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PubMed2025

A meta-analysis of diagnostic yield and clinical utility of genome and exome sequencing in pediatric rare and undiagnosed genetic diseases.

PURPOSE: To systematically evaluate the diagnostic yield and clinical utility of genome sequencing (GS) and exome sequencing (ES; genome-wide sequencing [GWS]) in pediatric patients with rare and undiagnosed genetic diseases. METHODS: We conducted a meta-analysis of studies published between 2011 and 2023. To address study heterogeneity, comparative analyses included within-cohort studies using random-effects models. RESULTS: We identified 108 studies including 24,631 probands with diverse clinical indications. The pooled diagnostic yield among within-cohort studies (N = 13) for GWS was 34.2% (95% CI: 27.6-41.5; I2: 86%) vs 18.1% (95% CI: 13.1-24.6; I2: 89%) for non-GWS, with 2.4-times odds of diagnosis (95% CI: 1.40-4.04; P < .05). The pooled diagnostic yield among within-cohort studies (N = 3) for GS was 30.6% (95% CI: 18.6-45.9; I2: 79%) vs 23.2% (95% CI: 18.5-28.7; I2: 58%) for ES, with 1.7-times the odds of diagnosis (95% CI: 0.94-2.92; P = .13). In first-line testing, the diagnostic yield tended to be higher for GS than for ES across clinical subgroups. The pooled clinical utility among patients with a positive diagnosis was 58.7% (95% CI: 47.3-69.2; I2: 81%) for GS and 54.5% (95% CI: 40.7-67.6; I2: 87%) for ES. CONCLUSION: GS appears to have a higher diagnostic yield than ES, with similar clinical utility per positive diagnosis.

Child↗

PubMed2026

Investigating the Role of MicroRNA396 (miR396) Gene in Regulating Wheat Yield and Grain Nitrogen Concentration.

Nitrogen (N) is essential for crop growth, yet excessive fertilization causes environmental issues, highlighting the need to sustain yield and grain N concentration under reduced N input. miR396s are known to regulate plant development and stress responses. Here, we examined whether and how miR396 affects wheat yield and N status under high and low N conditions. TaMIM396 (transforming with the target mimicry construct of miR396) overexpression significantly increased plant height, spike length, grain yield, and grain N concentration under both N treatments. Physiological data showed TaMIM396 enhanced dry matter (DM) and N accumulation at anthesis and maturity, as well as improved post-anthesis remobilization of DM and N to grains. RNA-seq analysis revealed that, under low N, TaMIM396 specifically upregulated key photosynthetic antenna genes, including Lhca3 and Lhcb1/2/3/5, which are critical for light harvesting, suggesting improved photosynthetic efficiency that promotes DM accumulation under N limitation. Collectively, our results demonstrate that TaMIM396 acts as a broad-spectrum N-efficiency gene, coordinating carbon and N remobilization while boosting photosynthetic capacity, thereby supporting stable yield and grain N concentration across N supply levels. Therefore, TaMIM396 is a promising candidate for breeding N-efficient wheat cultivars compatible with sustainable high-yield agriculture.

TaMIM396↗

PubMed1976

Bacterial yields on methanol, methylamine, formaldehyde, and formate.

Several bacteria utilizing C1-compounds as sole carbon sources were grown on these substrates in continuous culture. The molar yield values (g of cell dry wt/mol of substrate utilized) of bacteria which utilize C1-compounds via the ribulose monophosphate pathway were between 15.7 to 17.3 when grown on methanol; while the molar yield values of bacteria which use the serine pathway for the assimilation of C1-compounds varied between 9.8 and 13.1. The molar yield values of different bacteria which use the serine pathway decreased as the oxidation levels of the C1-growth substrates increased. On formaldehyde the values were between 7.2 to 9.6, whereas on formate the values varied from 3.3 to 6.9. It appears that bacteria utilize C1-compounds more efficiently via the ribulose monophosphate pathway than via the serine pathway. The oxidation step from methanol to formaldehyde (and from methylamine to formaldehyde) in the bacteria studied may be energy yielding. A comparison has been made between the experimental yield values obtained and theoretical values.

