gebhart/patrepeval huggingface dataset:
Cell transplantation in the treatment of liver diseases (2007)

The liver performs multiple functions that are essential for life, the most crucial being its role in the body metabolism. Impairment of this function, because of liver insufficiency, can be partially restored by medical management but OLT remains the ultimate therapeutic treatment. Because not always indicated or available, other alternatives are proposed such as LCT. Compared to OLT, this procedure is less invasive, less expensive, and fully reversible. More than 50 patients have thus far benefited of this technique and are reviewed here. Indications were multiple including inborn errors of metabolism, FHF, acute on chronic diseases, and decompensated end-stage cirrhosis. Documented results were encouraging, especially for metabolic disorders, with medium-term efficacy up to two yr. Related complications were exceptional. On this basis, LCT has entered its phase of clinical application and current indications and protocols are detailed. Ongoing lines of research are discussed, including cell quality, stem cell field, and rejection prevention. Further improvement of the procedure is therefore expected and should lead to broader applications of LCT.
Characterising covalent warhead reactivity (2019)

Many drugs currently used are covalent inhibitors and irreversibly inhibit their targets. Most of these were discovered through serendipity. Covalent inhibitions can have many advantages from a pharmacokinetic perspective. However, until recently most organisations have shied away from covalent compound design due to fears of non-specific inhibition of off-target proteins leading to toxicity risks. However, there has been a renewed interest in covalent modifiers as potential drugs, as it possible to get highly selective compounds. It is therefore important to know how reactive a warhead is and to be able to select the least reactive warhead possible to avoid toxicity. A robust NMR based assay was developed and used to measure the reactivity of a variety of covalent warheads against serine and cysteine - the two most common targets for covalent drugs. A selection of these warheads also had their reactivity measured against threonine, tyrosine, lysine, histidine and arginine to better understand our ability to target non-traditional residues. The reactivity was also measured at various pHs to assess what effect the environment in the active site would have on these reactions. The reactivity of a covalent modifier was found to be very dependent on the amino acid residue.
Macitentan and Morbidity and Mortality in Pulmonary Arterial Hypertension (2013)

Macitentan significantly reduced morbidity and mortality among patients with pulmonary arterial hypertension in this event-driven study. (Funded by Actelion Pharmaceuticals; SERAPHIN ClinicalTrials.gov number, NCT00660179.).
Improving biophysical properties of a bispecific antibody scaffold to aid developability (2013)

While the concept of Quality-by-Design is addressed at the upstream and downstream process development stages, we questioned whether there are advantages to addressing the issues of biologics quality early in the design of the molecule based on fundamental biophysical characterization, and thereby reduce complexities in the product development stages. Although limited number of bispecific therapeutics are in clinic, these developments have been plagued with difficulty in producing materials of sufficient quality and quantity for both preclinical and clinical studies. The engineered heterodimeric Fc is an industry-wide favorite scaffold for the design of bispecific protein therapeutics because of its structural, and potentially pharmacokinetic, similarity to the natural antibody. Development of molecules based on this concept, however, is challenged by the presence of potential homodimer contamination and stability loss relative to the natural Fc. We engineered a heterodimeric Fc with high heterodimeric specificity that also retains natural Fc-like biophysical properties, and demonstrate here that use of engineered Fc domains that mirror the natural system translates into an efficient and robust upstream stable cell line selection process as a first step toward a more developable therapeutic.
Overlapped block motion compensation: an estimation-theoretic approach (1994)

We present an estimation-theoretic analysis of motion compensation that, when used with fields of block-based motion vectors, leads to the development of overlapped block algorithms with improved compensation accuracy. Overlapped block motion compensation (OBMC) is formulated as a probabilistic linear estimator of pixel intensities given the limited block motion information available to the decoder. Although overlapped techniques have been observed to reduce blocking artifacts in video coding, this analysis establishes for the first time how (and why) OBMC can offer substantial reductions in prediction error as well, even with no change in the encoder's search and no extra side information. Performance can be further enhanced with the use of state variable conditioning in the compensation process. We describe the design of optimized windows for OBMC. We also demonstrate how, with additional encoder complexity, a motion estimation algorithm optimized for OBMC offers further significant gains in compensation accuracy. Overall mean-square prediction improvements in the range of 16 to 40% (0.8 to 2.2 dB) are demonstrated.
pH-dependent Perforation of Macrophage Phagosomes by Listeriolysin O from Listeria monocytogenes (1997)

