gebhart/patrepeval huggingface dataset:
Clinical and prognostic significance of the expression of the c-erbB-2 and c-erbB-3 oncoproteins in primary and metastatic malignant melanomas and breast carcinomas. (1997)

Several growth factors and proto-oncogenes play a leading regulatory role during human carcinogenesis. In this systematic immunocytochemical study we observed the expression (overexpression) of the c-erbB-2 and c-erbB-3 oncoproteins in 30 primary cutaneous malignant melanomas (CMMs), 10 already metastasized malignant melanomas (MMMs) and 15 lymph-node negative breast carcinomas (BCs). Both oncoproteins were expressed as a result of either oncogene amplification or post-translational stabilization c-erbB-2 alone is unable to bind neuregulins, but it is able to act as a pan c-erbB receptor subunit. Heterodimerization between cerbB-2 and c-erbB-3 is required to initiate neuregulin directed signal transduction. We employed an indirect, four step streptavidinbiotin conjugated immunocytochemical technique for antigen detection. The visualization of the primary antigen-antibody reaction was carried out with alkaline phosphatase or immunoperoxidase labeling and the use of the appropriate enzymatic substrates. The presence of c-erbB-2 oncoprotein was detected in 12/30 CMMs, 8/10 MMMs and 6/15 BCs, while c-erbB-3 was identified in 14/30 CMMs, 7/10 MMMs and 6/15 BCs. The intensity of the cell membrane localized immunoreactivity was observed to be greater when the c-erbB-2 oncoprotein was targeted (A, AB and B). The c-erbB-3 oncoprotein was also detected in the cytoplasm with medium intensity (B, BC and C). Unfortunately, little is known concerning the range of oncoprotein overexpression after formalin fixation and paraffin embedding. We demonstrated overexpression localized to several cell clones within the oncoprotein positive population of malignant cells. The immunocytochemically defined extent of expression of both oncoproteins was between 10-40% (+ to +2) of the total cell population in the malignant melanomas and 20-35% (+2) of the total cell population in the BCs. In conclusion a) the results of the present study demonstrate the presence of c-erbB-2 and c-erbB-3 oncoprotein expression (overexpression) in melanoma and breast carcinoma, and b) oncogene receptor directed immunotherapy, as part of a more individualized anti-cancer treatment, represents a potentially valuable targeted treatment for the future.
Mild therapeutic hypothermia shortens intensive care unit stay of survivors after out-of-hospital cardiac arrest compared to historical controls (2008)

Therapeutic hypothermia was found to significantly shorten ICU stay and time of mechanical ventilation in survivors after out-of-hospital cardiac arrest. Moreover, profound improvements in both neurological outcome and 1-year survival were observed.
Monitoring temperature-sensitive vaccines and immunologic drugs, including anthrax vaccine (1999)

The experience of the U.S. Army Medical Materiel Center, Europe (USAMMCE), in monitoring temperature-sensitive vaccines and immunologic drugs, including anthrax vaccine, during storage and shipment is discussed. USAMMCE uses an electronic monitoring device to monitor and archive the time-temperature history of shipments of various vaccines, immunoglobulins, and other drugs requiring refrigeration. Using these monitors, USAMMCE can track its carriers' performance, reduce product loss, and validate quality. USAMMCE trains people to pack refrigerated items and to activate and place the monitoring device inside the packing container. Over 1200 temperature-monitor readings from 44 U.S. military logistical depots, hospitals, and clinics located outside the United States are evaluated annually by the USAMMCE pharmacist; each reading represents one shipment or packed box. When deactivated during unpacking, the device flashes green for a successful shipment (all temperature readings within the ideal range) or red for a potentially problematic shipment. From January through October 1998, the device was used in 750 temperature-sensitive shipments; 72% of the devices were returned to USAMMCE in green condition and the remainder in red. Of the red-flashing monitors, 15% were determined to signal that the drugs were received in unacceptable condition. USAMMCE successfully shipped more than 26,000 vials of anthrax vaccine from February through October 1998 within the manufacturer's guidelines for storage temperature. Temperature monitoring is essential for proper storage and transport of vaccines and immunologic drugs.
Cloning of type XVII collagen. Complementary and genomic DNA sequences of mouse 180-kilodalton bullous pemphigoid antigen (BPAG2) predict an interrupted collagenous domain, a transmembrane segment, and unusual features in the 5‘-end of the gene and the 3‘-untranslated region of the mRNA. (1993)

