gebhart/patrepeval huggingface dataset:
First, Gather the Data (2006)

It is a cornerstone of medical practice to “first, do no harm.” Yet the body of evidence that is sufficient to demonstrate efficacy for a new drug is rarely large enough to provide absolute assurance that harmful side effects do not exist. Thus, ongoing surveillance is necessary to detect adverse events.There are many reasons why the randomized trials that are adequate for demonstrating drug efficacy may not be adequate for the recognition of important side effects (see table). Randomized trials may be too small to permit the detection of adverse events. For instance, for a continuous outcome such as . . .
Preservation of avian blood and tissue samples for DNA analyses (1991)

A problem frequently faced by researchers involved in collecting tissues for DNA isolation is the preservation of samples in the field prior to and during their transportation to the laboratory. Prevention of DNA degradation is usually achieved through freezing. As this is not always practical, we have tested the efficiency of chemical solutions containing high concentrations of salts (e.g., NaCl, EDTA, and diaminocyclohexanetetraacetate) and detergent at preserving DNA in bird tissue and blood samples stored at ambient temperature for extended periods of time. For blood samples, we recommend the use of a buffer that lyses the cells and nuclei and contains 0.01 M Tris, 0.01 M NaCl, 0.01 M EDTA, and 1% n-lauroylsarcosine, Ph 7.5. Tissue samples are best preserved as small pieces in a saline solution made of 20% dimethyl sulfoxyde, 0.25 M EDTA, saturated with NaCl, pH 8.0. DNA extracted from samples preserved in these solutions for up to 24 weeks was compared with DNA recovered from tissue samples stored at −70 °C and blood samples stored at −70 and −20 °C. Yields were similar, averaging 300 μg/0.2 g of tissue and 500 μg/50 μL of blood. Quality of DNA in terms of fragment size, ability to be cut by restriction enzymes, and ability to hybridize to radioactive probes was also similar between cryopreserved and chemically preserved samples. Yields of DNA recovered from tissue samples preserved in 70% ethanol for 6 or 11 weeks was very low and significant degradation was observed. We have also examined how DNA contained in crude avian blood samples withstands freeze–thaw cycles. We found normal yields and no significant degradation of DNA in samples that experienced up to six cycles. We encourage field researchers who refrain from preserving tissue samples because of logistical problems, such as transporting liquid nitrogen containers in the field, to consider using these solutions. Both solutions can also facilitate exchanges of samples between laboratories, and they form an alternative to storage of samples at −70 °C for laboratories and museums with limited access to deep-freezing facilities.
Settlement of barnacle larvae is governed by Euclidean and not fractal surface characteristics (1999)

1. Extensive research has been carried out on the biological, physical and chemical characteristics of surfaces that promote, or prevent, marine fouling. The texture of the substratum is probably the most important factor affecting settlement of the Acorn Barnacle Semibalanus balanoides in the field. The aim of this study was to examine the relationship between fractal and Euclidean descriptions of substratum surface complexity and settlement of the Acorn Barnacle. 2. Replicate settlement panels with smooth, fine, medium and coarse surfaces were manufactured using a precise and accurate technique. Two‐dimensional profiles were measured using a laser profilometer, and two surface complexity indices, potential settling sites (PSS) and the Minkowski fractal dimension (MFD) were calculated. PSS is a Euclidean measure of the surface complexity taking into account the body size and settlement behaviour of the barnacle larvae, whereas MFD is a fractal dimension related to the complexity of the surface at a variety of scales. 3. In a field experiment, settlement density of S. balanoides was positively related to both PSS and MFD. To break the correlation between PSS and MFD, surfaces were modified by sandblasting with either 64–125‐μm or 250–500‐μm grains. This decreased MFD but did not affect PSS. 4. A further field experiment found that this erosion using small‐scale sand particles had no effect on settlement of the barnacle. It was concluded that S. balanoides larvae were responding to characteristics of the surface related to PSS and not MFD. 5. Although a correlation was found between species abundance and the fractal complexity of its habitat, further experimentation showed that there was no causality in this relationship. Many surveys, with no experimentation, of aquatic and terrestrial communities have shown relationships between organisms and their habitat and assumed causality; however, care must be taken in interpretation of such studies.
The prognostic value of CD44 isoforms in prostate cancer patients treated by radical prostatectomy. (1997)