Formaldehyde↗

PubMed1978

Different yield and properties of mitochondria from skeletal muscle of normal hamsters.

Yield and properties of mitochondria, isolated from hind leg muscles of normal hamsters, are different, when 4 preparation procedures are applied simultaneously: 1. mechanical homogenization of muscle with a glass-Teflon homogenizer followed by rehomogenization of the isolated nuclear fraction for 1--6 times. The procedure yields impure mitochondria showing the highest amounts of mitochondrial enzymes (50--65% of total), protein and DNA; the isolated mitochondria exhibit disrupted outer membranes and loosened inner membranes causing a better supply with substrates of enzymes located at the inner membrane and in the matrix. 2. Single mechanical homogenization of muscle for increasing periods (2--40 min) yields lower amounts of all constituents (25--40% of total). 3. The yields of Nagarse treatment with one step of 2 min mechanical homogenization range between 20--35% of total. Mitochondria isolated with the latter procedure exhibit compact membranes and are very pure, but still contaminated with Nagarse, causing destructions of mitochondrial membranes already after 24 h storage in buffer with sucrose and mannitol at 2 degrees C. 4. One single Nagarse treatment of muscle for 40 min produces a minor yield of these these constituents. Therefore, at least two different isolation procedures are proposed for optimum investigation of skeletal muscle mitochondria.

Animals↗

PubMed1992

Thermoluminescence and flash-induced oxygen yield in herbicide resistant mutants of the D1 protein in Synechococcus PCC7942.

Several strains of Synechococcus PCC7942 carrying point mutations in the gene psbA were studied by thermoluminescence and polarographic measurement of flash-induced oxygen yield. The following results were obtained: (a) Replacement of Ser-264 in D1 by Ala (mutant Di1) or Gly (mutant G264) resulting in DCMU and atrazine resistance leads to a downshift of the thermoluminescence (TL) B-band peak temperature from 40 degrees C in wild-type thylakoids to about 30 degrees C. In dark adapted samples of both mutants the TL and oxygen yield pattern induced by a train of single turnover flashes were strongly damped indicative of a high miss factor. (b) In contrast to Ser-264 mutants, replacement of Phe-255 in D1 by Tyr (mutant Tyr5) induced strong resistance to atrazine but not to DCMU and did not affect the peak termperature of the B-band and the flash-induced TL and oxygen yield patterns. In this respect mutant Tyr5 resembles the wild type. (c) No significant differences have been found between strains with single site mutations in psbAI and normal psbAII/psbAIII genes, and strains with same mutations in psbAI but additional deletion of psbAII and psbAIII. Obviously in strains were psbAI is present, PS II complexes containing gene products of psbAII and psbAIII are not assembled in detectable amounts. (d) Strains with double mutations at positions 264 and 255 display a downshift of the B-band peak temperature. Their oscillatory patterns of B-band intensity and oxygen yield are highly damped. This behaviour is similar to strains D1 and G264 which are modified at position 264 only. We extend reports on additivity of mutation effects on herbicide binding to binding of QB. (e) Mutations at the QB site not only influence the binding of QB and herbicides but also change the thermoluminescence quantum yield and the lifetimes of the redox states S2 and S3 of the water oxidase. This finding might indicate long ranging effects on Photosystem II exerted by structural modifications of the QB site. From these data we conclude that Ser-264 is essential for binding of atrazine, DCMU and QB, whereas Phe-255 is involved in atrazine binding and its substitution by Tyr does not markedly affect QB or DCMU binding in Synechococcus PCC7942.

Atrazine↗

PubMed1976

The effect of changes in dose rate on the yield of chromosome aberrations in human lymphocytes exposed to gamma radiation.

