gebhart/patrepeval huggingface dataset:
Dade County Medical Examiner Department Florida ABD ile İlgili İzlenimler (1997)

1996-1997 Kasım ayları arasında 1 yıl süreyle asistanlık yaptığım Dade County Medical Examiner Department’taki (Florida-Amerika Birleşik Devletleri) uygulamalar ile ilgili izlenimlerimi meslektaşlarımla paylaşmak istiyorum. Bölümün kurucusu, 1950’li yıllardan beri adli tıbba hizmet veren Pıof.Dr.Joseph H. Davis’dir. 1996 yılında emekli olmasına rağmen halen aynı merkezde çalışmaktadır. 1980’li yıllarda bugünkü modern yapılarına kavuşan merkezin yıllık olgu sayısı 3600 civarındadır. Olgulardan yaklaşık 600 kadarının ölüm sertifikası dış muayene ile imzalanmakta, geri kalanına otopsi yapılmaktadır. Otopsi olgularının 1200 kadarı doğal ölümler, 800 kadarı kazalar, 600 kadarı cinayet ve yaklaşık 400’ü de intihardır. Amerika Birleşik Devletleıi’nin en kapsamlı ve en modem otopsi merkezlerinden biri olarak kabul edilen merkez, yaklaşık 2 milyon 250 bin nüfuslu Dade County’ye hitap etmektedir. 75 çalışanı bulunan bölümde otopsi işlemleri hafta sonu ve resmi tatil günlerinde de devam etmektedir. Gerek olgu spektrumu, gerek teknik kapasitesi, gerek işleyişi, gerekse çalışanlarının bilgi düzeyi açısından örnek seviyede olan merkezin Miami Üniversitesi ile de resmi bağlantısı bulunmaktadır. Amerika Birleşik Devletleri’nde adli ölüm olaylarının tıbbi incelenmesinde temelde iki sistem mevcuttur. Bunlardan biri “medical examiner” diğeri “coroner” sistemidir. Bu uygulamalar eyaletlere göre değişmektedir. “Medical Examiner’lar” genelde adli patolog iken “Coroner’ler” genelde pratisyen hekimlerden oluşmaktadır. “Dade County Medical Examiner Department” idari, araştırma-soruşturma, morg, yazım, arşiv, toksiko- loji, histopatoloji, özlük hakları, antropoloji, adli görüntüleme ve bilgi işlem bölümlerinden oluşmaktadır. Aynı anda 15 olguya otopsi yapacak kapasitede bir otopsi salonu, yaklaşık 300 cesedi barındıracak kapasitede morgu, çürümüş veya enfekte cesetlere otopsi yapmak için morg vs. tesislerini de içeren ayrı bir binası bulunmaktadır. Departman üç ayrı binadan oluşmaktadır. Bölümün bütün kapıları, sadece çalışan per- .sonele dağıtılmış olan özel manyetik kartlarla açılabilmektedir. Bütün girişler ve birimlerin çalışma alanları, güvenlik kameraları ile 24 saat izlenmektedir. Yetkili kişilerin herhangi bir terminalden herhangi bir olguyla ilgili bilgilere ulaşmasını mümkün kılacak şekilde, bölüm içinde bir bilgisayar ağı mevcuttur.
The active site structure of methane monooxygenase is closely related to the binuclear iron center of ribonucleotide reductase (1992)

Methane monooxygenase (MMO) catalyses the biological transformation of methane to methanol at a binuclear iron site. Guided by the three-dimensional structure of the R2 protein of E. coli ribonucleotide reductase (RNR), we have aligned the sequences of two different MMOs with the sequences of the iron coordinating four helix bundle in R2. The model suggests that the central four helix bundle of R2 is present also in MMO. The iron coordination is similar in MMO and R2 with two histidine ligands and four carboxyl ligands in both cases. The residues lining the proposed oxygen binding site in MMO are significantly smaller in MMO than in R2 allowing binding of both molecular oxygen and methane at this site. This binding site is lined by residues Cys151, Thr213, Ile217 and Ile(Val)239.
Photophysical, Photochemical and Photocatalytic Aspects of Metal Nanoparticles (2002)

