gebhart/patrepeval huggingface dataset:
Effect of the Molecular Nature of Mutation on the Efficiency of Intrachromosomal Gene Conversion in Mouse Cells (1987)

With the intent of further exploring the nature of gene conversion in mammalian cells, we systematically addressed the effects of the molecular nature of mutation on the efficiency of intrachromosomal gene conversion in cultured mouse cells. Comparison of conversion rates revealed that all mutations studied were suitable substrates for gene conversion; however, we observed that the rates at which different mutations converted to wild-type could differ by two orders of magnitude. Differences in conversion rates were correlated with the molecular nature of the mutations. In general, rates of conversion decreased with increasing size of the molecular lesions. In comparisons of conversion rates for single base pair insertions and deletions we detected a genotype-directed path for conversion, by which an insertion was converted to wild-type three to four times more efficiently than was a deletion which maps to the same site. The data are discussed in relation to current theories of gene conversion, and are consistent with the idea that gene conversion in mammalian cells can result from repair of heteroduplex DNA (hDNA) intermediates.
Green Chemistry: Theory and Practice (1998)

1: Introduction. 2: What is Green Chemistry?. 3: Tools of Green Chemistry. 4: Principles of Green Chemistry. 5: Evaluating the Impacts of Chemistry. 6: Evaluating Feedstocks and Starting Materials. 7: Evaluating Reaction Types. 8: Evaluation of Methods to Design Safer Chemicals. 9: Illustrative Examples. 10: Future Trends in Green Chemistry
Extension of the Applicable Range of Fluorescein: A Fluorescein‐Based Probe for Western Blot Analysis (2005)

The new star of Westerns: A highly sensitive fluorescence probe for alkaline phosphatase (ALP) based on a fluorescein derivative has been prepared and found to be suitable for use in Western blot analysis. The probe 1 is nonfluorescent but undergoes hydrolysis in the presence of ALP to yield a green-fluorescent derivative 2 and may be used in multicolor labeling in combination with other probes. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501542_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Site-specific Mutagenesis of a Recombinant Anti-single-stranded DNA Fab (1997)

The heavy chain complementarity-determining region 3 (HCDR3) of the anti-oligo(dT) recombinant antibody fragment, DNA-1, contributes significantly to antigen binding (Komissarov, A. A., Calcutt, M. J., Marchbank, M. T., Peletskaya, E. N., and Deutscher, S. L. (1996) J. Biol. Chem. 271, 12241-12246). In the present study, the role of separate HCDR3 residues of DNA-1 in interaction with oligo(dT) was elucidated. Based on a molecular model of the combining site, residues at the base (Arg98 and Asp108) and in the middle (Tyr101-Arg-Pro-Tyr-Tyr105) of HCDR3 were predicted to support the loop conformation and directly contact the ligand, respectively. Twenty-five site-specific mutants were produced as hexahistidine-tagged proteins, purified, and examined for binding to (dT)15 using two independent methods. All mutations in the middle of HCDR3 led to either abolished or diminished affinity. Tyr101 likely participates in hydrogen bonding, while Tyr104 and Tyr105 may be involved in aromatic-aromatic interactions with the ligand. The residues Arg102 and Pro103 were not as critical as the tyrosines. It is speculated that HCDR3 interacts with the thymines, rather than the phosphates, of the ligand. A 3-fold increase in affinity was observed by mutation of Asp108 to alanine. The highly conserved Arg98 and Asp108 do not appear to form a salt bridge.
Amino Acids (2013)

Amino acid biochemistry and nutrition spans a broad range of fields including biochemistry, metabolism, physiology, immunology, reproduction, pathology, and cell biology. In the last half-century, there have been many conceptual and technical advancements, from analysis of amino acids by high-performance liquid chromatography and mass spectrometry
Complex regional pain syndrome (2011)

