gebhart/patrepeval huggingface dataset:
Synthesizing Filamentary Structured Images with GANs (2017)

This paper aims at synthesizing filamentary structured images such as retinal fundus images and neuronal images, as follows: Given a ground-truth, to generate multiple realistic looking phantoms. A ground-truth could be a binary segmentation map containing the filamentary structured morphology, while the synthesized output image is of the same size as the ground-truth and has similar visual appearance to what have been presented in the training set. Our approach is inspired by the recent progresses in generative adversarial nets (GANs) as well as image style transfer. In particular, it is dedicated to our problem context with the following properties: Rather than large-scale dataset, it works well in the presence of as few as 10 training examples, which is common in medical image analysis; It is capable of synthesizing diverse images from the same ground-truth; Last and importantly, the synthetic images produced by our approach are demonstrated to be useful in boosting image analysis performance. Empirical examination over various benchmarks of fundus and neuronal images demonstrate the advantages of the proposed approach.
1H, 13C‐NMR and X‐ray Absorption Studies of Copper(I) Glutathione Complexes (1996)

The tripeptide glutathione (gamma-L-Glu-L-Cys-Gly, GSH) is an important intracellular reducing agent for Cu(II) and complexation agent for Cu(I). We have studied the complexation of Cu(I) to GSH in aqueous solution at a range of pH values and Cu(I):GSH molar ratios by 1H-NMR and 13C-NMR spectroscopy and X-ray absorption spectroscopy. The NMR data are consistent with formation of a complex with approximate 1:1 stoichiometry [Cu(SG)] as the major species with only thiolate sulfur of GSH binding to Cu(I). The rate of exchange of GSH with GS-Cu was determined to 13 s(-1) at 283 K, pH 6.8. X-ray absorption spectroscopic measurements showed that Cu(I) is coordinated to 3.1+/-0.3 sulfur atoms at approximately 0.222 nm in solutions (and solids) containing GSH:Cu in 1:1 and 2:1 mol ratios. The possible structures of polymeric Cu(I)-glutathione complexes are discussed. The high thermodynamic stability of Cu(I)-S bonds in Cu(I)-glutathione complexes coupled with their kinetic lability may provide efficient and specific pathways for the transport of copper in cells.
Assembly of Nitrogenase MoFe Protein (2008)

Assembly of nitrogenase MoFe protein is arguably one of the most complex processes in the field of bioinorganic chemistry, requiring, at least, the participation of nifS, nifU, nifB, nifE, nifN, nifV, nifQ, nifZ, nifH, nifD, and nifK gene products. Previous genetic studies have identified factors involved in MoFe protein assembly; however, the exact functions of these factors and the precise sequence of events during the process have remained unclear until the recent characterization of a number of assembly-related intermediates that provided significant insights into this biosynthetic "black box". This review summarizes the recent advances in elucidation of the mechanism of FeMoco biosynthesis in four aspects: (1) the ex situ assembly of FeMoco on NifEN, (2) the incorporation of FeMoco into MoFe protein, (3) the in situ assembly of P-cluster on MoFe protein, and (4) the stepwise assembly of MoFe protein.
Characterization of Synthetic Peptide Substrates for p34cdc2 Protein Kinase (1991)

