gebhart/patrepeval huggingface dataset:
Endocrine complications of bone marrow transplantation in children (1999)

Eighty-seven patients had a bone marrow transplantation (BMT) at our institution between 1980 and 1992. We wished to study the endocrine complications that accompany this procedure as long-term survival is now much more common. Forty-three patients were retrospectively available for review and their records were examined for evidence of thyroid, pubertal, and growth complications. Fifteen per cent of the patients showed evidence of thyroid involvement. Pubertal delay or gonadal damage was almost universal in pubertal-aged girls treated with busulfan/cyclophosphamide. Gonadal involvement was more frequent in girls than in boys (70% vs. 47%). Sixty per cent of children were shorter or grew at a slower rate. Sixty-five per cent of the children presented with one or more endocrine complications. These are the combined effects of different treatment regimens (chemotherapy, radiotherapy, combined therapy). It is essential to know the natural history of these patients in order to offer proper guidance and treatment as survival rates are increasing.
Artificial-Intelligence Approach for Biomedical Sample Characterization Using Raman Spectroscopy (2005)

An artificial-intelligence approach is proposed to differentiate various biomedical samples via Raman spectroscopy technology to obtain accurate medical diagnosis and decision making. The complete process consists of noise filtering, fluorescence identification, optimization and elimination, spectral normalization, multivariate statistical analysis, and data clustering, as well as the final decision making. Numerous modeling, intelligent control, and system-identification schemes have been employed. By means of fuzzy control, genetic algorithms, and principal component analysis (PCA), as well as system identification, a systematic intelligent-control approach is formulated, which is capable of classifying diversified biomedical samples. Raman spectra are weak signals whose features are sensitive to a variety of noises, which have to be reduced to an acceptable level. Fuzzy logic has been known to interpret uncertainty, imprecision, and vague phenomena. Thus, a fuzzy controller is used for noise filtering. On the other hand, background fluorescence acts as a secondary intensity component within a raw Raman spectrograph, so its spectral baseline should be determined. By removing background fluorescence, intrinsic Raman spectrum can be extracted in consequence. To optimize this detrend process, genetic algorithms have been implemented for baseline-function global optimization by selecting an optimal combination of individual spectroscopic functions. Normalization is performed by standard normal variate (SNV) afterwards to compensate for scattering effects. Normalized intrinsic spectra can be used for sample differentiation, where the PCA approach distinguishes some signatures from different samples in terms of dominant principal components. Eventually, various principal components are accumulated for clustering using scatter plots. The long-term objective of this intelligent-control approach is to create a real-time technique for sample analysis, using a Raman spectrometer directly mounted at the end-effectors of medical robots, which is to enhance the robotic surgery.
V2O5 xerogel electrodes with much enhanced lithium-ion intercalation properties with N2 annealing (2009)

V2O5 xerogel films were fabricated by casting V2O5 sols onto FTO glass substrates and annealing at 300 °C for 3 hours in nitrogen and air. The films annealed in nitrogen and air possessed different grain size and crystallinity. Optical absorption measurements and electrochemical impedance analyses revealed a reduced optical bandgap and enhanced electrical conductivity of N2 annealed V2O5 film. Lithium ion intercalation measurements showed that at a charge/discharge current density of 600 mAg−1, the N2 annealed sample possessed noticeably better lithium ion storage capability. In contrast to the air annealed sample, which started with a discharge capacity of 152 mAhg−1 but after 50 cycles the capacity had decreased to a low value of only 44 mAhg−1, the N2 annealed sample started with a low value of 68 mAhg−1 but the capacity increased sharply to a high value of 158 mAhg−1 at the 24th cycle, followed by little capacity degradation in later cycles and after 50 cycles, the discharge capacity was still as high as 148 mAhg−1. Much improved lithium ion intercalation capacity and cyclic stability could be attributed to surface defects V4+ and/or V3+ and associated oxygen vacancies introduced by N2annealing as well as much less crystallized vanadium oxide.
Balloon‐assisted tracking: A must‐know technique to overcome difficult anatomy during transradial approach (2013)

