Empirically determining the sample size for large-scale gene network inference algorithms.

The performance of genome-wide gene regulatory network inference algorithms depends on the sample size. It is generally considered that the larger the sample size, the better the gene network inference performance. Nevertheless, there is not adequate information on determining the sample size for optimal performance. In this study, the author systematically demonstrates the effect of sample size on information-theory-based gene network inference algorithms with an ensemble approach. The empirical results showed that the inference performances of the considered algorithms tend to converge after a particular sample size region. As a specific example, the sample size region around ≃64 is sufficient to obtain the most of the inference performance with respect to precision using the representative algorithm C3NET on the synthetic steady-state data sets of Escherichia coli and also time-series data set of a homo sapiens subnetworks. The author verified the convergence result on a large, real data set of E. coli as well. The results give evidence to biologists to better design experiments to infer gene networks. Further, the effect of cutoff on inference performances over various sample sizes is considered. [Includes supplementary material].

Local network-based measures to assess the inferability of different regulatory networks.

The purpose of this study is to compare the inferability of various synthetic as well as real biological regulatory networks. In order to assess differences we apply local network-based measures. That means, instead of applying global measures, we investigate and assess an inference algorithm locally, on the level of individual edges and subnetworks. We demonstrate the behaviour of our local network-based measures with respect to different regulatory networks by conducting large-scale simulations. As inference algorithm we use exemplarily ARACNE. The results from our exploratory analysis allow us not only to gain new insights into the strength and weakness of an inference algorithm with respect to characteristics of different regulatory networks, but also to obtain information that could be used to design novel problem-specific statistical estimators.

[Ofloxacin treatment of salmonella infections]. / Salmonella enfeksiyonlarinda ofloksasin tedavisi.

In the present study, 33 adult patients with salmonella infections consisting of 13 typhoid fever, 9 paratyphoid fever, 8 enterocolitis, 2 carriers, 1 acute gastroenteritis have been treated with ofloxacin. The duration of treatment was 10 days for typhoid fever, 7 days for paratyphoid fever, 5 days for enterocolitis, 3 days for acute gastroenteritis and 7 days for asymptomatic carriers. All the patients recovered without any complication and fever declined to normal levels within a mean of 3.0 +/- 1.34 days. Two carriers of S. enteritidis became salmonella free after 7 days of ofloxacin treatment. One of the patients who had severe S. paratyphi B bacteremia remained carrier for about 6 months. None of the patients have relapsed. The antibiotic therapy proposals on salmonella in adults were discussed in the light of our results and the other studies.

[Development of resistance in bacteria interacting with subinhibitory antibiotic concentrations]. / Subinhibitör antibiyotik konsantrasyonlarinin bakterilerde direnç gelisimi üzerine etkileri.

In order to determine the role of subinhibitory concentrations of antibiotics in resistance development, we performed an in vitro trial in which E. coli gained resistance after exposure to low concentrations of ampicillin in serial passages, while MIC values for amikacin and gentamicin increased 2 and 4 times, respectively. Pseudomonas also became resistant to ceftazidime whereas the MIC value for ciprofloxacin increased 10 times. There was not any significant change in susceptibility of S. aureus to vancomycin and amoxicillin + clavulanate.

[In vitro activity of various antibiotics against Shigella strains]. / Cesitli antibiyotiklerin Shigella suslarina in-vitro etkinlikleri.

The in-vitro activity of ampicillin, chloramphenicol, oxytetracycline, trimethoprim-sulfamethaxazole (TMP-SMX), cefoperazone, ceftriaxone, cefotaxime, ceftizoxime, ofloxacin, pefloxacin, ciprofloxacin and fleroxacin against clinically isolated strains of Shigella spp. (n 42) have been determined in this study. The minimum inhibitory concentrations (MICs) were established using the microtube dilution technique. In shigella strains relatively high percentage of resistance was found against ampicillin (% 36.5), chloramphenicol (% 34), oxytetracycline (% 35), and TMP-SMX (% 25.6). The antibiotic therapy proposals reviewed according to these results.

[The susceptibility of Salmonella sp. to various antibiotics]. / Salmonella cinsi bakterilerin çesitli antibiyotiklere duyarliliklarinin arastirilmasi.

