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PubMed2026

Optimization of protoplast based DNA isolation and genome analysis in a gamma-irradiated Aspergillus niger mutant strain.

Aspergillus niger is an important industrial fungus widely used for citric acid production and a range of biotechnological applications. In this study, a protoplast-based DNA isolation protocol was optimized for a gamma-irradiated A. niger AN-L103_M1 mutant strain, followed by whole-genome sequencing and functional genome analysis. Protoplast yield was strongly influenced by enzyme concentration and the molarity of the osmotic stabilizer. The highest yield was achieved at an enzyme concentration of 50 mg/mL (2.487 ± 0.04 × 10⁸ cells/mL) and 0.8 M KCl (2.550 ± 0.06 × 10⁸ cells/mL), with both factors showing significant effects (p < 0.0001) in GraphPad Prism 11.0.0. Whole-genome sequencing performed using an Illumina NovaSeq 6000 platform yielded a 37.06 Mb draft genome assembled into 537 contigs, with an N50 of 363,084 bp and a GC content of 48.2%. BUSCO 14 analysis showed high completeness (97.95% complete BUSCOs). Functional annotation and KEGG pathway mapping identified genes involved in glycolysis, the tricarboxylic acid cycle, and citrate biosynthesis, while biosynthetic gene cluster analysis revealed diverse potential for secondary metabolite production. These findings provide an optimized workflow for protoplast-based DNA isolation and genome-scale functional analysis in A. niger, proposing a basis for future comparative genomics, transformation studies, and experimentally validated metabolic engineering.

Aspergillus niger↗

PubMed1991

Ability, disability, and the functional capacity of patients with cardiovascular disease.

Assessment of functional capacity, of ability and disability among patients with cardiovascular disease raises a number of problems and issues for which there are currently only imperfect or incomplete answers. Emphasis must be placed on the lack of predictable relationship of anatomic abnormality and functional abnormality. For example, the percentage obstruction of the coronary artery documents the anatomic extent of the disease, rather than the limitation of functional capacity; the same lack of predictive value characterizes the decrease in resting ventricular ejection fraction. The response to a challenge of activity or exertion currently appears to offer the optimal method of assessing functional capacity for work, although a brief continuous exercise test may not be the optimal exercise protocol by which to evaluate endurance. As an example, in our laboratory, comparing a low-level continuous exercise test protocol with one with an intermittent exercise design (i.e., periods of exercise alternating with periods at rest), patients typically can perform at least one additional stage of exercise on the discontinuous or intermittent test protocol. This occurred without significant differences in the final heart rate, blood pressure, or rate-pressure product, probably because most patients so tested were limited not by myocardial ischemia but by musculoskeletal problems, fatigue, or dyspnea (8). An unmet need is a comparison of exercise test protocols for the assessment of functional capacity, possibly the development of new test protocols for patients with limited functional capacity, and the evaluation of the relationship of these test data to eight hours of occupational activity in the workplace setting. It appears logical that a diagnostic exercise test should differ from one designed to determine functional capacity, but the results of a variety of exercise test protocols should be compared with the actual physical activity able to be performed in the workplace, as well as with reported symptoms. It should be defined whether testing is to be performed on optimal medical therapy, which I believe should be the case; or whether the technique used for diagnostic exercise testing, that of the minimal medication possible, is to be employed. Next, the time after surgical intervention or following a prolonged hospitalization at which to test should be delineated in that the deconditioning effect of immobilization may substantially decrease effort tolerance, unrelated to the severity of the underlying cardiovascular disease. Finally, should exercise rehabilitation be recommended or required before testing for cardiovascular impairment; major improvement in functional capacity has occurred in previously sedentary patients with a variety of cardiovascular diseases, including those with important manifestations of myocardial ischemia and ventricular dysfunction.(ABSTRACT TRUNCATED AT 400 WORDS)

Cardiovascular Diseases↗

PubMed1993

Biokinetics of technetium-99m-tetrofosmin: myocardial perfusion imaging agent: implications for a one-day imaging protocol.