The yield of chromosome aberrations was studied in Go human peripheral blood lymphocytes following in vitro exposure to 100, 250 and 500 rad of caesium-137 gamma radiation. The doses were given at various rates up to 400 rad per h with the longest exposures lasting for approx. 50 h. At 500 and 250 rad the dicentric yields fell by 66 and 64% when the dose rate was reduced from 400 to 10 rad per h whereas at 100 rad the reduction was only 29%. Reductions were also noted in frequency of acentric aberrations. At the higher dose rates (greater than 150 R/h) the aberration yield was constant and agreed with data published elsewhere for 3000 R/h. The dose rate at which the decline in aberration yield became apparent was dose dependent and, for dicentrics, occurred at about 150, 100 and 25 rad/h respectively for the 500-, 250- and 100-rad doses. The data are interpreted in terms of the quadratic model of aberration induction in which the dose-squared term represents dose rate dependent two-track aberrations which constitute an increasingly important component of yield as dose increases. The implications of this work for cytogenetic dosimetry are discussed.

Chromosome Aberrations↗

PubMed1977

Dicentric yields induced by gamma-radiation and chromosome arm number in primates.

To evaluate the effect of the chromosome arm number on the yield of dicentric chromosomes, frequencies of gamma-ray-induced chromosome aberrations were examined with peripheral lymphocytes from three different primate species, Saimiri sciureus (arm number, 77), Macaca fascicularis (arm number, 83) and Nycticebus coucang (arm number, 99). Irradiated blood samples were cultured by the same standard technique as that commonly used for human lymphocytes. The yields of dicentrics and dicentrics plus rings at doses of 100, 200 and 300 rad of gamma-irradiation were not significantly different among the three species, in spite of the difference in the chromosome arm number. Furthermore, dose-response relationships for these species were consistent with that for man. Statistical analysis indicated that the expected dicentric yields calculated from the arm number model were significantly different from the observed yields at 200 and 300 rad doses (P less than 0.01). From these results it can be pointed out that there is no correlation between the yield of dicentrics and the effective chromosome arm number, and that the chromosomal radiosensitivity of these primates is essentially the same as that of man, at least in the lymphocyte system.

Animals↗

PubMed1976

Effect of phosphate fertilization and seed inoculation with ""Okadin'' at high rate on yield of broadbean and lentil.

The effect of phosphate fertilization and seed inoculation with ""Okadin'' preperation of rhizobia strains on the yield of broadbean and lentil was tested in field experiments during the seasons 1969 to 1972 in the farm of Faculty of Agriculture, Assiut University. Superphosphate was added at the rate of 0, 50, 100, or 200 kg/fa., and ""Okadin'' preparation, specific for the kind of legume planted, was applied to the seeds at 10 times the recommended rate. Application of superphosphate at any of the tested rates did not significantly affect total yield obtained, seeds yield, or the nitrogen content of seeds of lentil or braodbean. Seed inoculation with Okadin showed no significant effect on the yield of broadbean, but resulted in significant reduction in the yield of lentil seeds in the two seasons of the experiment.

Agriculture↗

PubMed1976

Effect of feeding fat to dairy cows receiving a fat-deficient basal diet. I. Milk yield and composition.

The effects of supplementing a basal diet, in which the low level of fatty acids limited milk production, with soya oil, a palm oil/palmitic acid mixture and tallow, on the yield of milk and of its constituents, and on the composition of the milk, are reported. The yields of milk and milk fat were greatly increased by all the oil-supplemented diets; the mean daily yield of solids-not-fat (SNF) was also increased, but supplementation with soya oil caused the yield of crude protein (CP) to decrease, whereas the other fat-rich concentrate mixtures gave the same mean yield of protein as did the low-fat, control diet. All 3 oil-supplemented diets lowered the proportion of CP in the milk, but the SNF content was unchanged by any treatment. Dietary soya oil tended to lower the proportion of fat in the milk, whilst the palm oil/palmitic acid mixture raised it, with the tallow exerting no effect. The results are discussed in relation to previous work in which these dietary oils have been used, but in which the intake of fatty acids from the control diets did not limit milk production to the extent reported here.

Animals↗

PubMed2026

Transcriptional and phytohormonal regulation of positional ear development reveals yield strategies in maize.