CD44 forms a group of transmembranous glycoproteins formed by alternative splicing of a single mRNA. The expression of v6 exon-containing variants correlates with metastasis and poor prognosis in a number of malignancies. The distribution and prognostic value of CD44s, CD44v5, and CD44v6 were studied immunohistochemically in the radical prostatectomy specimens of 97 patients with prostate cancer and in 12 lymph node metastases. The mean follow-up period was 84 months. The percentage of CD44-immunoreactive cells was scored semiquantitatively. CD44 mRNA expression was studied in nine prostate cancer and eight benign prostatic hyperplasia (BPH) samples by reverse transcriptase-PCR. Benign prostatic glands almost always expressed CD44s, CD44v6, and, at a lower intensity, CD44v5. CD44 scores decreased from low- to high-grade prostatic intraepithelial neoplasia. CD44s, CD44v5, and CD44v6 were expressed in 86, 23, and 69% of the adenocarcinomas, respectively. Gleason sum score (GSS) and pT stage were correlated inversely with CD44s and CD44v6 scores. CD44 was not found in the lymph node metastatic tumor cells. At the mRNA level, 89% of the tumors and all BPH samples expressed CD44s. CD44v6-v10 mRNA was present in 44 and 75% of the tumors and BPH samples, respectively. Loss of CD44s and CD44v6 predicted an adverse prognosis at univariate analysis. The independent prognosticators identified by multivariate analysis were: GSS, pT stage, and CD44s for clinical progression; GSS and CD44s for prostate-specific antigen progression; and GSS for tumor-specific survival. Loss of CD44s expression in prostate adenocarcinoma predicts a poor prognosis, independent of stage and grade.
Virulence of Staphylococcus aureus in a mouse mastitis model: studies of alpha hemolysin, coagulase, and protein A as possible virulence determinants with protoplast fusion and gene cloning (1985)

Mutants of a genetically well-characterized strain of Staphylococcus aureus [SA113(83A)] were isolated after mutagenization. Alpha-hemolysin- (hla), coagulase- (coa), and protein A- (spa) negative mutants were characterized by more than 90 biochemical tests for production of extracellular proteins and biochemical profile to exclude pleiotropy. Protoplast fusion was then used to isolate double-defective (hla and coa) recombinants and recombinants with regained properties, i.e., production of alpha-hemolysin and coagulase. Studies of such mutants and recombinants in the mouse mastitis model showed that one alpha-hemolysin [SA113(83A) hla-5] and one coagulase-negative [SA113(83A) coa-147] mutant were lower in virulence compared with the wild-type strain SA113(83A). The double-negative mutant SA113(83A) hla-5 coa-147 showed a drastic decline in virulence and only induced very mild changes, as determined by microscopic examinations of infected mammary gland tissue. The recombinant with regained properties, however, was as virulent as the wild-type strain. This suggests that alpha-hemolysin and coagulase are virulence determinants of S. aureus. A high-level protein A-producing mutant (U300) showed the same virulence as the parent strain SA113(83A) in this model. One low virulence protein A-negative mutant (U320) did not markedly increase in virulence when a plasmid containing the cloned gene for protein A (pSPA15) was introduced into this mutant. By these and earlier observations, it seems likely that protein A is not an important virulence determinant in mastitis of mice. The reduced virulence of the protein A-negative mutant U320 compared with the wild-type SA113(83A) may be due to pleiotropic loss of some other unknown virulence determinant(s). Our data confirm earlier findings that pleiotropic changes are common in protein A-negative mutants.
Influence of Hyperglycemia on Oxidative Stress and Matrix Metalloproteinase-9 Activation After Focal Cerebral Ischemia/Reperfusion in Rats (2007)

Hyperglycemia increases oxidative stress and MMP-9 activity, exacerbating BBB dysfunction after ischemia/reperfusion injury. Superoxide overproduction may be a causal link among hyperglycemia, MMP-9 activation, and BBB dysfunction.
Enzymic properties of thermopsin. (1990)