Tetrofosmin is a 99mTc-labeled myocardial perfusion imaging agent that has shown encouraging results in Phase I and II clinical trials. The purpose of this study was to determine the biokinetics of this agent following administration during exercise and at rest in order to determine an optimal imaging protocol. Twenty patients with suspected coronary artery disease underwent symptom-limited treadmill exercise. Six to 8 mCi of 99mTc-tetrofosmin was injected at peak exercise and 22-24 mCi was injected 4 hr later at rest. Serial 5-min planar images were obtained in the left anterior oblique view at 5, 10, 15, 30, 60, 120 and 180 min after the radiotracer injection. Regions of interest were drawn on the serial images around the entire heart and portions of liver, lung, spleen, gallbladder and gastrointestinal tract. Average decay-corrected counts per pixel in each organ were plotted against time. In addition, heart-to-adjacent organ ratios were also determined. On stress images, the heart had the highest activity at all times, with the exception of gallbladder in the first 15 min. On rest images, the gallbladder, liver and gastrointestinal tract initially had higher activity than the heart; but the activity in these organs cleared rapidly over the subsequent 30-60 min. Heart-to-adjacent organ ratios were > 1.0 at all times in the stress images. Heart-to-organ ratios were < 1.0 in the first 15 min on the rest images for the liver and gastrointestinal tract. However, 30 min later, all ratios on the rest images were > or = 1.0. Technetium-99m-tetrofosmin images were considered to be of good to excellent quality with good myocardial delineation and adequate contrast between the heart and background. These These observations indicate that a convenient one-day tetrofosmin imaging protocol similar in duration to conventional 201Tl imaging is feasible.

Adult↗

PubMedDate not supplied

Optimization of techniques in screening CT of the sinuses.

The number of screening examinations of the sinuses performed with CT has markedly increased owing to the widespread and increasing use of endoscopic sinonasal surgery. We reviewed scans from 500 patients who had screening CT examinations of the sinuses for preendoscopic evaluation of inflammatory sinonasal disease to better define an optimal imaging protocol. Three aspects of direct coronal imaging of the paranasal sinuses were investigated: (1) preparation of the patient prior to the examination; (2) technical factors of the CT study, including positioning of the patient, optimal coronal angle, slice thickness, and CT exposure factors; and (3) data display. Our experience indicates that pretreatment of the patient with maximal medical therapy enables the best preendoscopic definition of anatomy, disease pattern, and nonreversible disease component for the treating surgeon. CT technical factors are optimized with scanning in the prone position with thin (3-mm) sections obtained through the anterior paranasal sinuses. This allows optimal visualization of the ostiomeatal unit. The remaining posterior portions of the sinuses are adequately imaged with thicker slices (5 mm). The coronal scan angle used is less critical. Exposure factors (mAs) can be reduced dramatically without image compromise. Data display is optimized when the bone algorithm is used to acquire the data and with image display at intermediate window center and width level. Use of the techniques outlined in this article results in a cost-effective yet diagnostic scan of the sinuses with decreased radiation exposure to the patient.

Cost-Benefit Analysis↗

PubMed1999

Lower esophageal sphincter dysfunction often precludes safe gastric feeding in stroke patients.

OBJECTIVES: To determine the relationship between stroke and lower esophageal dysfunction with vomiting and to identify an optimal nutrition protocol based on our findings. PATIENTS AND METHODS: The lower and upper esophageal sphincter functions were assessed in 35 patients who had an acute stroke to determine whether gastric or jejunal enteral feeding was the optimal route. Stroke was due to unilateral ischemia in 20 patients, unilateral intracerebral hemorrhage in 8 patients, and global ischemia in 7 patients. Our study consisted of 18 men and 17 women with an average age of 64 years. RESULTS: Using standard esophageal manometric definitions, the lower esophageal sphincter function was below normal in 24 patients: 3 had global anoxia, 5 had unilateral hemorrhage, and 16 had unilateral ischemia. The upper esophageal sphincter function was low in 30 patients: 6 had global anoxia, 7 had unilateral hemorrhage, and 17 had unilateral ischemia. Based on lower esophageal sphincter pressure, 7 patients underwent tube gastrostomy and 13 patients underwent tube jejunostomy placement. All tolerated enteral alimentation well. Prior to lower esophageal sphincter assessment, 4 patients had percutaneous endoscopy gastrostomy feedings that led to aspiration pneumonitis and consultation for tracheostomy; 2 terminally ill patients were referred to the ethics service, and 2 were converted to feeding via jejunostomy tube at the time of tracheostomy and did well. CONCLUSIONS: Vomiting with aspiration due to lower esophageal sphincter dysfunction is common after acute strokes. Esophageal manometry serves as a guide to find the optimal feeding route.

