P < .05) with regard to both riboflavin and niacin contents. Little variation was observed in riboflavin and niacin content of five bison from the same producer and two bison from another producer. These content values may be used in estimating the riboflavin and niacin content of bison meat.

Vitamin B-6 inadequacy is prevalent in rural and urban Indonesian children.

The vitamin B-6 status of Indonesian children was evaluated by determining their dietary vitamin B-6 intakes, erythrocyte alanine aminotransferase activity coefficients and plasma pyridoxal phosphate (PLP) concentrations. Thirty-eight third-grade elementary school children (ages = 8-9 y) in rural and 39 in urban areas of Bogor, West Java, Indonesia, voluntarily served as subjects. The subjects included 39 male and 38 female students. The mean vitamin B-6 intake of the subjects was 0.57 mg/d. Fifty-five percentage of the children reported consuming <0.5 mg/d of vitamin B-6 (the 1998 Estimated Average Requirement for those 4-8 y). Erythrocyte alanine aminotransferase activity coefficients >/= 1.25 were observed in 30%, and plasma PLP concentrations

[Intubation using a submental approach]. / Intubation par voie sous-mentale.

Authors report a case of sub-mental approach for endotracheal intubation in maxillo-facial surgery. This unusual technique was simple to perform and remained uncomplicated.

[Results of the conservative surgical and irradiation treatment of 132 nonpalpable ductal carcinomas in situ of the breast]. / Résultats du traitement par chirurgie conservatrice et irradiation de 132 carcinomes canalaires in situ non palpables du sein.

PURPOSE: Retrospective analysis of results of treatment of 132 subclinical ductal carcinomas in situ, non-palpable. MATERIAL AND METHODS: Patients were treated with limited surgery and 70 Gy radiation therapy (70 Gy). RESULTS: With a median follow-up of 7 years, the total recurrence rate was 6%, and the actuarial rate at 5 years 4% and at 10 years 13% at. These have no influence on recurrence on the specific actuarial survival rate which was 100% at 10 years. In spite of five infiltrating recurrences of seven, no metastasis appeared 48 months after the salvage surgery. The global rate of breast preservation was 92% at 7 years. DISCUSSION AND CONCLUSION: Therapeutic indications were developed taking into account the present analysis and a literature review (2,338 in situ ductal carcinomas, palpable or not, treated with conservative surgery, with or without adjuvant radio-therapy).

Problems Associated with Crop Rotation for Management of Pratylenchus penetrans on Easter Lily.

In Humboldt and Del Norte counties of California and Curry County, Oregon, Easter lilies (Lilium longiflotum) are grown commercially in a 3- to 6-year rotation with pasture for cattle and sheep. Bulbs are sold to greenhouse operations to produce flowering plants. The lesion nematode, Pratylenchus penetrans, is a serious detriment to Easter lily production. Both soil and planting stock are often infested; typically, a dual nematicide application is used consisting of a preplant soil fumigation followed by an at-planting application of an organophosphate or carbamate. Nematicide usage has resulted in ground-water contamination. Several factors that could lead to an improved crop rotation program were examined in five field trials in Oregon. Examining the relative nematode host status of crops for feeding cattle and sheep indicated differences in host suitability among clovers and fescues that could prove useful in development of pasture mixes. Populations of P. penetrans under continuous fallow and pasture were monitored for 4 years following harvest of Easter lilies. Populations fluctuated in both situations but generally increased on pasture plants and decreased under fallow. Nematodes were still detectable at the end of 4 years of weed-free fallow. Populations of P. penetrans on Easter lilies were followed over two successive crops. Numbers in soil peaked in July and then decreased while numbers within roots continued to increase until harvest in October.

Concentrations of selected vitamins and selenium in bison cuts.

We analyzed individual cuts from clod (Triceps brachii), ribeye (Longissimus thoracis), top round (semimembranosus), and top sirloin (Gluteus medius) from 12 fed bison bulls for content of selected vitamins and selenium. The bulls came from producers in the United States and Canada and had consumed concentrate diets plus hay free choice for at least 180 d. The mean nutrient concentrations of all of the bison cuts combined were as follows (per 100 grams of wet weight): .045 mg thiamin, .253 mg vitamin B6, 2.131 microg vitamin B12, no detectable vitamin C, .848 microg vitamin A, .047 mg alpha-tocopherol, .013 mg tau-tocopherol, and 25.464 microg selenium. The nutrient content values did not differ (P > .05) among the cuts of meat. Cuts from individual bulls were different (P < .05) with regard to alpha- and tau-tocopherols, selenium, and vitamin A but not with regard to thiamin, vitamin B6, and vitamin B12. Nutrient concentrations, with the exception of one nutrient, of five bison from the same producer were similar. Great variation was observed between the alpha- and tau-tocopherols, selenium, and vitamin A contents among bison bulls but not among cuts of meat.

Determination of traces of pesticides in water by solid-phase extraction and liquid chromatography-ionspray mass spectrometry.

A multi-residue analytical method for six pesticides (atrazine, hydroxyatrazine, carbofuran, promecarb, linuron and monolinuron) in drinking water has been developed. The method combines liquid chromatography and mass spectrometry using an ionspray interface. The linearity domain, as well as the limits of detection and quantification, were determined for each compound. Although satisfactory performance could be achieved, present drinking water regulations (0.1 microgram l-1 for single pesticide) requires a pre-concentration step. This was performed using solid-phase extraction with octadecyl-bonded silica cartridges. The analytical procedure was tested on water samples spiked at the 0.04 and 0.08 microgram l-1 levels, and allowed the determination of the investigated pesticides (except hydroxyatrazine) at these trace concentrations.

beta-Carotene and alpha-tocopherol inhibit the development of atherosclerotic lesions in hypercholesterolemic rabbits.

Male New Zealand White rabbits were made hypercholesterolemic by feeding an atherogenic diet (0.5% cholesterol, 3% peanut oil, and 3% coconut oil) with or without (control) antioxidants for 8 weeks. The antioxidant treatments were intravenous injection of beta-carotene (25 mg/kg/BW, twice weekly), dietary supplementation of alpha-tocopherol (0.5%), and a combination of both. Antioxidant treatments significantly increased plasma and LDL antioxidant levels in the above three groups. Intravenous injection of beta-carotene significantly decreased total and LDL cholesterol concentrations, thoracic atherosclerotic lesion area, and intimal thickness, but had no effects on LDL oxidation ex vivo as compared to control. Added dietary alpha-tocopherol significantly decreased the susceptibility of LDL to oxidation ex vivo, aortic atherosclerotic lesion area and intimal thickness, but had no effects on plasma cholesterol levels as compared to control. Combination of both antioxidants significantly decreased total and LDL cholesterol concentrations, susceptibility of LDL to oxidation ex vivo, as well as atherosclerotic lesion area and intimal thickness at aortic arch and thoracic aorta as compared to control, but not beta-carotene or alpha-tocopherol groups. These data suggest that the antihypercholesterolemic effects of beta-carotene and antioxidant effects of alpha-tocopherol may benefit rabbits fed an atherogenic diet by inhibiting the development of atherosclerotic lesions.