BAT technique was useful to address the anatomical issues and tortuosities of radial, brachial, and subclavian vasculature during TRA.
Incoherent Combining and Atmospheric Propagation of High-Power Fiber Lasers for Directed-Energy Applications (2008)

High-power fiber lasers can be incoherently combined to form the basis of a directed high-energy laser system which is highly efficient, compact, robust, low-maintenance and has a long operating lifetime. This approach has a number of advantages over other beam combining methods. We present results of the first field demonstration of incoherent beam combining using kilowatt-class, single-mode fiber lasers. The experiment combined four fiber lasers using a beam director consisting of individually controlled steering mirrors. Propagation efficiencies of ~90%, at a range of 1.2 km, with transmitted continious-wave power levels of 3 kW were demonstrated in moderate atmospheric turbulence. We analyze the propagation of combined single-mode and multimode beams in atmospheric turbulence and find good agreement between theory, simulations and experiments.
Rosiglitazone ameliorates cisplatin-induced renal injury in mice (2006)

These results showed that pre-treatment with rosiglitazone attenuates cisplatin-induced renal damage through the suppression of TNF-alpha overproduction and NF-kappaB activation.
Insects Represent a Link between Food Animal Farms and the Urban Environment for Antibiotic Resistance Traits (2014)

Antibiotic-resistant bacterial infections result in higher patient mortality rates, prolonged hospitalizations, and increased health care costs. Extensive use of antibiotics as growth promoters in the animal industry represents great pressure for evolution and selection of antibiotic-resistant bacteria on farms. Despite growing evidence showing that antibiotic use and bacterial resistance in food animals correlate with resistance in human pathogens, the proof for direct transmission of antibiotic resistance is difficult to provide. In this review, we make a case that insects commonly associated with food animals likely represent a direct and important link between animal farms and urban communities for antibiotic resistance traits. Houseflies and cockroaches have been shown to carry multidrug-resistant clonal lineages of bacteria identical to those found in animal manure. Furthermore, several studies have demonstrated proliferation of bacteria and horizontal transfer of resistance genes in the insect digestive tract as well as transmission of resistant bacteria by insects to new substrates. We propose that insect management should be an integral part of pre- and postharvest food safety strategies to minimize spread of zoonotic pathogens and antibiotic resistance traits from animal farms. Furthermore, the insect link between the agricultural and urban environment presents an additional argument for adopting prudent use of antibiotics in the food animal industry.
Identification of p130 cas as a Substrate for the Cytosolic Protein Tyrosine Phosphatase PTP-PEST (1996)

PTP-PEST is a ubiquitously expressed, cytosolic, mammalian protein tyrosine phosphatase (PTP) which exhibits high specific activity in vitro. We have investigated the substrate specificity of PTP-PEST by a novel substrate-trapping approach in combination with in vitro dephosphorylation experiments. We initially identified a prominent 130-kDa tyrosine-phosphorylated protein in pervanadate-treated HeLa cell lysates which was preferentially dephosphorylated by PTP-PEST in vitro. In order to identify this potential substrate, mutant (substrate-trapping) forms of PTP-PEST were generated which lack catalytic activity but retain the ability to bind substrates. These mutant proteins associated in stable complexes exclusively with the same 130-kDa protein, which was identified as p130(cas) by immunoblotting. This exclusive association was observed in lysates from several cell lines and in transfected COS cells, but was not observed with other members of the PTP family, strongly suggesting that p130(cas) represents a major physiologically relevant substrate for PTP-PEST. Our studies suggest potential roles for PTP-PEST in regulation of p130(cas) function. These functions include mitogen- and cell adhesion-induced signalling events and probable roles in transformation by various oncogenes. These results provide the first demonstration of a PTP having an inherently restricted substrate specificity in vitro and in vivo. The methods used to identify p130(cas) as a specific substrate for PTP-PEST are potentially applicable to any PTP and should therefore prove useful in determining the physiological substrates of other members of the PTP family.
Simple preparation and characterization of cationic liposomes associated with a monoclonal antibody against glioma-associated antigen (immunoliposomes) (1995)