Adult↗

PubMed1995

High-efficiency retroviral-mediated gene transfer into human and nonhuman primate peripheral blood lymphocytes.

Peripheral blood lymphocytes (PBLs) are primary targets for gene therapy of inherited and acquired disorders of the immune system. We describe the development of an optimized transduction system that provides for high-efficiency retrovirus-mediated gene transfer into primary PBLs. This optimized transduction protocol combines centrifugation of the lymphocytes (1000 x g) at the inception of transduction with phosphate depletion, low-temperature incubation (32 degrees C), and the use of the packaging cell line PG13. Gene marking studies of human and primate PBLs using these optimized transduction conditions demonstrated that the transduction efficiency exceeded 50% of the total lymphocyte population. The optimized transduction efficiency of PBLs with amphotropic retroviral vectors was in excess of 25%. The transduction procedure does not alter phenotype, viability, or expansion of the transduced cells. Our data indicate that this optimized transduction system leads to high-efficiency gene transfer into primary human lymphocytes, which obviates the requirement for selection of transduced cells prior to gene-therapy procedures. Thus, large quantities of healthy retrovirally transduced lymphocytes containing a broad immunological repertoire can be generated for use in clinical protocols. Our results represent a significant improvement in the methodology for the transduction of lymphocytes for gene therapy.

Animals↗

PubMed2026

Optimizing focal vibration therapy for balance and gait: A systematic review.

OBJECTIVE: This systematic review evaluated the efficacy of focal (localized) vibration therapy (FVT) applied to muscles/tendons on balance, gait, and mobility, with a specific focus on defining optimal vibration protocols (frequency, amplitude, dosing) and muscle-targeting strategies to maximize sensorimotor recovery. METHODS: A systematic review was conducted across six databases (CINHAL, Embase, Medline, Web of Science, Scopus, CENTRAL) from January 2000 to May 2025. Studies were included if they involved human participants, applied FVT therapeutically, and reported balance, gait, or mobility outcomes. Data extraction included study characteristics, intervention protocols, and outcomes. Methodological quality was assessed using the PEDro scale. RESULTS: Sixty-two studies (n = 2090 participants) were included. Methodological quality assessment (PEDro scale) indicated 44% of studies met high-quality standards. Biomechanical analysis identified the quadriceps, gastrocnemius/soleus, and plantar muscles as the most effective vibration sites, given their critical roles in gait propulsion and postural stability. The synthesis of protocol data indicated a promising therapeutic window characterized by a vibration frequency of 80-120 Hz (primarily fixed sinusoidal waveforms at a single frequency) and an amplitude of 0.2-0.5 mm (reported only in 12 studies; amplitude was not reported in 23 studies), applied bilaterally for a minimum of 3 sessions per week over 4-12 weeks, which could lead to improved balance and gait performance with benefits sustained for up to 5 months. CONCLUSION: FVT shows potential to improve gait and balance, particularly when targeting lower-extremity muscles with optimized vibration parameters. To advance the field, future research must prioritize the development of standardized protocols and investigate neurophysiological mechanisms to refine FVT as a precision bioengineering solution for mobility deficits.

Humans↗

PubMed1986

MR imaging of the lumbar spine: anatomic correlations and the effects of technical variations.