Synthetic peptide substrates for the cell division cycle regulated protein kinase, p34cdc2, have been developed and characterized. These peptides are based on the sequences of two known substrates of the enzyme, Simian Virus 40 Large T antigen and the human cellular recessive oncogene product, p53. The peptide sequences are H-A-D-A-Q-H-A-T-P-P-K-K-K-R-K-V-E-D-P-K-D-F-OH (T antigen) and H-K-R-A-L-P-N-N-T-S-S-S-P-Q-P-K-K-K-P-L-D-G-E-Y-NH2 (p53), and they have been employed in a rapid assay of phosphorylation in vitro. Both peptides show linear kinetics and an apparent Km of 74 and 120 microM, respectively, for the purified human enzyme. The T antigen peptide is specifically phosphorylated by p34cdc2 and not by seven other protein serine/threonine kinases, chosen because they represent major classes of such enzymes. The peptides have been used in whole cell lysates to detect protein kinase activity, and the cell cycle variation of this activity is comparable to that measured with specific immune and affinity complexes of p34cdc2. In addition, the peptide phosphorylation detected in mitotic cells is depleted by affinity adsorption of p34cdc2 using either antibodies to p34cdc2 or by immobilized p13, a p34cdc2-binding protein. Purification of peptide kinase activity from mitotic HeLa cells yields an enzyme indistinguishable from p34cdc2. These peptides should be useful in the investigation of p34cdc2 protein kinase and their regulation throughout the cell division cycle.
Algebraic Immunity of S-Boxes Based on Power Mappings: Analysis and Construction (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The algebraic immunity of an S-box depends on the number and type of linearly independent multivariate equations it satisfies. In this paper, techniques are developed to find the number of linearly independent, multivariate, bi-affine, and quadratic equations for S-boxes based on power mappings. These techniques can be used to prove the exact number of equations for any class of power mappings. Two algorithms to calculate the number of bi-affine and quadratic equations for any <emphasis emphasistype="italic"><formula formulatype="inline"> <tex Notation="TeX">$(n,n)$</tex></formula></emphasis> S-box based on power mapping are also presented. The time complexity of both algorithms is only <emphasis emphasistype="italic"><formula formulatype="inline"><tex Notation="TeX">$O(n^2)$</tex> </formula></emphasis>. To design algebraically immune S-boxes, four new classes of S-boxes that guarantee zero bi-affine equations and one class of S-boxes that guarantees zero quadratic equations are presented. The algebraic immunity of power mappings based on Kasami, Niho, Dobbertin, Gold, Welch, and inverse exponents are discussed along with other cryptographic properties and several cryptographically strong S-boxes are identified. It is conjectured that a known Kasami-like highly nonlinear power mapping is differentially <emphasis emphasistype="italic"><formula formulatype="inline"><tex Notation="TeX">$4$</tex> </formula></emphasis>-uniform. Finally, an open problem to find an <emphasis emphasistype="italic"><formula formulatype="inline"><tex Notation="TeX">$(n,n)$</tex> </formula></emphasis> bijective nonlinear S-box with more than <emphasis emphasistype="italic"><formula formulatype="inline"><tex Notation="TeX">$5n$</tex></formula></emphasis> quadratic equations is solved. </para>
Looking Beyond Highly Active Antiretroviral Therapy: Drug‐Related Hepatotoxicity in Patients with Human Immunodeficiency Virus Infection (2002)

Management of human immunodeficiency virus (HIV) has become increasingly complex since the introduction of highly active antiretroviral therapy (HAART). Patients with HIV have become exposed to an increasing array of drugs to treat HIV, prevent opportunistic infections and immune dysfunction, and manage comorbid illnesses and therapeutic complications. Hepatic complications have become common and may lead to discontinuation of treatment and significant morbidity. Up to 90% of patients with acquired immunodeficiency syndrome (AIDS) receive at least one drug that can cause hepatotoxicity. Clinicians treating patients with HIV frequently face difficulty distinguishing abnormal liver transaminase levels and toxicities in patients receiving several drugs. Some potential causes of hepatic dysfunction are viral infections, alcohol and substance abuse, and hepatotoxic drugs such as HAART. Recent reports have focused on the hepatotoxicity of HAART and the role of hepatitis viruses to the exclusion of many other agents prescribed for patients with HIV. Many of the common antibiotics, antifungals, antivirals, and ancillary agents prescribed for patients with HIV are independently associated with hepatotoxicity. Clinicians should be aware of the potential non-antiretroviral hepatotoxic agents that are frequently administered in HIV management.
Postmenopausal serum androgens, oestrogens and breast cancer risk: the European prospective investigation into cancer and nutrition (2005)