Complex regional pain syndrome (CRPS) previously known as reflex sympathetic dystrophy is a chronic neurological disorder involving the limbs characterized by disabling pain, swelling, vasomotor instability, sudomotor abnormality, and impairment of motor function. CRPS is not uncommon after hand surgery and may complicate post-operative care. There is no specific diagnostic test for CRPS and the diagnosis is based on history, clinical examination, and supportive laboratory findings. Recent modifications to diagnostic criteria have enabled clinicians to diagnose this disease more consistently. This review gives a synopsis of CRPS and discusses the diagnosis, pathophysiology, and treatment options based on the limited evidence in the literature.
Evaluation and Floating Enhancement of Levodopa Sustained Release Floating Minitablets Coated with Insoluble Acrylic Polymer (2008)

This article describes the in vitro evaluation and the enhancement of the floating properties of coated sustained release (SR) minitablets (MTs). The evaluated system consisted of a 3-mm drug-containing gas-generating core prepared by melt granulation and subsequent compression, which was then coated with a flexible polymeric membrane. Eudragit RL30D and acetyl triethylcitrate were used as a film former and a plasticizer, respectively. The coating level was fixed at 20% (wt/wt). The optimally coated floating MTs floated within 10 min and remained buoyant for more than 13 h, regardless of the pH of the test medium. By evaluating the dissolution profiles of levodopa at different pH, it was found that the release of levodopa was sustained for more than 12 h regardless of the pH, even if the coating did not cancel the effect of the pH-dependent solubility of the active drug. Finally, the robustness of the coated floating MTs was assessed by testing the drug release variability in function of the stirring conditions during dissolution tests.
Sclerostin is a delayed secreted product of osteocytes that inhibits bone formation (2005)

Osteocytes are the most abundant cells in bone and are ideally located to influence bone turnover through their syncytial relationship with surface bone cells. Osteocyte-derived signals have remained largely enigmatic, but it was recently reported that human osteocytes secrete sclerostin, an inhibitor of bone formation. Absent sclerostin protein results in the high bone mass clinical disorder sclerosteosis. Here we report that within adult iliac bone, newly embedded osteocytes were negative for sclerostin staining but became positive at or after primary mineralization. The majority of mature osteocytes in mineralized cortical and cancellous bone was positive for sclerostin with diffuse staining along dendrites in the osteocyte canaliculi. These findings provide for the first time in vivo evidence to support the concept that osteocytes secrete sclerostin after they become embedded in a mineralized matrix to limit further bone formation by osteoblasts. Sclerostin did not appear to influence the formation of osteocytes. We propose that sclerostin production by osteocytes may regulate the linear extent of formation and the induction or maintenance of a lining cell phenotype on bone surfaces. In doing so, sclerostin may act as a key inhibitory signal governing skeletal microarchitecture.
The molecular mechanism of dicarboxylic acid transport in escherichia coli K 12 (1977)

It is the purpose of this communication to review the properties of the dicarboxylic acid transport system in Escherichia coli K 12, in particular the role of various dicarboxylate transport proteins, and the disposition of these components in the cytoplasmic membrane. The dicarboxylate transport system is an active process and is responsible for the uptake of succinate, fumarate, and malate. Membrane vesicles prepared from the EDTA, lysozyme, and osmotic shock treatment take up the dicarboxylic acids in the presence of an electron donor. Genetic analysis of various transport mutants indicates that there is only one dicarboxylic acid transport system present in Escherichia coli K 12, and that at least 3 genes, designated cbt, dct A, and dct B, are involved in this transport system. The products corresponding to the 3 genes are: a periplasmic binding protein (PBP) specified by cbt, and 2 membrane integral proteins, SBP 1 and SBP 2, specified by dct B and dct A, respectively. Components SBP 1 and SBP 2 appear to be exposed on both the inner and outer surfaces of the membrane, and lie in close proximity to each other. The substrate recognition sites of SBP 2 and SBP 1 are exposed on the outer and inner surfaces of the membrane respectively. The data presently available suggest that dicarboxylic acids may be translocated across the membrane via a transport channel. A tentative working model on the mechanism of translocation of dicarboxylic acids across the cell envelope by the periplasmic binding protein, and the 2 membrane carrier proteins is presented.
Aberrant Regulation of the Agouti Pigment Pattern in the Viable Yellow Mouse (1974)