Maize (Zea mays L.) is a vital global crop, contributing ∼37% of annual grain production. Enhancing yield per unit area is crucial for food security, yet research has primarily focused on single-ear traits, overlooking the regulation of double ears-a key determinant of prolificacy. While secondary ears drive yield variability under prolificacy-favoring conditions, the mechanisms governing ear formation across shoot positions remain poorly understood. Here, we performed high-resolution transcriptomic analysis of 66 samples from three ear types (primary, secondary and third) in maize inbred B73. We uncovered distinct hormonal developmental dynamics: strigolactone (SL) signaling genes, particularly SBP transcription factors, dominated in primary (I) ears, whereas ethylene-related genes (e.g., ZmEREB131, ZmACCO35) were enriched in third (III) ears. Functional validation confirmed that knockout of ZmEREB131 and ZmACCO35 accelerated development and elongated ears compared to wild-type, implicating ethylene (ETH) signaling in ear maturation arrest. Notably, SL inhibitor application synchronized primary and secondary ear development, boosting total yield by >20% without compromising primary ear performance. Our study elucidates the transcriptional networks underlying differential ear development and provides actionable strategies for yield improvement through targeted hormonal modulation. These findings advance the understanding of maize inflorescence biology and offer molecular tools for breeding high-yielding varieties.

RNA-seq↗

PubMed1976

Metabolism and growth yields in Bacteroides ruminicola strain b14.

Metabolism of D-glucose by Bacteroides ruminicola subsp. brevis, strain B14, has been examined. Growth yield studies gave molar growth yields, corrected for storage polysaccharide, of approximately 66 g (dry weight)/mol of glucose fermented. The storage polysaccharide amounted to about 14% of the total dry weight, or 55% of the total cellular carbohydrate, at full growth. After correcting glucose utilization for incorporation into cellular carbohydrate, measurement of product formation showed that 1.1 succinate, 0.8 acetate, and 0.35 formate are produced and 0.5 CO2 net is taken up during the fermentation of 1 glucose under the conditions used. The implication of these results with respect to adenosine 5'-triphosphate (ATP) molar growth yield calculations is discussed. If substrate-level phosphorylation reactions alone are responsible for ATP generation, then the ATP molar growth yield must be about 23 g (dry weight)/mol of ATP. Alternatively, if anaerobic electron transfer-linked phosphorylation also occurs, the ATP molar growth yield will be lower.

Acetates↗

PubMed2026

Prenatal SNP-array chromosomal microarray analysis in 3,549 pregnancies: indication-specific yields and clinical implications.

BACKGROUND: SNP-based chromosomal microarray analysis (CMA) is widely used in invasive prenatal diagnosis, yet real-world performance across contemporary referral pathways, especially in the NIPT era, remains incompletely characterized. METHODS: We retrospectively analyzed 3,549 prenatal invasive samples tested by SNP array, and evaluated diagnostic yield overall and by referral indication and ultrasound phenotype. RESULTS: In total, we identified 398 pathogenic or likely pathogenic (P/LP) variants across 386 fetuses, resulting in an overall diagnostic yield of 10.9% (386/3,549). These findings comprised 223 aneuploidies and 175 pathogenic CNVs. In contrast, variants of uncertain significance (VOUS) were detected in 12.0% (426/3,549) of cases. Diagnostic yields were heavily stratified by indication: yields peaked in NIPT high-risk referrals (38.9%) and were intermediate in ultrasound-based cases (~ 11%), but dropped significantly in the advanced maternal age (AMA; 4.2%) and serum screening (~ 5-6%) groups. Conversely, VOUS rates remained remarkably stable across all referral categories. Sub-analysis of ultrasound abnormalities revealed that multisystem anomalies conferred the highest risk (27.3%), driven predominantly by aneuploidies; among soft markers, increased nuchal translucency (NT) emerged as the strongest predictor of chromosomal pathology. CONCLUSIONS: In our cohort, SNP-array identified clinically actionable findings in 10.9% of cases. NIPT enriched diagnostic yields, particularly for aneuploidies, and NT thickness was strongly associated with pathogenic findings. These results support an indication-based approach to genomic testing, with NIPT as a triage tool for aneuploidy and CMA for high-risk populations, while improving VOUS counseling.