Considerable experimental and epidemiological evidence suggests that elevated endogenous sex steroids - notably androgens and oestrogens - promote breast tumour development. In spite of this evidence, postmenopausal androgen replacement therapy with dehydroepiandrosterone (DHEA) or testosterone has been advocated for the prevention of osteoporosis and improved sexual well-being. We have conducted a case-control study nested within the European Prospective Investigation into Cancer and Nutrition. Levels of DHEA sulphate (DHEAS), (Delta4-androstenedione), testosterone, oestrone, oestradiol and sex-hormone binding globulin (SHBG) were measured in prediagnostic serum samples of 677 postmenopausal women who subsequently developed breast cancer and 1309 matched control subjects. Levels of free testosterone and free oestradiol were calculated from absolute concentrations of testosterone, oestradiol and SHBG. Logistic regression models were used to estimate relative risks of breast cancer by quintiles of hormone concentrations. For all sex steroids -the androgens as well as the oestrogens - elevated serum levels were positively associated with breast cancer risk, while SHBG levels were inversely related to risk. For the androgens, relative risk estimates (95% confidence intervals) between the top and bottom quintiles of the exposure distribution were: DHEAS 1.69 (1.23-2.33), androstenedione 1.94 (1.40-2.69), testosterone 1.85 (1.33-2.57) and free testosterone 2.50 (1.76-3.55). For the oestrogens, relative risk estimates were: oestrone 2.07 (1.42-3.02), oestradiol 2.28 (1.61-3.23) and free oestradiol (odds ratios 2.13 (1.52-2.98)). Adjustments for body mass index or other potential confounding factors did not substantially alter any of these relative risk estimates. Our results have shown that, among postmenopausal women, not only elevated serum oestrogens but also serum androgens are associated with increased breast cancer risk. Since DHEAS and androstenedione are largely of adrenal origin in postmenopausal women, our results indicated that elevated adrenal androgen synthesis is a risk factor for breast cancer. The results from this study caution against the use of DHEA(S), or other androgens, for postmenopausal androgen replacement therapy.
Chemical synthesis of an octadecapeptide with the biological and immunological properties of human heat-stable Escherichia coli enterotoxin (1984)

An eighteen-amino-acid peptide having the linear amino acid sequence of human heat-stable enterotoxin (ST) has been synthesized by solid phase peptide synthesis. The purified peptide could be obtained in yields approaching 25% after purification by size, charge, and high-performance ligand chromatography. This material was pure and identical to native ST by analytical high-performance ligand chromatography, amino acid analysis, paper electrophoresis and thin-layer chromatography. The formation of the disulfide bonds was critical for biological and immunological activity and were tentatively determined to be between cysteines 5 and 14, 6 and 10, and 9 and 17. This synthetic peptide had full immunological and biological activity when compared to native ST by enzyme-linked immunosorbent assay and the suckling mouse assay respectively.
IgG Biosynthesis: No “Immunoregulatory Feedback” (1997)

THE PLASMA CONCENTRATION of IgG has a direct bearing on the health of the host. Of all Ig deficiencies, only agammaglobulinemia is associated with certain fatal outcome in the absence of supplementation therapy. Since the time of Ehrlich[1][1] in the 1890s, the transmission of immunity from mother
Tumor‐Specific Transplantation Resistance in Mice after Treatment of Initial Tumors with Streptococcus thermophilus (1996)

Antitumor activity observed by treatment with Streptococcus thermophilus was further investigated. The mice cured from fibrosarcoma by treatment with heat-killed preparation of S. thermophilus, when challenged with fibrosarcoma failed to take up the tumor. However, these cured mice when challenged with sarcoma-180 or Ehrlich ascites carcinoma, did not show significant changes in tumor take and/or survival compared to their respective controls. Similarly, mice cured from sarcoma-180 were challenged with fibrosarcoma, sarcoma-180 or Ehrlich ascites carcinoma. Though there was no change in the mean survival time (MST) of the dying mice regarding sarcoma-180 or Ehrlich ascites carcinoma, there was 50 and 30% increase in the number of mice that showed total regression respectively over controls. However, there was no difference in the growth rate of fibrosarcoma. Similar observations were made with mice cured from Ehrlich ascites carcinoma, challenged with these tumors. These findings thus suggest that the antitumor response was tumor-specific and that tumor-associated antigens may have a role in imparting this specificity. Bacterial treatment non-specifically augmented this primary response.
Signature Pattern Analysis: A Method for Assessing Viral Sequence Relatedness (1992)