In this study we prepared and characterized monoclonal antibody associated cationic liposomes (immunoliposomes) to be used as a vehicle for human gene therapy of malignant glioma. This association method is especially amenable to mass production. The immunoliposomes consist of N-(a-trimethylammonio-acetyl)-didodecyl-D-glutamate chloride (TMAG), dilauroyl phosphatidylcholine (DLPC), and dioleoyl phosphatidyl- ethanolamine (DOPE) in a molar ratio of 1:2:2 as TMAG:DLPC:DOPE. Their preparation required only the addition of a solution containing plasmid DNA and a monoclonal antibody against glioma-associated antigen to a lipid film of the above three lipids. The association of antibody on the surface of immunoliposomes was confirmed by an immunochemical procedure. Liposome-mediated LacZ gene transfection of human glioma cells resulted in p-galactosidase activity about 2- to 3-fold higher when immunoliposomes were used as compared to control liposomes that were not associated to antibody. Also, the production of human (3-interferon (HuIFN-P) into the medium was 2- to 7-fold higher when HuIFN-P gene was transfected. Based on the present results, the immunoliposomes associating a monoclonal antibody against glioma-associated antigen may become effective carriers for gene transfer to human glioma cells.
Gene Expression Studies in Systemic Lupus Erythematosus (2006)

In a single assay, gene microarrays generate tens of thousands of measurements for the relative levels of messenger RNA expression, and thus hold promise to uncover the regulation of transcriptional responses behind clinical phenotypes of various diseases. Systemic lupus erythematosus (SLE) offers a unique opportunity to study gene expression both systemically and organ specific, as the tissues involved and specifically peripheral blood cells are readily accessible for molecular analysis. In the current review we highlight the current knowledge related to gene microarray in SLE. We approached the following questions: 1) Can gene microarray technology be used to translate molecular profiles into meaningful and applicable clinical information? 2) Does the assessment of differential gene expression provide specific signatures that may contribute to diagnostic and prognostic markers of SLE? 3) Can clinicians be helped in monitoring disease activity by identification of drug response gene profile? 4) Does evaluation of differential gene expression provide clues to detect previously unrecognized genes associated with the disease? It is evident that though not all questions can be currently answered appropriately, gene expression studies in SLE have important implications and will not only be beneficial for SLE patients, but will also lead to a better understanding of other autoimmune inflammatory diseases, thereby leading to novel diagnostic and therapeutic strategies in autoimmunity.
Deposition and Resorption of Calcified Matrix in Vitro by Rat Marrow Cells (1991)

Rat bone marrow derived cells were cultured using a-Minimal Essential Medium supplemented with antibiotics, ascorbic acid and !3-glycerphosphate in the presence of 10-8M dexamethasone, on polystyrene and hydrophilic fluorocarbon substrata for periods of 2 - 4 weeks. During this time, a large yield of bone nodules was achieved and the elaborated tissue was examined by both scanning and transmission electron microscopy. The matrix produced by the cells contacting the underlying substratum was an afibrillar, globular, calcified material which formed a layer approximately 0.5μm thick. The calcium and phosphorus content of this material was confirmed by energy dispersive X-ray dot mapping analysis. The collagenous matrix of the forming bone nodules was intimately associated with, and anchored to, this layer. The bulk of the bone nodule, above the interfacial zone, was of a normal appearance with osteocytes buried in a collagenous matrix exhibiting spheritic foci of mineralization. The cells, but not the extracellular matrix, of this culture were then removed using a trypsin citrate saline solution and the dishes containing these nodules reseeded with fresh bone marrow cells. These second stage cultures were maintained in supplemented medium, without dexamethasone. During this second period, osteoclasts resorbed both the afibrillar and collagen containing calcified matrices laid down in the first stage of the culture, producing characteristic scalloped osteoclast resorption lacunae.
Radiotherapy or Surgery for Prostate Cancer? Ten and Fifteen-Year Results of External Beam Therapy (1991)