The pore-forming toxin listeriolysin O (LLO) is a major virulence factor implicated in escape of Listeria monocytogenes from phagocytic vacuoles. Here we describe the pH-dependence of vacuolar perforation by LLO, using the membrane-impermeant fluorophore 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) to monitor the pH and integrity of vacuoles in mouse bone marrow-derived macrophages. Perforation was observed when acidic vacuoles containing wild-type L. monocytogenes displayed sudden increases in pH and release of HPTS into the cytosol. These changes were not seen with LLO-deficient mutants. Perforation occurred at acidic vacuolar pH (4.9-6.7) and was reduced in frequency or prevented completely when macrophages were treated with the lysosomotropic agents ammonium chloride or bafilomycin A1. We conclude that acidic pH facilitates LLO activity in vivo.
Tissue Engineered Bone Repair of Calvarial Defects Using Cultured Periosteal Cells (1998)

Periosteum has been demonstrated to have cell populations, including chondroprogenitor and osteoprogenitor cells, that can form both cartilage and bone under appropriate conditions. In the present study, periosteum was harvested, expanded in cell culture, and used to repair critical size calvarial defects in a rabbit model. Periosteum was isolated from New Zealand White rabbits, grown in cell culture, labeled with the thymidine analog bromodeoxyuridine for later localization, and seeded into resorbable polyglycolic acid scaffold matrices. Thirty adult New Zealand White rabbits were divided into groups, and a single 15-mm diameter full-thickness calvarial defect was made in each animal. In group I, defects were repaired using resorbable polyglycolic acid implants seeded with periosteal cells. In group II, defects were repaired using untreated polyglycolic acid implants. In group III, the defects were left unrepaired. Rabbits were killed at 4 and 12 weeks postoperatively. Defect sites were then studied histologically, biochemically, and radiographically. In vitro analysis of the cultured periosteal cells indicated an osteoblastic phenotype, with production of osteocalcin upon 1,25(OH)2 vitamin D3 induction. In vivo results at 4 weeks showed islands of bone in the defects repaired with polyglycolic acid implants with periosteal cells (group I), whereas the defects repaired with untreated polyglycolic acid implants (group II) were filled with fibrous tissue. Collagen content was significantly increased in group I compared with group II (2.90 +/- 0.80 microg/mg dry weight versus 0.08 +/- 0.11 microg/mg dry weight, p < 0.006), as was the ash weight (0.58 +/- 0.11 mg/mg dry weight versus 0.35 +/- 0.06 mg/mg dry weight, p < 0.015). At 12 weeks there were large amounts of bone in group I, whereas there were scattered islands of bone in groups II and III. Radiodensitometry demonstrated significantly increased radiodensity of the defect sites in group I, compared with groups II and III (0.740 +/- 0.250 OD/mm2 versus 0.404 +/- 0.100 OD/mm2 and 0.266 +/- 0.150 OD/mm2, respectively, p < 0.05). Bromodeoxyuridine label, as detected by immunofluorescence, was identified in the newly formed bone in group I at both 4 and 12 weeks, confirming the contribution of the cultured periosteal cells to this bone formation. This study thus demonstrates a tissue-engineering approach to the repair of bone defects, which may have clinical applications in craniofacial and orthopedic surgery.
Expression of major surface protein 2 antigenic variants during acute Anaplasma marginale rickettsemia (1996)