Unique electronic and chemical properties of metal nanoparticles have drawn the attention of chemists, physicists, biologists, and engineers who wish to use them for the development of new generation nanodevices. Metal nanoparticles such as gold and silver show noticeable photoactivity under UV−visible irradiation as is evident from the photoinduced fusion and fragmentation processes. Binding a photoactive molecule (e.g., pyrene) to metal nanoparticle enhances the photochemical activity and renders the organic−inorganic hybrid nanoassemblies suitable for light-harvesting and optoelectronic applications. The nature of charge-transfer interaction of fluorophore with gold surface dictates the pathways with which the excited-state deactivates. Obtaining insight into energy and electron-transfer processes is important to improve the charge separation efficiencies in metal−fluorophore nanoassemblies and photocatalytic activity of metal−semiconductor composites.
Mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK) inhibitors restore anoikis sensitivity in human breast cancer cell lines with a constitutively activated extracellular-regulated kinase (ERK) pathway. (2002)

Anchorage-independent growth is a hallmark of oncogenic transformation. We reported that the mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK) inhibitor U0126 inhibited anchorage-independent growth of Ki-ras-transformed rat fibroblasts by simultaneously blocking both extracellular signal-regulated kinase (ERK) and mammalian target of rapamycin (mTOR)-p70(S6K) pathways. Here, we examined the effects of U0126 on the growth of eight human breast cancer cell lines. U0126 selectively repressed anchorage-independent growth of MDA-MB231 and HBC4 cells, two lines with constitutively activated ERK. Loss of contact with substratum triggers apoptosis in many normal cell types, a phenomenon termed anoikis. U0126 sensitized MDA-MB231 and HBC4 to anoikis, i.e., upon treatment with U0126, cells deprived of anchorage entered apoptosis, whereas adherent cells remained viable. Another MEK inhibitor PD98059 also induced anoikis sensitivity in MDA-MB231 cells but not in HBC4 cells. However, HBC4 cells were sensitized to anoikis when PD98059 was combined with the mTOR inhibitor rapamycin. To study the biochemical basis for induction of anoikis sensitivity, we examined the effects of the MEK inhibitors on ERK and p70(S6K) pathways in anchored versus nonanchored cells. As in Ki-ras-transformed rat fibroblasts, U0126 reduced activation of both ERK and p70(S6K) in MDA-MB231 and HBC4 cells, irrespective of anchorage. PD98059, in anchored cells, was more selective for the ERK pathway and did not significantly block the p70(S6K) pathway. Removal of anchorage substantially sensitized p70(S6K) to PD98059 in MDA-MB231 cells, whereas p70(S6K) in suspended HBC4 cells remained fairly refractory. U0126 was either without effect or less inhibitory on p70(S6K) in MDA-MB453 and SKBR3, two cell lines in which anoikis sensitivity was not induced. Thus, susceptibility of the p70(S6K) pathway to MEK inhibitors appeared to be an important determinant of anoikis sensitivity. The results indicate that concurrent inhibition of MEK-ERK and mTOR-p70(S6K) pathways induces apoptosis in MDA-MB231 and HBC4 cells when cells are deprived of anchorage but not when anchored. Inhibitors of MEK-ERK and mTOR-p70(S6K) pathways may provide a therapeutic strategy to selectively target neoplasms proliferating at ectopic locations, with acceptable effects on normal cells in their proper tissue context.
Accurate SHAPE-directed RNA structure determination (2008)

Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure-function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75-155 nt) with accuracies of up to 96-100%, which are comparable to the best accuracies achievable by comparative sequence analysis.
Transplantation of photoreceptors to light-damaged retina. (1989)