Humans↗

PubMed1992

Estimates of subprimal yields from beef carcasses as affected by USDA grades, subcutaneous fat trim level, and carcass sex class and type.

One hundred beef carcasses were selected to represent the mix of cattle slaughtered across the United States. Selection criteria included breed type (60% British/continental European, 20% Bos indicus, and 20% dairy carcasses), sex class (beef and Bos indicus: 67% steers, 33% heifers; dairy: 100% steers), USDA quality grade (4% Prime, 53% Choice, and 43% Select), USDA yield grade (10% YG 1, 43% YG 2, 40% YG 3, and 7% YG 4), and carcass weight (steers: 272.2 to 385.6 kg, heifers: 226.8 to 340.2 kg). One side of each carcass was fabricated into boneless subprimals and minor cuts following Institutional Meat Purchase Specifications. After fabrication, subprimals were trimmed progressively of fat in .64-cm increments beginning with a maximum of 2.54 cm and ending with .64 cm. Linear regression models were developed for each individual cut, including fabrication byproduct items (bone, fat trim) to estimate the percentage yield of those cuts reported by USDA Market News. Strip loin, top sirloin butt, and gooseneck rounds from heifers tended to have a higher percentage yield at the same USDA yield grade than the same cuts from steers, possibly resulting from increased fat deposition on heifers. Percentage of fat trimmed from dairy steers was 2 to 3% lower than that from other sex-class/carcass types; however, due to increased percentage of bone and less muscle, dairy steers were lower-yielding. Fat trimmed from carcasses ranged from 7.9 to 15.6% as the maximum trim level decreased from 2.54 to .64 cm.

Adipose Tissue↗

PubMed1979

Health care requirements of dairy cattle. I. Response to milk yield selection.

To measure direct response to single trait selection for milk yield and correlated response in health problems, two homologous base populations were formed by pairing 66 Holstein females by sire. Base populations and descendants were managed identically except for selection by milk yield. One base and lineage were mated with sires with highest predicted difference milk (selection group); other base and lineage were mated with average sires in 1964 (control group). Milk yield, supplemental labor, and veterinary and semen expense were recorded specific to each cow. Over 9 yr, 130 selection and 163 control cows were observed. Selection cows yielded more milk but with increase in labor and expense for health care. Estimates of labor for the selection group were greater for mammary, locomotion, and digestion categories and for expense in mammary, respiration, first insemination, and later insemination categories. Labor and expense for reproduction did not differ for genetic groups. Differences between groups in annual estimated labor and expense totaled $27.00. Extra income over feed cost more than compensated for greater health care and semen cost; however, the magnitude of the latter indicates a need for them to be considered when economically evaluating breeding programs where major emphasis is on milk yield.

Animals↗

PubMed1992

Time series cross-correlation analysis of postparturient relationships among serum metabolites and yield variables in Holstein cows.

Time series cross-correlation analysis was used to determine relationships among serum beta-hydroxybutyrate, glucose, FFA, cholesterol, milk yield, DMI, and estimated net energy balance for 42 d postpartum for 14 multiparous cows. Milk yield was positively associated with beta-hydroxybutyrate concentrations on the same day, and milk yield was a primary determinant of metabolic change. Dry matter intake was negatively correlated with beta-hydroxybutyrate concentrations 3 d later and on the same day. The data supported in vitro studies showing that FFA are positively associated with beta-hydroxybutyrate production, showed that glucose concentrations are negatively cross-correlated with beta-hydroxybutyrate concentrations, and found that estimated net energy balance is negatively cross-correlated with beta-hydroxybutyrate. Analyses suggested that serum glucose and cholesterol concentrations significantly decreased with increased milk yield; analyses also suggested that elevated beta-hydroxybutyrate concentrations were associated with decreases in milk yield 6 d later. beta-Hydroxybutyrate and FFA concentrations 3 to 9 d before parturition were positively related to cholesterol concentrations, and relationships were positive between estimated net energy balance and cholesterol, suggesting that cholesterol concentrations increased as precursors for cholesterol synthesis were available. Time series cross-correlation analysis was a useful tool in examining relationships among variables when repeated samples were obtained from the same individuals.