Antigenic variants of Anaplasma marginale major surface protein 2 (MSP-2), a target of protective immune responses, have been detected by use of copy-specific monoclonal antibodies reactive with some, but not all, organisms during acute rickettsemia. The presence of polymorphic msp-2 genes was confirmed by cloning and sequencing two gene copies, 11.2 and DF5, each of which encodes a full-length MSP-2 with a unique amino acid sequence. Transcription of msp-2 genes during acute rickettsemia was analyzed by use of cDNA cloning of hybrid-selected msp-2 mRNA. Sequencing of cDNA clones, designated AR1 to AR14, indicated that DF5 msp-2 was transcribed during acute rickettsemia. Two classes of variant msp-2 genes were also transcribed during acute rickettsemia. The first class of variant transcripts, typified by clones AR3, AR4, AR7, and AR14, each encoded a single or small number of amino acid substitutions relative to DF5. The second type, AR5, encoded a large region of amino acid polymorphism, including additions, deletions, and substitutions, as compared to DF5. Specific antibody directed against the AR5 polymorphic region bound a unique MSP-2 expressed on A. marginale that was not recognized by antibody generated against DF5. Similarly, anti-AR5 peptide antibody reacted with a different MSP-2 that was not bound by anti-DF5 antibody. This expression confirmed that variant msp-2 transcripts encode structurally distinct MSP-2 molecules which bear unique B-cell epitopes. These results support the hypothesis that the large msp-2 gene family, which constitutes a minimum of 1% of the genome, encodes antigenic variants critical to evasion of protective immune response directed against surface MSP-2 epitopes.
ADMINISTRATION OF DIHYDROXYPHENYLALANINE TO PARKINSONIAN PATIENTS. (1964)

Dihydroxyphenylalanine (dopa), the metabolic precursor of dopamine, was administered to 10 parkinsonian patients in oral doses of 1-5 g. and intravenous doses of 0.2-0.5 g. Increases in dopamine excretion of 100- to 1000-fold following the dopa administration indicated that dopa was being absorbed and metabolized. Only two of the 10 patients showed any objective improvement on this treatment. Although dopa did not show sufficient beneficial results in this study to be considered a useful therapeutic agent, its slight activity is consistent with other evidence suggesting that some extrapyramidal cells are sensitive to dopamine.
The contribution of glycoprotein VI to stable platelet adhesion and thrombus formation illustrated by targeted gene deletion (2003)

Platelet interaction with exposed adhesive ligands at sites of vascular injury is required to initiate a normal hemostatic response and may become a pathogenic factor in arterial diseases leading to thrombosis. We report a targeted disruption in a key receptor for collagen-induced platelet activation, glycoprotein (GP) VI. The breeding of mice with heterozygous GP VI alleles produced the expected frequency of wild-type, heterozygous, and homozygous genotypes, indicating that these animals had no reproductive problems and normal viability. GP VInull platelets failed to aggregate in response to type I fibrillar collagen or convulxin, a snake venom protein and known platelet agonist of GP VI. Nevertheless, tail bleeding time measurements revealed no severe bleeding tendency as a consequence of GP VI deficiency. Ex vivo platelet thrombus formation on type I collagen fibrils was abolished using blood from either GP VInull or FcR-gammanull animals. Reflection interference contrast microscopy revealed that the lack of thrombus formation by GP VInull platelets could be linked to a defective platelet activation following normal initial tethering to the surface, visualized as lack of spreading and less stable adhesion. These results illustrate the role of GP VI in postadhesion events leading to the development of platelet thrombi on collagen fibrils.
A Comprehensive Review of Opioid-InducedHyperalgesia (2011)