Ten and 15-year outcome results are reviewed that demonstrate the role of radiation therapy in the management of prostate cancer. Patients with favorable T2a (B1) cancers of unknown nodal status are shown to have equal 15-year survival whether treated with external beam radiation therapy or radical prostatectomy. Patients of unknown nodal status treated for T2b (stage B2) cancer with external beam radiation therapy show superior survival and disease-free survival when compared to results with radical prostatectomy. the role of radical prostatectomy in these patients is unproven. Patients with lymph node dissection negative clinical stages T1b (A2) and T2 (B) treated with external beam radiation therapy exceed their expected survival at 10 years (65% vs 60%), and 70% are free of any failure at 10 years with the majority of failures due to metastasis, not local disease. Similar results are obtained in selected surgical centers with radical prostatectomy in highly selected patients. Patients with stage T3,4 (stage C) prostate cancer show 10 and 15-year survivals that offer curative therapy and hope to patients with these locally advanced cancers. No long-term data support a role for radical prostatectomy in these patients.
The Saccharomyces cerevisiae ACR3 Gene Encodes a Putative Membrane Protein Involved in Arsenite Transport (1997)

The cluster of three genes, ACR1, ACR2, and ACR3, previously was shown to confer arsenical resistance in Saccharomyces cerevisiae. The overexpression of ACR3 induced high level arsenite resistance. The presence of ACR3 together with ACR2 on a multicopy plasmid was conducive to increased arsenate resistance. The function of ACR3 gene has now been investigated. Amino acid sequence analysis of Acr3p showed that this hypothetical protein has hydrophobic character with 10 putative transmembrane spans and is probably located in yeast plasma membrane. We constructed the acr3 null mutation. The resulting disruptants were 5-fold more sensitive to arsenate and arsenite than wild-type cells. The acr3 disruptants showed wild-type sensitivity to antimony, tellurite, cadmium, and phenylarsine oxide. The mechanism of arsenical resistance was assayed by transport experiments using radioactive arsenite. We did not observe any significant differences in the accumulation of 76AsO33- in wild-type cells, acr1 and acr3 disruptants. However, the high dosage of ACR3 gene resulted in loss of arsenite uptake. These results suggest that arsenite resistance in yeast is mediated by an arsenite transporter (Acr3p).
Advances in the Medical Treatment of Diabetic Retinopathy (2009)

Proliferative diabetic retinopathy (PDR) remains the leading cause of blindness among working-age individuals in developed countries (1). Diabetic macular edema (DME), another important event that occurs in diabetic retinopathy, is more frequent in type 2 than type 1 diabetes (2). Whereas PDR is the most common sight-threatening lesion in type 1 diabetes, DME is the primary cause of poor visual acuity in type 2 diabetes. Because of the high prevalence of type 2 diabetes, DME is the main cause of visual impairment for diabetic patients (2). In addition, DME is almost invariably present when PDR is detected in type 2 diabetes (3). Neovascularization caused by severe hypoxia is the hallmark of PDR, whereas vascular leakage caused by the breakdown of the blood retinal barrier (BRB) is the main event involved in the pathogenesis of DME (4,5).

Although tight control of both blood glucose levels and hypertension is essential to prevent or arrest progression of the disease, the recommended goals are difficult to achieve in many patients and, consequently, diabetic retinopathy develops during the evolution of the disease. When PDR or clinically significant DME do appear, argon-laser photocoagulation is currently indicated, which the efficacy of has been widely demonstrated (6). However, the optimal period for laser treatment has frequently passed; moreover, it is not uniformly successful in halting visual decline. In addition, argon-laser photocoagulation is associated with moderate visual loss, some diminished visual field, reduced color vision, and reduced contrast sensitivity. The presence of these symptoms led to the prevailing thinking that laser treatment prevents vision loss but rarely results in visual improvement.