Thus far, 16 distinct vertebrate collagens (types I-XVI) have been delineated. In this study, we have cloned a mouse collagenous protein, the 180-kDa bullous pemphigoid antigen (BPAG2). Isolation of over-lapping clones, together with 5' and 3' rapid amplification of cDNA ends, allowed delineation of the entire coding sequence. The 5' and 3' ends of the mRNA transcripts were confirmed by primer extension and anchored reverse transcription polymerase chain reaction analyses. The deduced polypeptide contained 1,433 amino acids, including a collagenous domain that consisted of 13 separate segments. Computer analysis of the deduced amino acid sequence demonstrated the presence of a membrane-associated segment. Examination of the 5' end of the BPAG2 gene revealed that the 295-base pair (bp) exon 1 contained two segments of (T)13AA and TT(A)11, whereas exon 2 was shown to contain the translation initiation codon. The 3' end of the mRNA transcript identified two 6-bp inverted repeat sequences that could form a stem for a 30-bp hairpin loop followed by a series of U residues. Comparison of mouse and human BPAG2 sequences demonstrated 86% homology and the unit of evolutionary period of 4.2 million years. In summary, we have cloned full-length mouse BPAG2 cDNA sequences that encode a collagenous polypeptide. We propose that this polypeptide be designated as the alpha 1-chain of type XVII collagen.
Impact of Different Target Sequences on Type III CRISPR-Cas Immunity (2016)

CRISPR-Cas loci protect bacteria and archaea from both phage infection and plasmid invasion. These loci harbor short sequences of phage and plasmid origin known as "spacers" that specify the targets of CRISPR-Cas immunity. The presence of a spacer sequence matching a phage or plasmid ensures host immunity against infection by these genetic elements. In turn, phages and plasmids constantly mutate their targets to avoid recognition by the spacers of the CRISPR-Cas immune system. In this study, we demonstrated that different spacer sequences vary in their ability to tolerate target mutations that allow phages and plasmids to escape from CRISPR-Cas immunity. These results uncover an unexpected complexity in the arms race between CRISPR-Cas systems and prokaryotic infectious genetic elements.
Distribution of pathogenicity islands in Salmonella spp (1996)

We investigated the phylogenetic distribution of the SPI-1 and SPI-2 pathogenicity islands in Salmonella spp. SPI-1 was present in representatives of all eight subspecific groups, but no SPI-2-hybridizing sequences were detected in group V (S. bongori). Our data suggest that SPI-2 was acquired by S. enterica after its split from S. bongori.
Isolation and Preliminary Characterization of a Purified Pig Zona Antigen (PPZA) from Porcine Oocytes (1983)

A protocol was developed for isolation of a purified pig zona antigen (PPZA) under nondissociating conditions. Heating of isolated zona-encased porcine oocytes at 73 degrees C for 20 min resulted in optimal solubilization of zona antigen activity (ZAA) as assessed by radioimmunoassay. Subsequent fractionation of solubilized proteins by ammonium sulfate precipitation, ultrafiltration, gel filtration, and ion exchange chromatography yielded PPZA. Sodium dodecyl sulfate polyacrylamide gel electrophoresis of PPZA yielded a major diffuse band at 58,000 Mr which stained for protein and carbohydrate and which possessed ZAA. Two-dimensional gel electrophoresis confirmed the identity of the 58,000 Mr glycoprotein and one of the three major charge heterogeneous glycoprotein families of the porcine zona pellucida. These experiments established that the principal macromolecular and antigenic component of PPZA is a 58,000 Mr glycoprotein originating from the zona pellucida. The nature of PPZA antigenic determinants recognized by a rabbit antiserum to PPZA was studied by radioimmunoassay. ZAA of PPZA was sensitive to the action of mercaptans and proteases, indicating a contribution of polypeptide chain to PPZA antigenicity. Loss of ZAA upon periodate oxidation of PPZA also implicated carbohydrate residues. PPZA retains antigenic determinants of the intact zona pellucida as assessed by reactivity with antiserum to intact porcine zonae. Likewise, rabbit antiserum to PPZA reacts avidly with intact porcine zonae. These results demonstrate that PPZA is a suitable target antigen for further studies on immunocontraception.
Gut microbiota role in irritable bowel syndrome: New therapeutic strategies (2016)