Opioid-induced hyperalgesia (OIH) is defined as a state of nociceptive sensitization caused by exposure to opioids. The condition is characterized by a paradoxical response whereby a patient receiving opioids for the treatment of pain could actually become more sensitive to certain painful stimuli. The type of pain experienced might be the same as the underlying pain or might be different from the original underlying pain. OIH appears to be a distinct, definable, and characteristic phenomenon that could explain loss of opioid efficacy in some patients. Findings of the clinical prevalence of OIH are not available. However, several observational, cross-sectional, and prospective controlled trials have examined the expression and potential clinical significance of OIH in humans. Most studies have been conducted using several distinct cohorts and methodologies utilizing former opioid addicts on methadone maintenance therapy, perioperative exposure to opioids in patients undergoing surgery, and healthy human volunteers after acute opioid exposure using human experimental pain testing. The precise molecular mechanism of OIH, while not yet understood, varies substantially in the basic science literature, as well as clinical medicine. It is generally thought to result from neuroplastic changes in the peripheral and central nervous system (CNS) that lead to sensitization of pronociceptive pathways. While there are many proposed mechanisms for OIH, 5 mechanisms involving the central glutaminergic system, spinal dynorphins, descending facilitation, genetic mechanisms, and decreased reuptake and enhanced nociceptive response have been described as the important mechanisms. Of these, the central glutaminergic system is considered the most common possibility. Another is the hypothesis that N-methyl-D-aspartate (NMDA) receptors in OIH include activation, inhibition of the glutamate transporter system, facilitation of calcium regulated intracellular protein kinase C, and cross talk of neural mechanisms of pain and tolerance. Clinicians should suspect OIH when opioid treatment's effect seems to wane in the absence of disease progression, particularly if found in the context of unexplained pain reports or diffuse allodynia unassociated with the original pain, and increased levels of pain with increasing dosages. The treatment involves reducing the opioid dosage, tapering them off, or supplementation with NMDA receptor modulators. This comprehensive review addresses terminology and definition, prevalence, the evidence for mechanism and physiology with analysis of various factors leading to OIH, and effective strategies for preventing, reversing, or managing OIH.
Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps (2010)

I propose a technique for reading the base sequence of a single DNA molecule using a graphene nanogap to read the DNA's transverse conductance. Because graphene is a single atom thick, single-base resolution of the conductance is readily obtained. The nonlinear current-voltage characteristic is used to determine the base type independent of nanogap-width variations that cause the current to change by 5 orders of magnitude. The expected sequencing error rate is 0% up to a nanogap width of 1.6 nm.
Application of enzymes to the synthesis of amino acid‐based bola and gemini surfactants (1998)

Abstract A facile and flexible chemoenzymatic route for the preparation of a variety of amino acid‐based surfactants ranging from simple monoesters to more complex bola‐ and gemini‐amphiphiles is described. The methodology is based on the observation that some lipases, notably immobilized Candida antarctica and Rhizomucor miehei , readily accept N ‐Cbzamino acids as substrates and catalyze their esterification/amidation with long‐chain alcohols and α,ω‐diols/α,ω‐diamines in excellent yield. The resulting alkanediyl‐α,ω‐bis‐( N ‐Cbz‐amino acid) can be either deprotected using conventional procedures to attain a number of multifunctional bola‐amphiphiles or further modified to obtain a range of amino acid‐based gemini surfactants.
Physical association of pyrimidine dimer DNA glycosylase and apurinic/apyrimidinic DNA endonuclease essential for repair of ultraviolet-damaged DNA. (1981)

T4 endonuclease V [endodeoxyribonuclease (pyrimidine dimer), EC 3.1.25.1)], which is involved in repair of UV-damaged DNA, has been purified to apparent physical homogeneity. Incubation of UV-irradiated poly(dA).poly(dT) with the purified enzyme preparations resulted in production of alkali-labile apyrimidinic sites, followed by formation of nicks in the polymer. The activity to produce alkali-labile sites was optimal in a relatively broad pH range (pH 6.0-8.5), whereas the activity to form nicks had a narrow optimum near pH 6.5. By performing a limited reaction with T4 endonuclease V at pH 8.5, irradiated polymer was converted to an intermediate form that carried a large number of alkali-labile sites but only a few nicks. The intermediate was used as substrate for the assay of apurinic/apyrimidinic DNA endonuclease activity [endodeoxyribonuclease (apurinic or apyrimidinic, EC 2.1.25.2]. The two activities, a pyrimidine dimer DNA glycosylase and an apurinic/apyrimidinic DNA endonuclease, were copurified and found in enzyme preparations that contained only a 16,000-dalton polypeptide. An enzyme fraction from cells infected with bacteriophage T4v1, a mutant that is sensitive to UV radiation, was defective in both glycosylase and endonuclease activities. Moreover, occurrence of an amber mutation in the denV gene caused a simultaneous loss of the two activities, and suppression of the mutation rendered both activities partially active. These results strongly suggested that a DNA glycosylase specific for pyrimidine dimers and an apurinic/apyrimidinic DNA endonuclease reside in a single polypeptide chain coded by the denV gene of bacteriophage T4. Because the two activities exhibited different thermosensitivity, it was further suggested that conformation of the active sites for these activities may be different.
Nonconjugated linseed vinyl ether by vinyl transetherification. Preparation procedure (1960)