The specificity of thermopsin, a thermostable acid protease from Sulfolobus acidocaldarius, was studied using oxidized insulin B chain as substrate followed by peptide isolation and identification. The following bonds were hydrolyzed: Leu-Val, Leu-Tyr, Phe-Phe, Phe-Tyr, and Tyr-Thr. Thus, the specificity of thermopsin is similar to that of pepsin, that is, it prefers large hydrophobic residues at both sides of the scissile bond. We confirmed this by the use of a synthetic substrate, Lys-Pro-Ala-Glu-Phe-p-nitro-phenylalanyl-Ala-Leu, which was cleaved by thermopsin between Phe and p-nitro-phenylalanyl. Using this substrate, enzyme inhibition and kinetic properties of thermopsin have been studied. Thermopsin optimally hydrolyzes this substrate at 75 degrees C and pH 2 with Km and kcat values under these conditions of 5.3 x 10(-5) M and 14.3 s-1, respectively. Pepstatin competitively inhibits thermopsin with a Ki of 2 x 10(-7) M. Other known aspartic protease inhibitors, diazoacetylnorleucine ethyl ester and 1,2-epoxy-3-(p-nitrophenoxy)propane inhibited thermopsin only slowly and with nonspecific reactions. Although thermopsin contains a single cysteine, iodoacetic acid and p-chloromercuric benzoate had no effect on activity. Mercuric chloride inhibited the enzyme, and the inhibition was reversible by mercaptoethanol. However, the enzyme was not labeled by [14C]iodoacetic acid either before or after sodium dodecyl sulfate denaturation. Thus, the thiol group is likely blocked, and the inhibition effect of mercuric ion is unrelated to the thiol group. These observations suggest that thermopsin has a different active site than the aspartic protease family but may have a similar transition state structure. The temperature dependence of Km and kcat was studied for thermopsin hydrolysis of the synthetic substrate between 26-78 degrees C. Both parameters increased with temperature, and the rise of kcat value was particularly sharp above 65 degrees C. Hydrolysis activity measured at high substrate concentration has a maximum at 76 degrees C, which is near the physiological temperature for the optimal growth of this organism. Thus, thermopsin appears to function best at high temperature and high substrate concentration. It may be utilized by the organism to response to the presence of high substrate concentration in the medium. Thermopsin is also competitively inhibited by urea, acetamide, and phenylalaninamide with Ki values of 0.5, 0.4, and 0.01 M, respectively.
Regulatory Mechanisms that Determine the Development and Function of Plasma Cells (2003)

Plasma cells are terminally differentiated final effectors of the humoral immune response. Plasma cells that result from antigen activation of B-1 and marginal zone B cells provide the first, rapid response to antigen. Plasma cells that develop after a germinal center reaction provide higher-affinity antibody and often survive many months in the bone marrow. Transcription factors Bcl-6 and Pax5, which are required for germinal center B cells, block plasmacytic differentiation and repress Blimp-1 and XBP-1, respectively. When Bcl-6-dependent repression of Blimp-1 is relieved, Blimp-1 ensures that plasmacytic development is irreversible by repressing BCL-6 and PAX5. In plasma cells, Blimp-1, XBP-1, IRF4, and other regulators cause cessation of cell cycle, decrease signaling from the B cell receptor and communication with T cells, inhibit isotype switching and somatic hypermutation, downregulate CXCR5, and induce copious immunoglobulin synthesis and secretion. Thus, commitment to plasmacytic differentiation involves inhibition of activities associated with earlier B cell developmental stages as well as expression of the plasma cell phenotype.
Prolactin in human systemic lupus erythematosus (2001)

In the last decade, evidence has accumulated to support the hypothesis that both mild and moderate elevations of serum prolactin (PRL) participate in the clinical expression and pathogenesis of systemic lupus erythematosus (SLE). Hyperprolactinemia (HPRL) has been found in 20-30% of patients with SLE. HPRL seems to be associated with clinical activity of SLE during pregnancy. Although the relationship between HPRL and active SLE in non-pregnant patients is controversial, recent clinical and experimental studies support the potential role of prolactin (PRL) as a promoter of clinical activity and severity of SLE. Mild elevations of serum PRL secondary to microadenoma could trigger the onset of SLE in a subset of patients. Elevated PRL and interleukin (IL)-6 have been found in the urine of patients with active lupus nephritis and in cerebrospinal fluid (CSF) of patients with active central nervous system (CNS) SLE. PRL may therefore participate in the pathogenesis of lupus nephritis and cerebritis, and the presence of PRL may reflect an abnormal communication between the immune system and the neuroendocrine system in active SLE. Lymphocytes from patients with active SLE produce increased amounts of PRL, and this extrapituitary PRL may participate in aberrant immune processes in SLE. There is exciting new evidence that HPRL in SLE may be explained by stimulation of pituitary PRL secretion by cytokines. In addition, defects in peptidergic modulators and dopamine metabolism have been described in patients with SLE. The interactions between PRL, cytoquines, autoantibodies and organ involvement suggest that PRL participates in local and generalized immune and inflammatory processes and acts as a bridge between the neuroendocrine and immune systems in SLE. Understanding the interactions between these systems in SLE will help us to understand and treat this important autoimmune disease.
Cognitive and Quantified Electroencephalographic Correlates of Cycloserine Treatment in Alzheimerʼs Disease (1995)