We investigated the possibility of reconstructing light-damaged retinas by photoreceptor transplantation. The outer nuclear layer containing the photoreceptor cells was eliminated in adult albino rat retinas by exposure to constant high-level illumination. Photoreceptors for transplantation were harvested from neonatal rats using a novel isolation technique that maintained the cellular organization of the outer nuclear layer. Transplantation was accomplished using a transcorneal approach to the subretinal space, which minimized trauma to the eye. The retina reattached to the back of the eye with transplanted photoreceptors interposed between the retina and the overlying tissues. Prelabelling with fluorescent dye enabled positive identification of the transplanted cells. The transplanted photoreceptors appeared to survive transplantation for at least 6 weeks and were immunohistochemically reactive for opsin. The antibody staining for opsin identifies the transplanted cells as photoreceptors and indicates that they are still capable of producing visual pigment and therefore may have the capacity to transduce light. These findings indicate that photoreceptors can be transplanted to form a new outer nuclear layer in a damaged mature retina.
Achieving nitritation and anammox enrichment in a single moving-bed biofilm reactor treating reject water (2011)

A biofilm with high nitrifying efficiency was converted into a nitritating and thereafter a nitritating-anammox biofilm in a moving-bed biofilm reactor at 26.5 (+/- 0.5) degrees C by means of a combination of intermittent aeration, low dissolved oxygen concentration, low hydraulic retention time, free ammonia and furthermore, also by elevated HCO3- concentration. Nitrite-oxidizing bacteria (NOB) were more effectively suppressed by an enhanced HCO3- concentration range of 1200-2350 mg/L as opposed to free-ammonia-based process control where NOBs recovered from inhibition; the respective total-nitrogen removal rates were 0.3 kg N/(m3 x d) and 0.2 kg N/(m3 x d). The biofilm modification strategies resulted in a shift in bacterial community as the NOB Nitrobacter spp. were replaced with NOB belonging to the genus Nitrospira spp. and were closely related to Candidatus Nitrospira defluvii. A community of anaerobic ammonium-oxidizing microorganisms -uncultured Planctomycetales bacterium clone P4 (closely related to Candidatus Brocadia fulgida)--was developed.
Flow Cytometry: First Principles (2001)

Preface. Acknowledgments (First Edition). Acknowledgments (Second Edition). The Past as Prologue. Setting the Scene. Instrumentation: Into the Black Box. Information: Harnessing the Data. Seeing the Light: Lasers, Fluorochromes, and Filters. Cells from Without: Leukocytes, Surface Proteins, and the Strategy of Gating. Cells from Within: Intracellular Proteins. Cells from Within: DNA in Life and Death. The Sorting of Cells. Disease and Diagnosis: The Clinical Laboratory. Out of the Mainstream: Research Frontiers. Flowing On: The Future. General References. Glossary. Figure Credits. Index.
Programs for pedigree analysis: Mendel, Fisher, and dGene (1988)

Peer Reviewed
Arylsulfatase in natural killer cells: its possible role in cytotoxicity. (1983)

Ultrastructural cytochemistry of natural killer cells enriched by Percoll gradient centrifugation showed them to possess arylsulfatase (aryl-sulfate sulfohydrolase, EC 3.1.6.1). The enzyme was located in vesicles, granules, and the parallel tubular arrays, organelles characteristic for cytotoxic lymphocytes. Biochemically, peak enzyme activity correlated with the Percoll fractions containing cells with cytotoxicity for melanoma target cells. Treatment of natural killer cells with Na2SO4, a competitive inhibitor of arylsulfatase, suppressed cytotoxicity by almost 50%. Electron microscopy of effector-target cell conjugates, which had been permitted to incubate for only 30 min, disclosed numerous arylsulfatase-positive sites at the points of contact between the effector/target cell membranes. Thus, the enzyme was translocated to the surface before lysis of the target cell was morphologically evident. It is postulated that the parallel tubular arrays play a role in this translocation and that arylsulfatase may function in the degradation of cerebroside sulfate ester components of the target cell membrane to initiate the lytic event.
TOPAS: An innovative proton Monte Carlo platform for research and clinical applications (2012)

We have demonstrated TOPAS accuracy and usability in a variety of proton therapy setups. As we are preparing to make this tool freely available for researchers in medical physics, we anticipate widespread use of this tool in the growing proton therapy community.
Architecture of High Performance Computers (1989)