A correlative anatomic study, a retrospective review of MR images performed in 35 patients, and a series of tests of the effectiveness of various MR scanning techniques were performed in order to improve comprehension of lumbar spine anatomy depicted on MR images, and thereby facilitate development of an optimal scanning protocol. Correlation of MR images with cryomicrotomed cadaver specimens enhanced understanding of the MR depiction of the intervertebral disks, ligamentum flavum, nerve roots, epidural fat, and epidural veins. Experiments were performed to assess the efficacy of a surface coil applied to the back, a solenoidal surface coil, a standard body coil, and an abdominal compression device in optimizing image quality. Experiments were also performed to determine the effect of alterations in the pulse sequence and variations of the phase-encoding axis. Based on these results, a protocol is proposed for routine imaging of the lumbar spine that yields high-resolution sagittal and oblique images and that does not require a surface coil. The recommended protocol employs heavily T1-weighted images with phase encoding along the z axis for sagittal images and along the x axis for axial images. This protocol yields multiple sagittal and oblique axial images through each of the lumbar disks, a larger field of view than obtained with surface coils, and a reduction of total imaging time to as little as 10 min.

Cadaver↗

PubMedDate not supplied

Noncompetitive immunoassays using bifunctional unilamellar vesicles or liposomes.

Small unilamellar vesicles (SUVs) functionalized with an enzyme label and with specific ligands for biological molecules are useful as signal enhancement vehicles in the development of enzyme-linked immunoadsorbent assays and other biosensor applications. Bifunctional vesicles were prepared by covalently attaching horseradish peroxidase (HRP) and an antibody to the outside of the lipid bilayer of an SUV. The reaction conditions were optimized to obtain 7-12 antibody molecules and 100-200 HRP molecules per vesicle. The enzyme retained 70-80% of its specific activity after immobilization, and the presence of immobilized proteins on the vesicle surface apparently increased the vesicle stability. To minimize the background signal and maximize the specific signal, the immunoassay protocol was optimized with respect to (1) the type and concentration of blocking agent, (2) the diluents for HRP-antibody-vesicles and sample, (3) the incubation period, and (4) the incubation temperature. The bifunctional vesicles were used in a noncompetitive immunoassay to detect d-dimer, a fibrin dimer formed at the early stages of thrombosis. A second conjugate, HRP-antibody, was prepared, characterized, and used as a control against which to compare the assay using vesicles. The assay results using vesicles led to a detection limit for d-dimer in human plasma 9 times lower than what was achieved using the conventional enzyme-antibody conjugate assay.

Antibodies↗

PubMed1985

Theoretical considerations for optimizing intensity differences between primary musculoskeletal tumors and normal tissue with spin-echo magnetic resonance imaging.

In the radiographic assessment of primary musculoskeletal tumors, it is important for therapy planning to accurately define the extent of a tumor. Using a double spin-echo pulse sequence, the T1 and T2 relaxation times and relative hydrogen densities of several neoplastic tissues and of several normal tissues in four patients were measured. Neoplasms measured included one fibrosarcoma, two osteosarcomas, and one giant cell tumor. Normal tissues measured included normal muscle, fat, and bone marrow. Using a mathematical model of the double spin-echo pulse sequence, the intensity difference between each tumor and each normal tissue for multiple values of TR and TE was calculated. These calculated intensity differences were then used to plot isodifference contour curves for each tissue pair. These plots enabled us to pick combinations of TR and TE that optimized the signal difference between tumor and normal tissue. When comparing tumor with predominantly fatty tissue such as marrow or subcutaneous fat, optimal signal difference in our imager occurred at a TR of 600 to 800 msec and a very short TE. When comparing tumor with muscle, optimal signal difference occurred with very long TR times, and TE times ranging from 30 to 90 msec. These preliminary results suggest that an optimal scanning protocol for primary musculoskeletal tumors should contain at least two different pulse sequences with widely separated TR values (500 and 2000 msec in our instrument), and short to intermediate values of TE (28 and 56 msec in our instrument). It is believed that analysis of isodifference contour plots is a useful method for optimizing intensity differences between any two tissue types.

Bone Neoplasms↗

PubMed1994

Management of patients with acute asthma: what do we know? What do we need to know?