Journal Article Aberrant Regulation of the Agouti Pigment Pattern in the Viable Yellow Mouse Get access DONALD B. GALBRAITH, DONALD B. GALBRAITH Biology Department, Trinity CollegeHartford, Connecticut 06106 Search for other works by this author on: Oxford Academic PubMed Google Scholar GEORGE L. WOLFF GEORGE L. WOLFF The Institute for Cancer ResearchPhiladelphia, Pennsylvania Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 65, Issue 3, May 1974, Pages 137–140, https://doi.org/10.1093/oxfordjournals.jhered.a108484 Published: 01 May 1974
Neuromuscular Electrical Stimulation for Quadriceps Muscle Strengthening After Bilateral Total Knee Arthroplasty: A Case Series (2004)

When NMES was added to a voluntary exercise program, deficits in quadriceps muscle strength and activation resolved quickly after TKA.
Large-scale production of murine monoclonal antibodies using hollow fiber bioreactors. (1988)

We have produced large quantities of murine monoclonal antibodies for in vivo human clinical trials using hollow fiber bioreactors (HFBRs). Thirty-three different hybridoma cell lines have been evaluated in various HFBR systems. Monoclonal antibody (Ab) productivity is highly dependent on the intrinsic secretory rate of each cell line. Other factors that affect Ab production include capillary membrane molecular weight cutoff, and HFBR design. Studies comparing HFBRs to static and suspension culture systems revealed similar Ab productivity. An advantage of the HFBR is that the Ab is concentrated in the extracapillary space, simplifying downstream processing.
Establishment of a continuous tumor‐cell line (PANC‐1) from a human carcinoma of the exocrine pancreas (1975)

An epithelioid cell line, started from a human pancreatic carcinoma of ductal cell origin, has been maintained in culture for over 2 years and has been subcultured more than 40 times. The PANC-1 cell line has a doubling time of 52 h and G6PD activity of the slow mobility of B type. Chromosome studies show a modal number of 63 with three distinct marker chromosomes and a small ring chromosome. The malignant nature of the PANC-1 cell line was verified by: (1) the ready growth of PANC-1 cells in soft agar and on top of a fibroblast monolayer; and (2) the formation of a progressively growing anaplastic carcinoma after injection of a nude-athymic mouse with PANC-1 cells.
[Determination of ten Chinese traditional medicines made in Jiangxi province by AAS]. (1999)

The quantities of 21 microelements were determined in 10 Chinese traditional medicines, using both flame and graphite oven atomic absorption spectrometry. We studied the efficacies of such Chinese medicaments. The result showed the efficacies related to the inorganic microelements.
Object-oriented development process and metrics (1996)

Part 1 Analysis: analysis concepts analysis process analysis metrics example. Part 2 Design: design concepts design process design metrics example. Part 3 Implementation: implementation concepts implementation process implementation metrics example. Part 3 Last words: one step beyond Appendices: category quality metric additional code fragments of example output.
Potential role of hematopoietic pre‐B‐cell leukemia transcription factor‐interacting protein in oral carcinogenesis (2014)

HPIP may play a critical role in oral carcinogenesis and is thus a potential target for anticancer therapy, with particular emphasis on its involvement in differentiation and migration/metastasis.
Tunable Bandgaps: Simulation Evidence of Hexagonal‐to‐Tetragonal ZnSe Structure Transition: A Monolayer Material with a Wide‐Range Tunable Direct Bandgap (Adv. Sci. 12/2015) (2015)

In article 1500290, X. C. Zeng and co-workers demonstrate simulation evidence for a structural transition in 2D ZnSe. The 2D tetragonal ZnSe monolayer exhibits highly tunable bandgap from 2 to 3 eV under the biaxial strain, suggesting its potential application as light-emitting material in red-green-blue light emission diodes or for visible-light driven water splitting through suitable band alignment.
Relapse-Related Molecular Signature in Lung Adenocarcinomas Identifies Patients With Dismal Prognosis (2009)

RRS-82 may be useful for identifying adenocarcinoma patients at very high risk for relapse, even those with cancer in the early stage.
The Yersinia pseudotuberculosis invasin protein and human fibronectin bind to mutually exclusive sites on the alpha 5 beta 1 integrin receptor. (1991)