Signature pattern analysis identifies particular sites in amino acid or nucleic acid alignments of variable sequences that are distinctly representative of a query set of sequences relative to a background set. We explore the merits of using signature patterns for analysis of HIV-1 (human immunodeficiency virus type 1) sequences in cases of epidemiological linkage and potential superinfection. For these purposes, query sets are viral sequences that are all derived from one HIV-1 infected individual, hence the signature pattern is the array of sites that are characteristic of the range of viral variants obtained from that person. Once a signature pattern has been objectively defined, it can be used to examine other viral sequences from other individuals for evidence of genetic relatedness. A computer program to facilitate this analysis, VESPA, is described and applied to sequence data gathered during the investigation of HIV-1 transmission in a dental practice. The implications of signature polymorphisms seen within an infected individual, and shared polymorphisms between linked individuals, are also considered. VESPA may also be applied to the molecular analysis of biological phenotypes.
Conditioning out‐of‐date bank‐stored red blood cells using a cell‐saver auto‐transfusion device: effects on numbers of red cells and quality of suspension fluid (2014)

We investigated the utility of a cell-saver device for processing out-of-date red blood cells, by washing twenty bags of red blood cells that had been stored for between 36 and 55 days. The volume of recovered cells, and the characteristics of the suspension fluid, were measured before and after treatment. The ratio of free haemoglobin to total haemoglobin was up to 0.02 before processing, and up to 0.011 afterwards, changing by between -0.013 and +0.003. This ratio met the current standard for free haemoglobin (less than 0.008 in more than 75% of samples), both before and after processing. Ninety-three percent of red blood cells survived the process. Potassium ion concentration fell from above 15 mmol.l(-1) in all cases, to a mean of 6.4 mmol.l(-1) (p < 0.001). The pH rose to a mean value of 6.44 (p = 0.001). Lactate ion concentration fell to a mean value of 14 mmol.l(-1) (p < 0.001). Sodium ion concentration rose from a mean value of 93 mmol.l(-1) to a mean value of 140 mmol.l(-1) (p < 0.001). A useful proportion of out-of-date red blood cells remained intact after conditioning using a cell-saver, and the process lowered concentrations of potentially toxic solutes in the fluid in which they were suspended.
Integration of gene expression profiling and clinical variables to predict prostate carcinoma recurrence after radical prostatectomy (2005)

Integration of gene expression signatures and clinical variables produced predictive models for prostate carcinoma recurrence that perform significantly better than those based on either clinical variables or gene expression information alone.
Cloning and sequence analysis of complementary DNA encoding an aberrantly rearranged human T-cell gamma chain. (1986)

Complementary DNA (cDNA) encoding a human T-cell gamma chain has been cloned and sequenced. At the junction of the variable and joining regions, there is an apparent deletion of two nucleotides in the human cDNA sequence relative to the murine gamma-chain cDNA sequence, resulting simultaneously in the generation of an in-frame stop codon and in a translational frameshift. For this reason, the sequence presented here encodes an aberrantly rearranged human T-cell gamma chain. There are several surprising differences between the deduced human and murine gamma-chain amino acid sequences. These include poor homology in the variable region, poor homology in a discrete segment of the constant region precisely bounded by the expected junctions of exon CII, and the presence in the human sequence of five potential sites for N-linked glycosylation.
Ambient Ionization and FAIMS Mass Spectrometry for Enhanced Imaging of Multiply Charged Molecular Ions in Biological Tissues (2016)