This second edition is presented as two volumes. Subtitled Uniprocessors and Vector Processors, Volume I is a revised and expanded version of the first edition; it deals mainly with the techniques use
A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription (1999)

The transcription factor VP1 regulates maturation and dormancy in plant seeds by activating genes responsive to the stress hormone abscisic acid (ABA). Although activation involves ABA-responsive elements (ABREs), VP1 itself does not specifically bind ABREs. Instead, we have identified and cloned a basic region leucine zipper (bZIP) factor, TRAB1, that interacts with both VP1 and ABREs. Transcription from a chimeric promoter with GAL4-binding sites was ABA-inducible if cells expressed a GAL4 DNA-binding domain::TRAB1 fusion protein. Results indicate that TRAB1 is a true trans-acting factor involved in ABA-regulated transcription and reveal a molecular mechanism for the VP1-dependent, ABA-inducible transcription that controls maturation and dormancy in plant embryos.
Analysis of Oct-4 expression and ploidy in individual human blastomeres (2001)

Oct-4, a decisive factor that maintains totipotency in murine embryonic and germ cells, is exclusively expressed in such cells. In mice, different levels of oct-4 expression in blastomeres predict development towards inner cell mass (ICM) (high oct-4) or trophectoderm (TE) (low oct-4). To address whether the mouse model also applies to human embryos, the cytoplasm of individual human blastomeres from normally and abnormally fertilized embryos was tested for Oct-4 expression by reverse transcription-polymerase chain reaction (RT-PCR). The nuclei of the same blastomeres were subjected to fluorescence in-situ hybridization (FISH) to determine ploidy. A significant difference in Oct-4 mRNA levels was revealed between blastomeres. The distribution of blastomeres with high Oct-4 levels varied according to the cleavage stage of the embryo: the more blastomeres, the lower the percentage with high Oct-4 levels. Aneuploid blastomeres did not exhibit lower Oct-4 mRNA levels than diploid ones. Thus, differential Oct-4 expression in individual human blastomeres appears to direct cells towards the ICM or TE lineages without regard to chromosomal status. Oct-4 might be used as a marker in preimplantation genetic diagnosis to identify embryogenic blastomeres.
Fundamental Examination of Cattle Red Blood Cells Damage with Ultrasound Exposure Microscopic System (UEMS) (1998)

In order to define the safety limit of the medical ultrasound equipment and to study the ultrasonic bioeffects, ultrasound exposure microscopic system (UEMS) was developed in our laboratory. We intended to observe the tissue damage caused by ultrasound exposure in real time. The change of size and shape of the cattle red blood cells was investigated experimentally with UEMS. It was observed that, at a driving frequency of 2.2 MHz, when the ultrasound intensity I SPTP was 28.4 W/cm 2 , the change of shape of the cattle red blood cells, due to the ultrasound exposure, occurred after 30 min of exposure. The change of size of the cattle red blood cells was investigated with a Coulter counter. The results, indicated that the size of the red blood cells after exposure to ultrasound was smaller than before exposure. Moreover, the results also indicated that, there was a tendency of the red blood cells to decrease in size after the ultrasound exposure when the ultrasound intensity was increased. At the two driving frequencies of 2.2 MHz and 0.55 MHz, in this study, the size of the cattle red blood cells decreased when the ultrasound intensities were increased.
Activation of the aryl hydrocarbon receptor affects activation and function of human monocyte-derived dendritic cells (2014)