Management of patients with acute, severe asthma mandates the use of comprehensive monitoring and aggressive therapeutic drug regimens. Global clinical and objective assessment criteria can help determine the severity of the acute episode and will also help determine optimal management protocols. The response to aggressive therapy, rather than the initial severity of the attack, predicts outcome. Beta 2 sympathomimetic agents are the treatment of choice for acute asthmatic episodes. Aminophylline and parasympatholytic agents may be useful adjuvants, but more data are needed before firm conclusions can be reached regarding risk-benefit ratios. The optimal timing of steroid therapy is not yet known, but even this form of treatment is slow in producing results.

Acute Disease↗

PubMed1987

Cryopreservation of in vitro cultured mouse preimplantation embryos.

We investigated two different freezing protocols on mouse embryos that were either grown in vivo or were grown in vitro for a certain period. Our results confirm that an extended in vitro culture period makes the embryo more susceptible for injury due to freezing and thawing. Furthermore when freezing two cell mouse embryos we could observe that this early stage is more dependent on optimal cryopreservation protocol parameters than later stages.

Animals↗

PubMed1982

Determination of half-dose depth in skin for soft x-rays.

Unlike superficial x-rays, the soft x-rays normally used in dermatologic practice spare unaffected underlying organs during treatment of cutaneous malignancies. However, since the dose with depth from soft x-rays varies markedly, it is important to know this relationship for optimal therapeutic results. The peak kilovoltage, and thus the energy of the beam, is generally selected so that the dose to the base of the lesion is one-half the surface dose. An absorbed dose of 3,400 rads to the surface and a dose of about one-half this amount to the base of most malignant lesions is one standard protocol for optimal therapeutic results. An accurate value of half-depth dose in skin is therefore necessary and is readily obtained from ordinary half-value layer measurements using the technic described.

Aluminum↗

PubMed1990

Optimization of multidimensional high-performance liquid chromatography for the determination of drugs in plasma by direct injection, micellar cleanup and photodiode array detection.

Improvements in a multidimensional liquid chromatography system for the direct determination of drug substances in blood plasma are reported. The system employs an on-line micellar chromatographic cleanup followed by a reversed-phase analytical separation. The limit of detection of propranolol is improved by a factor 10 compared to previously reported work. The technique is applied towards the determination of a multicomponent mixture of tricyclic anti-depressants in blood plasma. A protocol for optimization is described.

Chromatography, High Pressure Liquid↗

PubMed1996

Macrophage targeting with technetium-99m labelled J001 acylated poly-galactoside for scintigraphy of inflammation: optimization and assessment of imaging specificity in experimental arthritis.

J001, an acylated poly-(1,3)-galactoside purified from the membrane of Klebsiella pneumoniae, associates selectively with macrophages via the binding to CD11b and CD14 molecules. Inflammatory foci known to recruit macrophages could thus be imaged with technetium-99m labelled J001. This study aims to define the optimal scintigraphic protocol for 99mTc-J001 imaging and to evaluate the specificity of J001 scans. A dose range study was conducted in rabbits with immunological arthritis using six different specific activities ranging from 370 to 11840 MBq·mg-1 while the intravenously injected activity was constant (37 MBq) Radiochemical purity for each preparation was documented together with the in vivo stability of the 99mTc-J001 complex using exclusion-diffusion radioHPLC of serum collected 1 h after radiopharmaceutical administration. Scintigraphic images were recorded at 2, 3 and 4h and analysed using indexes calculated from regions of interest. Specificity of the macrophage imaging was assessed by comparison with scans obtained after administration of 99mTcO4(- )or 99mTc-albumin nanocolloids. A protocol of plasma transfusion was also used to inject 99mTc-J001 after complete removal of radioactive colloids likely to be generated during the labelling. For the higher specific activities (5920 and 11840 MBq.mg-1), radiochemical purity degradation and in vitro 99mTc transchelation were noted. To prevent transchelation and 99mTc bond hydrolysis likely to impair imaging specificity, 1480 MBq.mg-1 corresponding to 25microg injected J001 was found to be the optimal usable specific activity. Results obtained with the various tracers support the hypothesis that macrophage targeting is the main factor involved in the J001 imaging of arthritis.

Animals↗

PubMedDate not supplied

Childhood non-Hodgkin's lymphoma--results of treatment with ALL high-risk protocol.