Cycloserine acts as a potent and selective modulator of the N-methyl-D- aspartate (NMDA) receptor-associated glycine recognition site, which may be a possible mechanism for this compound's positive effects on memory formation and retrieval processes in animals. Studies in normal human volunteers have shown that cycloserine can have significant positive effects on cognitive processing in the elderly and can ameliorate memory deficits induced by subcutaneously administered scopolamine. Based on this profile, a double-blind, placebo controlled, parallel group (three drug dosages) study was conducted as part of a larger study to assess the efficacy and safety, as well as the cognitive and central nervous system (CNS) impact, of 6 months of cycloserine treatment in patients (N = 40) with probable dementia of the Alzheimer type (DAT). The Cognitive Drug Research Computerize Assessment System (CDR System) served as the primary outcome measure of efficacy. CNS activity was assessed using quantified electroencephalography (QEEG). Safety measures included adverse effects documentation and analysis of blood chemistry/hematology. Cycloserine proved to be a safe agent in this population at the doses given but failed to show any statistically significant effects in the areas of cognition and global clinical ratings and did not indicate significant CNS activity on QEEG. These findings suggest that cycloserine has no measurable therapeutic effect on Alzheimer's disease at the doses given.
X‐Ray Crystal Structure of Bone Marrow Kinase in the X Chromosome: A Tec Family Kinase (2011)

Bone marrow kinase in the X chromosome, a member of the Tec family of tyrosine kinases, plays a role in both monocyte/macrophage trafficking as well as cytokine secretion. Although the structures of Tec family kinases Bruton's tyrosine kinase and IL-2-inducible T-cell kinase are known, the crystal structures of other Tec family kinases have remained elusive. We report the X-ray crystal structures of bone marrow kinase in the X chromosome in complex with dasatinib at 2.4 Å resolution and PP2 at 1.9 Å resolution. The bone marrow kinase in the X chromosome structures reveal a typical kinase protein fold; with well-ordered protein conformation that includes an open/extended activation loop and a stabilized DFG-motif rendering the kinase in an inactive conformation. Dasatinib and PP2 bind to bone marrow kinase in the X chromosome in the ATP binding pocket and display similar binding modes to that observed in other Tec and Src protein kinases. The bone marrow kinase in the X chromosome structures identify conformational elements of the DFG-motif that could potentially be utilized to design potent and/or selective bone marrow kinase in the X chromosome inhibitors.
Polysialic acid engineering: synthesis of polysialylated neoglycosphingolipids by using the polysialyltransferase from neuroinvasive Escherichia coli K1. (1994)

The CMP-sialic acid:poly alpha 2,8sialosyl sialyltransferase (polyST) in neurotropic Escherichia coli K1 inner membranes catalyzes synthesis of the alpha 2,8-linked polysialic acid capsule. The capsule is a neurovirulent determinant associated with neonatal meningitis in humans. A functionally similar polyST in human neuroblastomas polysialylates neural cell adhesion molecules. While bacteria do not synthesize glycosphingolipids (GSLs), we report here that the E. coli K1 polyST can selectively polysialylate several structurally related GSLs, when added as exogenous sialyl acceptors. A structural feature common to the preferred sialyl acceptors (GD3 > GT1a > GQ1b = GT1b > GD2 = GD1b = GD1a > GM1) was the disialyl glycotope, Sia alpha 2,8Sia, alpha 2,3-linked to galactose (Sia is sialic acid). A linear tetrasaccharide with a terminal Sia residue (e.g., GD3) was the minimum length oligosaccharide recognized by the polyST. Endo-N-acylneuraminidase was used to confirm the alpha 2,8-specific polysialylation of GSL. Ceramide glycanase was used to release the polysialyllactose chains from the ceramide moiety. Size analysis of these chains showed that 60-80 Sia residues were transferred to the disialyllactose moiety of GD3. The significance of these findings is two-fold. (i) The E. coli K1 polyST can be used as a synthetic reagent to enzymatically engineer the glycosyl moiety of GSL, thus creating oligo- or polysialylated GSLs. Such "designer" GSLs may have potentially important biological and pharmacological properties. (ii) The use of GSLs as exogenous sialyl acceptors increases the sensitivity of detecting polyST activity. The practical advantage of this finding is that polyST activity can be identified and studied in those eukaryotic cells that express low levels of this developmentally regulated enzyme and/or its acceptor.
Prediction of Recurrence-Free Survival in Postoperative Non–Small Cell Lung Cancer Patients by Using an Integrated Model of Clinical Information and Gene Expression (2008)