The Yersinia pseudotuberculosis invasin protein promotes bacterial penetration into mammalian cells by binding to several beta 1 chain integrins. We show here that proteins containing the cell-binding domain of invasin bind to the fibronectin receptor alpha 5 beta 1 isolated from human placenta and immobilized on a filter membrane. Two forms of the receptor, each having a molecular weight of about 290,000, were immunodepleted by monoclonal antibodies specific for the beta 1 subunit or the alpha 5 beta 1 heterodimer. The binding of invasin to the receptor immobolized on the filter, or to whole JAR cells, reaches saturation after 90 min and has an apparent dissociation constant (Kd) of 5.0 x 10(-9) M. Invasin binding to alpha 5 beta 1 is inhibited by the 120-kDa chymotryptic fragment of fibronectin in a competitive manner with an inhibition constant (Ki) of 7.5 x 10(-7) M. Furthermore, invasin-receptor binding is also inhibited by the hexapeptide GRGDSP, and monoclonal antibodies that block cell attachment to invasin-coated surfaces also block cell attachment to fibronectin-coated surfaces. These results indicate that invasin and fibronectin bind to the same, or closely located sites on alpha 5 beta 1, although invasin binds with a much higher affinity than does fibronectin.
Ethanol‐induced cytochrome P4502E1 causes carcinogenic etheno‐DNA lesions in alcoholic liver disease†‡ (2009)

Our data support the assumption that ethanol-mediated induction of hepatic CYP2E1 leading inter alia to highly miscoding lipid peroxidation-derived DNA lesions may play a central role in hepatocarcinogenesis in patients with ALD.
Eribulin Mesylate: Mechanism of Action of a Unique Microtubule-Targeting Agent (2015)

Eribulin mesylate (eribulin), an analogue of the marine natural product halichondrin B, is a microtubule-depolymerizing drug that has utility in the treatment of patients with breast cancer. Clinical trial results have demonstrated that eribulin treatment provides a survival advantage to patients with metastatic or locally advanced breast cancer previously treated with an anthracycline and a taxane. Furthermore, a pooled analysis of two pivotal phase III trials has demonstrated that eribulin also improves overall survival in several patient subgroups, including in women with HER2-negative disease and triple-negative breast cancer. This review covers the preclinical research that led to the clinical testing and approval of eribulin, as well as subsequent research that was prompted by distinct and unexpected effects of eribulin in the clinic. Initial studies with halichondrin B demonstrated unique effects on tubulin binding that resulted in distinct microtubule-dependent events and antitumor actions. Consistent with the actions of the natural product, eribulin has potent microtubule-depolymerizing activities and properties that distinguish it from other microtubule-targeting agents. Here, we review new results that further differentiate the effects of eribulin from other agents on peripheral nerves, angiogenesis, vascular remodeling, and epithelial-to-mesenchymal transition. Together, these data highlight the distinct properties of eribulin and begin to delineate the mechanisms behind the increased survival benefit provided by eribulin for patients.
Prospects for prevention and treatment of vascular cognitive impairment. (2003)

With the aging population and rising prevalence of vascular disease in developed and developing countries, increasing numbers of individuals are at risk of cognitive impairment. Despite the potential of the therapeutics that are currently under investigation, none have yet fulfilled their promise for the prevention and treatment of dementia. The term vascular cognitive impairment (VCI) describes individuals with significant cognitive impairment arising from vascular disease. Risk factors predisposing to stroke correlate with brain changes, cognitive loss and Alzheimer's disease pathology. The volume of the infarcts and white matter changes, silent lacunar infarcts, and global and regional brain atrophy may be imaged non-invasively, targeted as surrogates of the dementia processes and considered parameters to be targeted for interventional strategies. As the greatest chance to prevent cognitive impairment and its progression is by intervening in the early stages or prior to any change, the development of preventative therapeutics is an important strategy. Non-invasive magnetic resonance imaging techniques may help to identify a subgroup of patients in whom infarct prevention, via risk factor control, may be of paramount importance. As the pathophysiology of dementia becomes more fully understood by coupling neuropsychological with neuroimaging, genetic and pathological features, there is the potential for the establishment of diagnostic criteria of the early phase of VCI and the testing of novel interventional strategies.
Transforming Growth Factor β Blocks Tec Kinase Phosphorylation, Ca2+ Influx, and NFATc Translocation Causing Inhibition of T Cell Differentiation (2003)