Intravitreal corticosteroids have been successfully used in the eyes of patients with persistent DME and loss of vision following the failure of conventional treatment (i.e., focal laser treatment and attention to systemic risk factors). However, …
Fiber Swap between Adenovirus Subgroups B and C Alters Intracellular Trafficking of Adenovirus Gene Transfer Vectors (1999)

Following receptor binding and internalization, intracellular trafficking of adenovirus (Ad) among subgroups B and C is different, with significant amounts of Ad serotype 7 (Ad7) (subgroup B) virions found in cytoplasm during the initial hours of infection while Ad5 (subgroup C) virions rapidly translocate to the nucleus. To evaluate the role of the fiber in these differences, we examined intracellular trafficking of Ad5, Ad7, and Ad5f7 (a chimeric vector composed of the Ad5 capsid with the fiber replaced by the Ad7 fiber) by conjugating Ad capsids directly with Cy3 fluorescent dye, permitting the trafficking of the capsids to be examined by fluorescence microscopy. The human lung carcinoma cell line A549 was infected with Cy3-conjugated viruses for 10 min followed by a 1-h incubation. Ad5 virions rapidly translocated to the nucleus (within 1 h of infection), while Ad7 virions were widely distributed in the cytoplasm at the same time point. Interestingly, chimeric Ad5f7 virions behaved similarly to Ad7 but not Ad5. In this regard, the percentages of nuclear localization of Ad5, Ad7, and Ad5f7 at 1 h following infection were 72% +/- 4%, 32% +/- 6%, and 38% +/- 2%, respectively. Consistent with these observations, fluorescence in situ hybridization demonstrated that most of the Ad5 DNA was detected at the nucleus after 1 h, but at the same time point, DNA of Ad7 and Ad5f7 was distributed in both the nucleus and cytoplasm. Quantification of the kinetics of Ad genomic DNA delivery to the nucleus using a fluorogenic probe-based PCR assay (TaqMan PCR) demonstrated that the percentages of nuclear association of Ad5 DNA and Ad5f7 DNA at 1 h postinfection were 80% +/- 13% and 43% +/- 1%, respectively. Although it has been generally accepted that Ad fiber protein mediates attachment of virions to cells and that fibers dissociate during endocytic uptake, these data suggest that in addition to mediating binding to the cell surface, fiber likely modulates intracellular trafficking as well.
[How I treat...persistent atrial fibrillation, by internal cardioversion, in a patient with exreme obesity]. (2001)

An ethylic hypertensive patient with a BMI of 51.4 developed persistent atrial fibrillation with high ventricular rates. External electrical cardioversion was attempted, but failed in spite of high energy shocks (350 joules). Sinus rhythm was restored by internal cardioversion (12 joules). The value and indications of the techniques are briefly discussed.
Amniotic Membrane Transplantation in the Human Eye (2011)

AMT is an established technique in the treatment of various diseases of the external eye. In the last few years, AMT has brought about major advances in the reconstructive surgery of the ocular surface.
Compression of FASTQ and SAM Format Sequencing Data (2013)

Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/.
Mechanism of autocatalytic oxidation of oxyhemoglobin by nitrite. (1987)

Oxidation of oxyhemoglobin by nitrite is characterized by the presence of a lag phase followed by autocatalysis. The stoichiometry of the overall reaction is described by the following equation: 4HbO2 + 4NO2- + 4H+ = 4Hb+ + 4NO3- + O2 + 2H2O (Hb denotes hemoglobin monomer). During the oxidation, we detected a free radical at g = 2.005, which is very similar to the methemoglobin free radical generated by the reaction with hydrogen peroxide. Nitrosylhemoglobin was not detected. The oxidation was delayed by the addition of KCN or catalase, but was not modified by superoxide dismutase in phosphate buffer. In bistris buffer, however, superoxide dimutase markedly prolonged the lag phase. The results suggest that during the oxidation, the methemoglobin peroxide compound is generated and converts nitrite into nitrogen dioxide by its peroxidatic activity. Nitrogen dioxide oxidizes oxyhemoglobin to methemoglobin and nitrite, yielding the autocatalytic phase.