We have developed an accurate, technically simple, and reproducible method for predicting individual recurrence risks. This model would potentially be useful in developing customized strategies for managing lung cancer.
Novel Cytidine-Based Orotidine-5′-Monophosphate Decarboxylase Inhibitors with an Unusual Twist (2012)

Orotidine-5'-monophosphate decarboxylase (ODCase) is an interesting enzyme with an unusual catalytic activity and a potential drug target in Plasmodium falciparum, which causes malaria. ODCase has been shown to exhibit unusual and interesting interactions with a variety of nucleotide ligands. Cytidine-5'-monophosphate (CMP) is a poor ligand of ODCase, and CMP binds to the active site of ODCase with an unusual orientation and conformation. We designed N3- and N4-modified CMP derivatives as novel ligands to ODCase. These novel CMP derivatives and their corresponding nucleosides were evaluated against Plasmodium falciparum ODCase and parasitic cultures, respectively. These derivatives exhibited improved inhibition of the enzyme catalytic activity, displayed interesting binding conformations and unusual molecular rearrangements of the ligands. These findings with the modified CMP nucleotides underscored the potential of transformation of poor ligands to ODCase into novel inhibitors of this drug target.
[Effect of ischemic preconditioning on cytokines during lung ischemia-reperfusion injury]. (2003)

Lung IPC has a marked protection effect against I/R injury. The effect was related to its inhibition of inflammatory cytokines such as TNFalpha, IL-6 and IL-8, thus reducing activation and infiltration of neutrophils.
Some new studies of the wear behavior of ultrahigh molecular weight polyethylene (1976)

The wear rate of ultrahigh molecular weight (UHMW) polyethylene over a long campaign of sliding distance is not constant. Both unfilled and graphite filled polyethylene show a high rate early, which reduces to a low value. The graphite-filled product shows a late stage increase in wear rate. Increased molding temperature reduces the molecular weight and increases the wear rate. Titanium articulating with UHMW polyethylene develops frequently an abnormally high wear rate with the generation of a black wear product.
Peroxisome Proliferator-Activated Receptor γ (PPARγ)-Independent Specific Cytotoxicity against Immature Adipocytes Induced by PPARγ Antagonist T0070907 (2013)

Peroxisome proliferator-activated receptor γ (PPARγ) plays indispensable roles in adipogenesis, which is frequently impaired under pathological conditions such as non-alcoholic steatohepatitis (NASH). Thus, a potent PPARγ antagonist, T0070907 is known as a useful tool for understanding such pathological conditions, while T007097 was also suggested to have PPARγ-independent actions. In the present study, we found that T0070907 inhibited adipogenesis concomitantly with the induction of rapid apoptosis of immature adipocytes within 2 h, whereas another PPARγ antagonist, SR-202 did not show such cytotoxicity. However, T0070907 did not affect the viabilities of pre-adipocytes, mature adipocytes, and NIH-3T3 fibroblasts. The cytotoxic effect of T0070907 was not inhibited by GW1929, a PPARγ agonist, but was inhibited by α-tocopherol, which was previously shown to provide clinical benefit to NASH patients. Interestingly, treatment with high amounts of α-tocopherol alone slightly increased the cellular lipid content in mature adipocytes, but did not affect PPARγ-dependent luciferase reporter expression in COS-7 cells. Moreover, other lipophilic antioxidants, such as tocotrienols, tert-butylhydroquinone, and butylated hydroxyanisole, also inhibited T0070907-induced apoptosis like α-tocopherol. Consequently, it is suggested that T0070907 efficiently inhibits adipogenesis, not only via PPARγ-dependent manner, but also through the induction of apoptosis specifically against immature adipocytes via oxidative stress in a PPARγ-independent manner.