In the last decade the impressive expansion of our knowledge of the vast microbial community that resides in the human intestine, the gut microbiota, has provided support to the concept that a disturbed intestinal ecology might promote development and maintenance of symptoms in irritable bowel syndrome (IBS). As a correlate, manipulation of gut microbiota represents a new strategy for the treatment of this multifactorial disease. A number of attempts have been made to modulate the gut bacterial composition, following the idea that expansion of bacterial species considered as beneficial (Lactobacilli and Bifidobacteria) associated with the reduction of those considered harmful (Clostridium, Escherichia coli, Salmonella, Shigella and Pseudomonas) should attenuate IBS symptoms. In this conceptual framework, probiotics appear an attractive option in terms of both efficacy and safety, while prebiotics, synbiotics and antibiotics still need confirmation. Fecal transplant is an old treatment translated from the cure of intestinal infective pathologies that has recently gained a new life as therapeutic option for those patients with a disturbed gut ecosystem, but data on IBS are scanty and randomized, placebo-controlled studies are required.
Photoelectrochemical water splitting at titanium dioxide nanotubes coated with tungsten trioxide (2006)

The photocatalytic splitting of water into hydrogen and oxygen using solar light is a potentially clean and renewable source for hydrogen fuel. Titanium oxide nanotubes coated with tungsten oxide were prepared to harvest more solar light for the first time and characterized their water splitting efficiency. The tungsten trioxide coatings significantly enhanced the visible spectrum absorption of the titanium dioxide nanotube array, as well as their solar-spectrum induced photocurrents. For the sample, upon white light illumination at 150mW∕cm2, hydrogen gas generated at the overall conversion efficiency of 0.87%.
The Fate and Distribution of Intra-Articularly Injected Osmium Tetroxide (Os-191) (1969)

SummaryIn nine cases of rheumatoid arthritis OsO4 labelled with Os-191 was injected into the knee joint. The radioactivity was measured from specimens of blood, urine and feces. In addition, the external radioactivity was measured above the injected and contralateral joint, the inguinal lymph nodes, the liver and the heart. The distribution of radioactivity in the injected joint was scanned.The resorption of the labelled OSO4 occurred in two phases. The half-life of the first phase was about one day and that of the second phase from 18 to 40 days.Os-191 was excreted from the body principally via the kidneys. The highest activity in the total blood volume remained below 10 per cent in every case.
Age-related thermal stability and susceptibility to proteolysis of rat bone collagen (1990)

The shrinkage temperature (Ts) and the pepsin-solubilizability of collagen fibrils in bone matrix obtained from decalcified femur diaphysis from 2-, 5-, 15- and 25-month-old rats were found to decrease with age. Digestion with human fibroblast collagenase dissolved less than half of the collagen, whereas sequential treatment by pepsin followed by collagenase resulted in its complete dissolution. This result shows that collagenase and a telopeptide-cleaving enzyme, when acting in an appropriate sequence, have a great potential for the degradation of bone collagen. The 'melting' profile of the pepsin-solubilized collagen showed a biphasic transition with transition peak at 35.9 degrees C and 40.8 degrees C. With increasing age an increasing proportion of the collagen 'melted' in the transition peak at 35.9 degrees C (pre-transition), and the 'melting' temperature (Tm) of the collagen decreased in parallel with Ts in relation to age. Both Ts and Tm decreased by 3 degrees C in the age span investigated. The age-related change in Ts could therefore be accounted for by the decrease in molecular stability. The collagenase-cleavage products of the bone collagen obtained by the sequential treatment with pepsin and collagenase showed only one peak transition (at 35.1 degrees C), and the Tm for the products was independent of age. The results indicate that the pre-transition for the pepsin-solubilized collagen is due to an age-related decrease in thermal stability may have implications for the mechanical strength and turnover of the bone collagen. In contrast with bone collagen, soft-tissue collagen showed neither the age-dependency of thermal stability nor the characteristic biphasic 'melting' profile.
Efficacy of a workplace osteoporosis prevention intervention: a cluster randomized trial (2016)

Australia New Zealand Clinical Trial Registry ACTRN12616000079448 . Registered 25 January 2016 (retrospectively registered).
Exposure of Patients to Human Immunodeficiency Virus through the Transfusion of Blood Components That Test Antibody-Negative (1989)