Between August 1984 and September 1990, 13 children with non-Hodgkin's lymphoma (NHL) were treated with ALL high-risk protocol (5 with TCLSG 842 regimen and 8 with TPOG 882B protocol) at Taichung Veterans General Hospital. Diagnosis of NHL was confirmed by histology. Nine had lymphoblastic lymphoma, three had histiocytic lymphoma and one had small non-cleaved cell lymphoma, according to the Rappaport classification. After thorough clinical evaluation eight children were NHL stage IV; four were stage III; and one was stage II. All these children had received chemotherapy as acute lymphocytic leukemia (ALL) high-risk protocol for a total of three years, including central nervous system (CNS) prophylaxis. Of the 13 patients, 9 (69.2%) gained complete remission. Over-all survival rate was 46.2%, with a median interval of 36 months. The complete remission rate and survival rate for the nine children with lymphoblastic lymphoma was better at 77.7% & 66.6% respectively. Within the nonresponsive group, two failed to remit because of early withdrawal from the protocol; the other two patients were refractory to treatment. Relapse was noted in one patient. As to the side effects, neutropenic fever was the most common problem encountered (9 occurrences in 13 patients). Other major complications included severe mucositis, massive GI bleeding, intracranial thrombosis induced by l-asparaginase and tumor lysis syndrome. Childhood NHL is often of diffuse types in pathology, and most affected children have advanced diseases at diagnosis. Choosing an optimal treatment protocol is important for good treatment results.

Adolescent↗

PubMed1997

An optimized PCR leads to rapid and highly sensitive detection of Borrelia burgdorferi in patients with Lyme borreliosis.

The present study aimed at developing an optimized PCR protocol fro the sensitive and specific detection of all three Borrelia burgdorferi genospecies pathogenic to humans in Lyme borreliosis patients. A rapid DNA extraction method using alkaline lysis was introduced and was found to be superior to other DNA extraction methods. Nested PCR was performed with primer sets targeting the plasmid-located ospA gene and a chromosomal gene segment encoding a 66-kDa protein (p66). In spiked synovial fluid (SF) fewer than three borreliae/sample were detected. The specificities of the amplicons were confirmed by Southern blot analysis with PCR-derived probes. Urine, cerebrospinal fluid (CSF), and SF specimens from 57 patients with Lyme borreliosis and from 58 controls were examined. In clinical samples the diagnostic sensitivity of PCR was 85% with SF samples, 79% with urine samples, and 91% with paired SF-urine samples from patients with Lyme arthritis and was 79% with CSF samples, 45% with urine samples, and 87% with paired CSF-urine specimens from neuroborreliosis patients. One patient each with neuroborreliosis and with Lyme arthritis had PCR-positive urine samples only. In 17% of all cases both primer sets yielded positive results, while the other patients were positive with only one primer set. Among these, more positive results were obtained with the p66 gene primer than with the ospA primer. The specificity exceeded 99%. We conclude that DNA from B. burgdorferi sensu lato species can sensitively and specifically be detected with the optimized PCR method described. At least two different primer sets should be used, and whenever possible, urine and CSF or SF should be analyzed in parallel to achieve maximum sensitivity of the test. This protocol, therefore, considerably enhances the diagnostic power of PCR in patients with B. burgdorferi infection.

Adolescent↗

PubMed1995

A reliable and sensitive method for non-radioactive northern blot analysis of nerve growth factor mRNA from brain tissues.

This report describes a sensitive, rapid and reproducible protocol for non-isotopic Northern blotting analysis. Church buffer and probes labeled with digoxigenin (DIG) were used for studying the expression of nerve growth factor (NGF) in the rat brain. Using the described method, NGF cRNA probe was hybridized to blotted RNA and the results were compared to Northern blot obtained using the method recommended by the manufacturer (Boehringer Mannheim). Comparison revealed that the blot treated with Church buffer detected at least 10-fold more NGF mRNA as compared to blot hybridized with formamide buffer. In summary, we have developed an optimal hybridization protocol to perform non-radioactive Northern blot analysis using antisense RNA as a probe. This method allowed us to detect the specific low-abundant mRNA and analyze the expression of neurotrophic factors in the rat brain.

Animals↗