Abstract An improved procedure is described for preparing nonconjugated linseed vinyl ether monomer by transetherification of linseed alcohol with ethyl vinyl ether. By use of a mercuric acetate‐oxalic acid catalyst mixture, an excess of ethyl vinyl ether, a reaction temperature of 45°C., and an evaporation, water‐extraction procedure for continuous removal of by‐product ethanol as the reaction proceeds, 91% of the linseed alcohol was converted to the fatty vinyl ether in 6 1/2 hrs. When mercuric acetate was used alone, more catalyst was required; at 90°C, and above, the over‐all rate and yield were reduced by partial deactivation of the catalyst. This reduction was attributed to a side reaction wherein the mercuric salt was added to the fatty acid radical at points of unsaturation. All the various methods that were compared for purifying the linseed monomer produced a product of polymerization quality. While vacuum distillation, followed by an alumina adsorption treatment, gave a monomer of the highest purity, a monomer, vacuum‐distilled only, should be of suitable polymerization quality for many purposes.
A Dominant Mutation That Alters the Regulation of INO1 Expression in Saccharomyces cerevisiae (1992)

A dominant, single nuclear gene mutation, CSE1, caused inositol auxotrophy in yeast cells. The inositol requirement was marked when choline was present in the medium. Inositol-1-phosphate synthase, the regulatory enzyme of inositol synthesis, is repressed by inositol, or more profoundly by a combination of inositol and choline in the wild type. In CSE1, the level of inositol-1-phosphate synthase was low and was greatly repressed on the addition of choline alone. In accordance with this, INO1 mRNA encoding the enzyme was low even under the depressed conditions and was profoundly decreased by choline in CSE1. But in the wild type, the addition of choline alone had little effect. An INO1-lacZ fusion was constructed and the control of the INO1 promoter in CSE1 was studied. lacZ expression was repressed not only by inositol, but also by choline in CSE1, whereas it was repressed by inositol, but only slightly by choline in the wild type. CSE1 was unlinked to the INO1 structural gene. Thus CSE1 was thought to be a regulatory mutation. Furthermore, when the CDP-choline pathway was mutationally blocked, choline did not affect INO1 expression, indicating that the metabolism of choline via the CDP-choline pathway is required for INO1 repression.
Level of circulating PD-L1 expression in patients with advanced gastric cancer and its clinical implications. (2014)

PD-L1 was elevated in advance gastric cancer patients and may play an important role in tumor immune evasion and patients prognosis.
Novel Enzymatic Method for the Production of Xylitol fromD-Arabitol byGluconobacter oxydans (2002)

Microorganisms capable of producing xylitol from D-arabitol were screened for. Of the 420 strains tested, three bacteria, belonging to the genera Acetobacter and Gluconobacter, produced xylitol from D-arabitol when intact cells were used as the enzyme source. Among them, Gluconobacter oxydans ATCC 621 produced 29.2 g/l xylitol from 52.4 g/l D-arabitol after incubation for 27 h. The production of xylitol was increased by the addition of 5% (v/v) ethanol and 5 g/l D-glucose to the reaction mixture. Under these conditions, 51.4 g/l xylitol was obtained from 52.4 g/l D-arabitol, a yield of 98%, after incubation for 27 h. This conversion consisted of two successive reactions, conversion of D-arabitol to D-xylulose by a membrane-bound D-arabitol dehydrogenase, and conversion of D-xylulose to xylitol by a soluble NAD-dependent xylitol dehydrogenase. Use of disruptants of the membrane-bound alcohol dehydrogenase genes suggested that NADH was generated via NAD-dependent soluble alcohol dehydrogenase.