The risk of transmission of the human immunodeficiency virus to recipients of blood transfusions exists chiefly during the period between the time a donor is infected and the time he or she has a positive blood test for HIV antibodies. Estimating the chance that blood will be donated during this period is an effective way to define the risk of HIV infection from transfusion. Using this approach, and employing data from over 17 million American Red Cross blood donations, we estimate that during 1987 the most likely number of units of blood infected with undetected HIV that were transfused was 131 (range, 67 to 227). For a patient, the odds of contracting HIV infection were 1:153,000 per unit transfused. A patient who received the average transfusion (5.4 units) had odds of 1:28,000. The risk has been decreasing by more than 30 percent a year. We estimate that donor-recruitment practices plus careful education and screening are eliminating 49 of every 50 donors likely to be HIV-positive and that testing is 92 to 97 percent effective, for a combined effectiveness of 99.9 percent. The risk of undetected infectious units can probably be further reduced by transfusing fewer units and units from fewer donors, recruiting more women and fewer men as new donors, and encouraging more frequent donations from donors who have been tested repeatedly.
Hedgehog Signaling in Pancreatic Fibrosis and Cancer (2016)

The hedgehog signaling pathway was first discovered in the 1980s. It is a stem cell-related pathway that plays a crucial role in embryonic development, tissue regeneration, and organogenesis. Aberrant activation of hedgehog signaling leads to pathological consequences, including a variety of human tumors such as pancreatic cancer. Multiple lines of evidence indicate that blockade of this pathway with several small-molecule inhibitors can inhibit the development of pancreatic neoplasm. In addition, activated hedgehog signaling has been reported to be involved in fibrogenesis in many tissues, including the pancreas. Therefore, new therapeutic targets based on hedgehog signaling have attracted a great deal of attention to alleviate pancreatic diseases. In this review, we briefly discuss the recent advances in hedgehog signaling in pancreatic fibrogenesis and carcinogenesis and highlight new insights on their potential relationship with respect to the development of novel targeted therapies.
Hyaluronic acid associated with the surfaces of cultured fibroblasts is linked to a serum-derived 85-kDa protein. (1990)

Hyaluronic acid (HA) was extracted from the cell layer of cultured mouse dermal fibroblasts with 6 M guanidine HCl in the presence of 8% (w/v) Zwittergent. HA could be separated from the bulk of extracted proteins by consecutive isopycnic centrifugation and gel and ion-exchange chromatography under dissociative conditions. The final preparation was the complex of HA (viscosity average molecular weight approximately 2 x 10(6)) and a protein of Mr approximately 85,000 in a molar ratio of 1:1. Since the extraction procedure employed has been shown to break most noncovalent bonds between HA and proteins, they would appear to be covalently linked. However, the HA-binding protein remained unlabeled even after long incubation of the cells in the presence of a highly radioactive amino acid mixture, suggesting that it is an exogenous protein derived from the fetal calf serum added to culture medium. The presence of a HA-binding 85-kDa protein could in fact be demonstrated in fetal calf serum as well as sera from various other sources. This protein cross-reacted with antibodies raised against the HA-protein complex purified from cultured mouse dermal cells and was retained on octyl-Sepharose. Like the cell-derived 85-kDa protein, the serum 85-kDa protein, once bound to HA, could not be released from the complex by various dissociative procedures. These results, taken together, suggest that the hydrophobic serum protein can be intercalated into cell surface membranes, thereby mediating the binding of HA to the cell surface.
Trimeric G‐proteins of the trans‐Golgi network are involved in the formation of constitutive secretory vesicles and immature secretory granules (1991)

Non-hydrolysable analogues of GTP, such as GTP gamma S and GMP-PNP, have previously been shown to inhibit the formation of constitutive secretory vesicles (CSVs) and immature secretory granules (ISGs) from the trans-Golgi network (TGN). Using a cell-free system, we show here that the formation of these vesicles is also inhibited by [A1F4]-, a compound known to act on trimeric G-proteins. Addition of highly purified G-protein beta gamma subunits stimulated, in a differential manner, the cell-free formation of both CSVs and ISGs. ADP-ribosylation experiments revealed the presence of a pertussis toxin-sensitive G-protein alpha subunit in the TGN. We conclude that trimeric G-proteins regulate the formation of secretory vesicles from the TGN.
Native Chemical Ligation at Valine (2008)