In this study, the in-vitro activity of ampicillin, chloramphenicol, trimethoprim-sulfamethoxazole (TMP-SMX), cefoperazone, ceftriaxone, cefotaxime, ceftizoxime, ofloxacin, pefloxacin, ciprofloxacin, and fleroxacin against recently isolated strains of S.typhi (20) and Salmonella group B (42) have been investigated. The minimum inhibitory concentrations (MICs) were determined using the microtube dilution technique except for TMP-SMX which was tested by agar dilution technique. All of S.typhi strains have been found to be susceptible to all antibiotics used in this study. In Salmonella group B bacteria relatively high percentage of resistance has been found against ampicillin (28.6%), chloramphenicol (33%), TMP-SMX (42.9%), cefoperazone (35.7%), and ceftizoxime (12%). All new quinolone derivatives tested were very active against all of the Salmonella strains. The antibiotic therapy proposals on salmonellosis in adults have been discussed in the light of our results, our clinical experience and the other studies.

[Anti-bacterial effect of ofloxacin--in vitro and in vivo results]. / Ofloxacin'in antibakteriyel etkisi - in vitro ve in vivo sonuçlar.

Gram (-) bacteria such as E. coli, B. proteus, Klebsiella and Pseudomonas sp were found to be sensitive to Ofloxacin 98.3%, 96.7%, 96.9%, and 89.1% respectively. Among Gram (+) bacteria, 98% of Staph aureus and 95% of Staph epidermidis were susceptible to this drug. The minimum inhibitory concentrations of Ofloxacin for the Shigella strains have been found to be between 0.1-0.05 mcg/ml (76%) and 0.05-0.025 mcg/ml (20%). Thirty three patients with various infection have been treated with ofloxacin; in acute cases the efficacy of the drug was 100%, but reinfections or relapse developed in about half of the patients with chronic and complicated urinary tract infections, 15-20 days after discontinuation of the drug. No serious side effect has been observed.

[Brucellosis and rheumatic fever]. / Brusellozis ve romatizmal ates.

Brucellosis and Acute Rheumatic Fever can not be verified by only clinical manifestations and the pattern of joint involvement. Four patients presented below had high fever, sweats, severe arthralgia and swelling of one or multiple joints, elevated sedimentation rate and positive C - reactive protein test and even leukocytosis. Therefore they were treated with anti - rheumatic drugs for 4 to 7 days after onset till brucellosis was considered or its specific tests became positive.

Identification and quantitation of embryonic and three types of fetal hemoglobin produced on induction of the human pluripotent leukemia cell line K-562 with hemin.

The hemoglobins synthesized by the pluripotent K-562 leukemia cell line of human origin after induction with hemin have been isolated by DEAE-cellulose chromatography and characterized by electrophoresis, high pressure liquid chromatography, and a radioimmunological assay. Six hemoglobin zones have been observed with the following likely compositions. Zone 1: alpha 2 epsilon 2, or HB Gower-2; zone 2: zeta 2 epsilon 2, or HB Gower-1; zone 3: zeta 2 gamma 2, or HB Portland-I; zone 4: Hb F, or alpha 2 gamma 2; zone 5: a mixture of acetylated HB Portland-I and Hb F; zone 6: Hb Bart's, or gamma 4. The embryonic Hbs (zones 1, 2, and 3) constituted 50%-75% of the total Hb present; the quantities varied from one experiment to the other. Both Hb Gower-1 and Hb Gower-2 were present. The gamma chain was heterogeneous and contained the G gamma, A gamma I, and A gamma T types in a ratio of about 4:2:1, indicating a heterozygosity for the Ile leads to Thr substitution at position gamma 75. The methodology used can be applied for additional studies evaluating quantitative changes in Hb types due to in vitro manipulations.

[Penicillinase activity of staphylococci and their sensitivity to penicillin G and oxacillin (author's transl)]. / Stafilokoklarin penicillinase aktivitesi ve penicillin G ile oxacillin'e duyarliligi.

The penicillinase activities of 169 strains of staphylococci isolated from outpatients were detected by a simple technique that gives the result in 10 minutes on benzylpenicillin and bromocresol purple absorbed Whatman No 1 filter papers. Seventy three out of 100 S. aureus strain and 4 out of 69 S. albus were found to have the enzyme. The ratio of penicillin G resistance among S. aureus and S. albus were found to be 89% and 41% respectively. Six strains (6%) of S. aureus and 5 (7%) S. albus were resistant to both antibiotics. When the findings were compared with those previously reported in Turkey, it was seen that the proportion of the penicillinase + strains and the incidence of resistance in staphylococci to both kinds of penicillins was increased.