Aryl hydrocarbon receptor (AhR) is well known for mediating the toxic effects of dioxin-containing pollutants, but has also been shown to be involved in the natural regulation of the immune response. In this study, we investigated the effect of AhR activation by its endogenous ligands 6-formylindolo[3,2-b]carbazole (FICZ) and 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE) on the differentiation, maturation and function of monocyte-derived DCs in Behçet's disease (BD) patients. In this study, we showed that AhR activation by FICZ and ITE down-regulated the expression of co-stimulatory molecules including human leucocyte antigen D-related (HLA-DR), CD80 and CD86, while it had no effect on the expression of CD83 and CD40 on DCs derived from BD patients and normal controls. Lipopolysaccharide (LPS)-treated dendritic cells (DCs) from active BD patients showed a higher level of interleukin (IL)-1β, IL-6, IL-23 and tumour necrosis factor (TNF)-α production. FICZ or ITE significantly inhibited the production of IL-1β, IL-6, IL-23 and TNF-α, but induced IL-10 production by DCs derived from active BD patients and normal controls. FICZ or ITE-treated DCs significantly inhibited the T helper type 17 (Th17) and Th1 cell response. Activation of AhR either by FICZ or ITE inhibits DC differentiation, maturation and function. Further studies are needed to investigate whether manipulation of the AhR pathway may be used to treat BD or other autoimmune diseases.
Primary structure of a constituent polypeptide chain (AIII) of the giant haemoglobin from the deep-sea tube worm Lamellibrachia. A possible H2S-binding site (1990)

The deep-sea tube worm Lamellibrachia, belonging to the Phylum Vestimentifera, contains two giant extracellular haemoglobins, a 3000 kDa haemoglobin and a 440 kDa haemoglobin. The former consists of four haem-containing chains (AI-AIV) and two linker chains (AV and AVI) for the assembly of the haem-containing chains [Suzuki, Takagi & Ohta (1988) Biochem. J. 255, 541-545]. The tube-worm haemoglobins are believed to have a function of transporting sulphide (H2S) to internal bacterial symbionts, as well as of facilitating O2 transport [Arp & Childress (1983) Science 219, 295-297]. We have determined the complete amino acid sequence of Lamellibrachia chain AIII by automated or manual Edman sequencing. The chain is composed of 144 amino acid residues, has three cysteine residues at positions 3, 74 and 133, and has a molecular mass of 16,620 Da, including a haem group. The sequence showed significant homology (30-50% identity) with those of haem-containing chains of annelid giant haemoglobins. Two of the three cysteine residues are located at the positions where an intrachain disulphide bridge is formed in all annelid chains, but the remaining one (Cys-74) was located at a unique position, compared with annelid chains. Since the chain AIII was shown to have a reactive thiol group in the intact 3000 kDa molecule by preliminary experiments, the cysteine residue at position 74 appears to be one of the most probable candidates for the sulphide-binding sites. A phylogenetic tree was constructed from nine chains of annelid giant haemoglobins and one chain of vestimentiferan tube-worm haemoglobin now determined. The tree clearly showed that Lamellibrachia chain AIII belongs to the family of strain A of annelid giant haemoglobins, and that the two classes of Annelida, polychaete and oligochaete, and the vestimentiferan tube worm diverged at almost the same time. H.p.l.c. patterns of peptides (Figs. 4-7), amino acid compositions of peptides (Table 2) and amino acid sequences of intact protein and peptides (Table 3) have been deposited as Supplementary Publication SUP 50154 (13 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1990) 265, 5.
Redirection of flux through the FPP branch‐point in Saccharomyces cerevisiae by down‐regulating squalene synthase (2008)

Saccharomyces cerevisiae utilizes several regulatory mechanisms to maintain tight control over the intracellular level of farnesyl diphosphate (FPP), the central precursor to nearly all yeast isoprenoid products. High-level production of non-native isoprenoid products requires that FPP flux be diverted from production of sterols to the heterologous metabolic reactions. To do so, expression of the gene encoding squalene synthase (ERG9), the first committed step in sterol biosynthesis, was down-regulated by replacing its native promoter with the methionine-repressible MET3 promoter. The intracellular levels of FPP were then assayed by expressing the gene encoding amorphadiene synthase (ADS) and converting the FPP to amorphadiene. Under certain culture conditions amorphadiene production increased fivefold upon ERG9 repression. With increasing flux to amorphadiene, squalene and ergosterol production each decreased. The levels of these three metabolites were dependent not only upon the level of ERG9 repression, but also the timing of its repression relative to the induction of ADS and genes responsible for enhancing flux to FPP.