Peptide ligation at hydrophobic sites is possible with a ligation–desulfurization strategy in which penicillamine serves as a precursor of valine. The β,β-dimethylcysteine peptides reacted surprisingly fast in native chemical ligation reactions. Even the sterically crowded and unpolar Leu–Val bond can be formed in high yield.
Affinity labeling of creatine kinase by N-(2,3-epoxypropyl)-N-amidinoglycine. (1979)

epoxycreatine, N-(2,3-epoxypropyl)-N-amidinoglycine; Hepes, 4-(2-hydroxyethyl)-l-piperazineethanesulfonic acid; HPLC, high performance liquid chromatography.
Characterization of the peptide substrate specificities of interstitial collagenase and 92-kDa gelatinase. Implications for substrate optimization (1994)

The peptide substrate specificities of two matrix metalloproteinases (MMPs), interstitial collagenase (MMP-1), and 92-kDa gelatinase (MMP-9), have been examined. Starting with the parent substrate, Dnp-Pro-Leu-Gly approximately Leu-Trp-Ala-D-Arg-NH2, four separate substrate mixtures were synthesized at subsites P2(Leu) through P2'(Trp). These mixtures contained either naturally occurring L-amino acids, D-amino acids, or either of two distinct sets of miscellaneous amino acids. Combined, these mixtures gave 88 unique substitutions at each position and, over the four subsites, represented 352 potential substrates. Optimal substrates were identified using a combined high performance liquid chromatography/mass spectrometry analysis as previously reported. The results gave an extended profile of the substrate specificities for both MMP-1 and MMP-9 at subsites P2(Leu) through P2'(Trp). Using the data obtained from the mapping, a new peptide substrate, Dnp-Pro-Cha-Abu approximately Smc-His-Ala-D-Arg-NH2 (where Dnp is 2,4-dinitrophenyl, Cha is cyclohexylalanine, Abu is alpha-aminobutyric acid, and Smc is S-methylcysteine) was designed and characterized. This peptide showed a 36-fold improvement in turnover (kcat/Km) versus the parent substrate by interstitial collagenase. In addition, some collagenase subsite specificities described here were found to be different from those previously reported. Experimental data show that the observed selectivity is dependent on the original peptide template employed, which has broader implications for substrate specificity studies.
Viral Genes Modify Herpes Simplex Virus Latency both in Mouse Footpad and Sensory Ganglia (1983)

Herpes simplex virus type 2 wild-type and 13 temperature-sensitive mutants have been examined for their ability to be recovered from latently infected Biozzi mice. After inoculation into the rear footpad, virus could be recovered from both the dorsal root ganglia (DRG) and the footpad (FP) at the site of inoculation (wt, ts 1, ts 2, ts 4, ts 6, ts 7 and ts 8), or from the DRG only (ts 11 and ts 13), or from FP only (ts 3, ts 9, ts 12). Two mutants (ts 5 and ts 10) have not been recovered from either site. Both DNA-positive and DNA-negative mutants have been shown to be capable of establishing latent infection.
Predicting dose‐volume histograms for organs‐at‐risk in IMRT planning (2012)

The results demonstrate that our mathematical framework and modest training cohorts successfully predict achievable OAR DVHs based on individual patient anatomy. The models correctly identified suboptimal plans that demonstrated further OAR sparing after replanning. This modeling technique requires no manual intervention except for appropriate selection of a training set with identical evaluation criteria. Clinical implementation is in progress to evaluate impact on real-time IMRT QC.
Immune Mechanisms and Therapeutic Potential of CpG Oligodeoxynucleotides (2006)

Unmethylated CpG motifs in bacterial DNA and synthetic oligodeoxynucleotides activate immune cells that express Toll-like Receptor 9. Activation through this receptor triggers cellular signaling that leads to production of a proinflammatory and a Th1-type, antigen-specific immune response. The immunostimulatory effects of CpG oligodeoxynucleotides confer protection against infectious disease, allergy and cancer in animal models, and clinical trials have been initiated. However, CpG oligodeoxynucleotides may exacerbate disease in some situations. We will review current concepts in the mechanisms of activating Toll-like Receptor 9 with CpG oligodeoxynucleotides and highlight opportunities for using large animal models to better determine the mechanisms of action.