[Brucellosis outbreak in Oltan village of Ankara (author's transl)]. / Ankara'nin Oltan köyündeki brusellozis salgini.

There has been significant increase in the number of brucellosis cases admitted to our clinic within first 6 months of 1979. Since most of the cases were from Ayas, Polatli and Oltan villages we visited Oltan and examined 97 persons 23 of whom had complaints of fever, arthralgia and sweating. In addition to previous 5 cases, 5 more patients were found to have antibody titers of 160-640. In the control group none of the randomly chosen outpatients had titers higher than 40. Three milk samples taken from 12 sheep also had antibodies against brucella. Six B. melitensis strains isolated from these and the other patients were sensitive to terramycin, rifampicin and streptomycin; but resistant to sulfonamide, chloramphenicol and clindamycin. Four of them were sensitive to bactrim and ampicillin. In this paper, the findings of 17 cases of brucellosis other than from those of Oltan have also been presented.

Radioimmunochemical characterization of hemoglobins Lepore and Kenya: unique antigenic determinants located on hybrid hemoglobins.

Antisera were produced in rabbits to the three known types of Lepore hemoglobins, which contain hybrid delta-beta non-alpha-chains, and to hemoglobin Kenya, which has a hybrid gamma-beta non-alpha-chain. By using a sensitive radioimmunoassay technique, the absorbed antisera were shown to contain an antibody population that was specific for the hybrid hemoglobin and did not cross-react with normal hemoglobins. However, with the absorbed Lepore-specific antisera, the three known types of Lepore hemoglobins were antigenically indistinguishable from each other, suggesting that antibodies are not produced to the primary structural differences which define the three non-alpha-chains of the Lepore hemoglobins. These studies demonstrate that the non-alpha-subunits of hemoglobins Lepore and Kenya possess unique antigenic determinant sites, evidently resulting from an altered polypeptide conformation.

Detection and quantitation of the fetal hemoglobin variant Hb F-Malta-I in adults.

A variant of fetal hemoglobin (Hb F-Malta-I) has been detected and quantitated in adult blood with a sensitive radioimmunoassay employing monospecific antisera. The concentration of Hb-F-Malta-I was 0.002-0.05%, with an average value of 0.011%. The ratio of Hb F-Malta-I/Hb F in adults was about 4.8%, compared to a ratio of about 27% in the newborn. Since the F-Malta-I variant is a product of a mutated Ggamma locus, which is one of the nonallelic structural genes directing the gamma chain synthesis, its presence in blood of adults shows that the synthesis of this gene is not completely suppressed after birth, as was previously suggested.

Radioimmunoassay for abnormal hemoglobins.

A sensitive and specific radioimmunoassay has been developed for the identification or quantification of the human hemoglobin variants S, C, D-Los Angeles, E, G Philadelphia, Russ, O Arab, Beograd, J Paris I, G San Jose, Q Iran, Korle Bu, and F Malta I. In the immunoassay, monospecific antibody preparations are used which recognize the single amino acid substitution in the variant polypeptide chail and do not cross-react with normal hemoglobins or hemoglobin variants containing a different amino acid exchange at the same position.

Specific radioimmunochemical identification and quantitation of hemoglobins A2 and F.

Hyperimmune antisera to chromatographically purified hemoglobins F and A2 were produced in rabbits and made specific for the immunogen by adsorption with normal human hemoglobin A conjugated to cyanogen bromide-activated agarose. A radioimmunoassay was established that permitted identification and quantitation of each of these two minor hemoglobins in hemolysates containing other hemoglobin components. The quantities of hemoglobins A2 and/or F present in hemolysates of individuals with beta-thalassemia, sickle cell anemia, Hb-C disease, and other hematological disorders were determined immunochemically, and the results were commpared to values obtained by microcolumn chromatography for the measurement of Hb-A2 or with the alkali denaturation technique in quantitating Hb-F. The immunoassay procedure has a greater sensitivity than other commonly employed techniques and can detect as little as 0.05 mug of these hemoglobins.