3-Hydroxybutyric Acid↗

PubMed1992

Milk yield, health, and reproduction of dairy cows given somatotropin (Somavubove) beginning early postpartum.

Cows (n = 210) were assigned to the following treatments: uninjected controls through 130 d postpartum; zero to high, uninjected through 60 d then injected with 14 mg of bST/d from 61 through 130 d postpartum; low, 5 mg of bST/d from 14 through 130 d postpartum; low to high, 5 mg of bST/d from 14 through 60 d then 14 mg of BST/d from 61 through 130 d postpartum; and high, 14 mg of bST/d from 14 through 130 d postpartum. Cows given 5 mg of bST/d (low and low to high treatments) yielded 1.2 kg of FCM/d more and high group cows yielded 1.3 kg of FCM/d more than control cows between 14 and 60 d postpartum. Cows given bST yielded 2.7 to 4.1 kg of FCM/d more than control cows during 61 to 130 d postpartum. Overall, control cows yielded 35.1 kg of FCM/d, and bST-dosed cows yielded 2.2 to 3.2 kg/d more FCM. Low group cows had improved pregnancy rate (80.0%) and conception rate (82.2%) compared with high group cows (57.2 and 60.3%). Neither pregnancy (70.0%) nor conception rates (71.5%) of controls differed from other groups. However, low group cows had first service conception rate of 57.8% compared with 34.3% for high and 38.2% for low to high group cows. First postpartum estrus was observed in high group cows about 13 to 16 d later than in low and low to high group cows, whereas low group cows came into first estrus 9 d sooner than controls. Cows of high group had lower body condition than controls (2.5 vs. 2.9), but other groups did not differ (2.7 to 2.9) from controls. Health was not adversely affected. Early postpartum bST administration at 5 mg/d increases FCM and, perhaps, reproductive performance of dairy cattle compared with herdmates.

Animals↗

PubMed1992

Fatty acids, calcium soaps of fatty acids, and cottonseeds fed to high yielding cows.

We examined the effects of dietary fat as cottonseed, fatty acids, or calcium soaps of fatty acids in the rations of high yielding lactating cows receiving low forage. Experiments were with isoenergetic, isonitrogenous diets containing equal amounts of forage. Inclusion of up to 510 g/d of fatty acids in the ration enhanced FCM yield. With cottonseed, increased FCM was mainly due to increased fat yield. Dietary fatty acids tended to increase milk in mid and late lactation and to decrease fat percentage. Calcium soaps of fatty acids enhanced FCM, particularly in early lactation. Feeding cottonseed and fatty acids together did not enhance yield. Effects described may be attributed in part to changes in ruminal fermentation in which cottonseed increased acetate concentrations and fatty acids decreased the ratio of acetate and butyrate to propionate and in part to enhanced efficiency of milk yield when fat was included in the ration.

Acetates↗

PubMed1976

Selection for increased semen yield in the turkey.

Selection was effective in greatly increasing semen yield in the turkey. After five generations of selection semen yield in the selected line was more than double that of the randombred control line from which the semen line was developed. The realized heritability of semen yield was .35 +/- .20. There was no consistent change in sperm concentration or frequency of bent sperm associated with the increased yield. Egg production was increased in the semen line. The increase occurred in the first generation of selection and was maintained throughout the remaining generations of selection. Body weight during the growing period exhibited an initial increase in the semen line but declined to randombred control levels in later generations. There was no consistent change in percent fertility, percent hatchability of fertile eggs or number of poults produced per hen which was associated with the genetic increases in semen yield.

Animals↗