Ambient ionization mass spectrometry imaging (MSI) has been increasingly used to investigate the molecular distribution of biological tissue samples. Here, we report the integration and optimization of desorption electrospray ionization (DESI) and liquid-microjunction surface sampling probe (LMJ-SSP) with a chip-based high-field asymmetric waveform ion mobility spectrometry (FAIMS) device to image metabolites, lipids, and proteins in biological tissue samples. Optimized FAIMS parameters for specific molecular classes enabled semitargeted detection of multiply charged molecular species at enhanced signal-to-noise ratios (S/N), improved visualization of spatial distributions, and, most importantly, allowed detection of species which were unseen by ambient ionization MSI alone. Under static DESI-FAIMS conditions selected for transmission of doubly charged cardiolipins (CL), for example, detection of 71 different CL species was achieved in rat brain, 23 of which were not observed by DESI alone. Diagnostic CL were imaged in a human thyroid tumor sample with reduced interference of isobaric species. LMJ-SSP-FAIMS enabled detection of 84 multiply charged protein ions in rat brain tissue, 66 of which were exclusive to this approach. Spatial visualization of proteins in substructures of rat brain, and in human ovarian cancerous, necrotic, and normal tissues was achieved. Our results indicate that integration of FAIMS with ambient ionization MS allows improved detection and imaging of selected molecular species. We show that this methodology is valuable in biomedical applications of MSI for detection of multiply charged lipids and proteins from biological tissues.
Pattern Formation by Cultured Human Epidermal Cells: Development of Curved Ridges Resembling Dermatoglyphs (1978)

In cultures made from disaggregated human epidermal cells, growth to a confluent cell layer is followed by the emergence of patterns resembling those of human dermatoglyphs. These patterns reflect intrinsic properties of kertinocytes. In vivo, only the epidermis of the volar surfaces forms patterns, but in culture, patterns are formed by epidermal cells from other sites as well. Patterns develop by a process of cell movement which first produces ridges and then curves the ridges into figures of increasing complexity, ultimately whorls.
Long-term Angiographic and Clinical Outcome After Percutaneous Transluminal Coronary Angioplasty and Intracoronary Radiation Therapy in Humans (1997)

These preliminary results demonstrate that ICRT after coronary intervention is feasible and is associated with an acceptable degree of complications and lower rates of angiographic restenosis indexes.
The role of the CC double bond in alcohol elimination from MH+ ions of unsaturated bicyclic esters upon chemical ionization (1995)

Abstract Methyl and ethyl endo ‐ and exo ‐bicyclo [2.2.2] oct‐5‐ene‐2‐carboxylates exhibit different mass spectral behaviour under i‐Bu‐chemical ionization (CI) conditions and upon collision‐induced dissociation (CID) of their MH + IONS. The endo ‐esters exhibit m / z 135 [MH  MeOH] + and [MH  EtOH] + ions, which are absent in the i‐Bu‐CI mass spectra of the exo ‐isomers. This stereospecific behavior is explained in terms of the proton bridging requirement in the alcohol elimination from MH + ions of esters. Such proton bridging between the alkoxycarbonyl group and the double bond is possible in the endo ‐esters, but not in the exo ‐isomers. Hydrogen‐deuterium exchange processes, observed in the CID spectra of the MD + ion of the endo ‐esters, support the proposed mechanistic pathway. Hydrogen bridging with the double bond also plays a role in the alcohol elimination processes of stereoisomeric bicyclo [2.2.2] oct‐5‐ene‐2,3‐dicarboxylates.
Nitrite-derived nitric oxide formation following ischemia-reperfusion injury in kidney (2004)

Nitric oxide (NO) is synthesized from l-arginine by nitric oxide synthase (NOS), and nitrite and nitrate are believed to be waste forms of NO. We previously reported an enzyme-independent pathway of NO generation from nitrite in acidic conditions. In this study, we show nitrite-derived NO formation in renal ischemia-reperfusion injury using electron paramagnetic resonance (EPR) spectroscopy. In this experiment, we utilized a stable isotope of [(15)N]nitrite as a source of nitrite to distinguish l-arginine-derived NO from [(15)N]nitrite-derived (15)NO. Intravenous infusion of a stable isotope of [(15)N]nitrite ((15)NO(2)(-)) facilitated the formation of Hb(15)NO during renal ischemia, which demonstrated that the origin of NO was nitrite. The EPR signal of Hb(15)NO in kidney appeared after 40 min of renal ischemia, and renal reperfusion decreased the Hb(15)NO level in the kidney and increased it in blood by contrast. In addition, the amount of HbNO was nitrite concentration dependent, and this formation was NOS independent. Our findings suggest that nitrite can be an alternative source of NO in ischemic kidney and that it binds with hemoglobin and then is spread by the circulation after reperfusion.