Transforming growth factor (TGF)-beta inhibits T cell proliferation and differentiation. TGF-beta has been shown to inhibit the expression of transcription factors such as GATA-3 and T-bet that play important roles in T cell differentiation. Here we show that TGF-beta inhibits T cell differentiation at a more proximal step. An early event during T cell activation is increased intracellular calcium levels. Calcium influx in activated T cells and the subsequent activation of transcription factors such as NFATc, events essential for T cell differentiation, are modulated by the Tec kinases that are downstream of the T cell receptor and CD28. We show that in stimulated CD4+ T cells, TGF-beta inhibits phosphorylation and activation of the Tec kinase Itk, increase in intracellular Ca2+ levels, NFATc translocation, and activation of the mitogen-activated protein kinase ERK that together regulate T cell differentiation. Our studies suggest that by inhibiting Itk, and consequently Ca2+ influx, TGF-beta limits T cell differentiation along both the Th1 and Th2 lineages.
Programming your way out of the past: ISIS and the META Project (1989)

The ISIS distributed programming system and the META Project are described. The ISIS programming toolkit is an aid to low-level programming that makes it easy to build fault-tolerant distributed applications that exploit replication and concurrent execution. The META Project is reexamining high-level mechanisms such as the filesystem, shell language, and administration tools in distributed systems.
Guidelines for the management of inflammatory bowel disease in adults (2004)

Ulcerative colitis (UC) and Crohn’s disease (CD) (collectively termed inflammatory bowel disease (IBD)) are complex disorders reflected by wide variation in clinical practice. These guidelines, commissioned by the Clinical Services’ Committee of the British Society of Gastroenterology (BSG) for clinicians and allied professionals caring for patients with IBD in the United Kingdom, provide an evidence based document describing good clinical practice for investigation and treatment. The guidelines are intended to bring consistency, but should not necessarily be regarded as the standard of care for all patients. Individual cases must be managed on the basis of all clinical data available for that case. Patient preferences should be sought and decisions jointly made between patient and health professional.

### 1.1 Development of guidelines

A comprehensive literature search was performed using electronic databases (Medline, PubMed, and Ovid; keywords: “inflammatory bowel disease”, “ulcerative colitis”, and “Crohn’s disease”) by Dr Carter. A preliminary document was drafted by Dr Carter, Dr Lobo, and contributing authors. This was summarised by Dr Travis and revised after circulation first to the committee and then to members of the IBD section of the BSG, before submission to the Clinical Services’ Committee.

### 1.2 Grading of recommendations1

The guidelines conform to the North of England evidence based guidelines development project. The grading of each recommendation is dependent on the category of evidence supporting it:





### 1.3 Scheduled review of guidelines

The content and evidence base …
Synthesis of a Pyridyl Disulfide End-Functionalized Glycopolymer for Conjugation to Biomolecules and Patterning on Gold Surfaces (2009)

A pyridyl disulfide end-functionalized polymer with N-acetyl-d-glucosamine pendant side-chains was synthesized by atom transfer radical polymerization (ATRP). The glycopolymer was prepared from a pyridyl disulfide initiator catalyzed by a Cu(I)/Cu(II)/2,2'-bipyridine system in a mixture of methanol and water at 30 degrees C. The final polymer had a number-average molecular weight (M(n)) of 13.0 kDa determined by (1)H NMR spectroscopy and a narrow polydispersity index (1.12) determined by gel permeation chromatography (GPC). The pyridyl disulfide end-group was then utilized to conjugate the glycopolymer to a double-stranded short interfering RNA (siRNA). Characterization of the glycopolymer-siRNA by polyacrylamide gel electrophoresis (PAGE) showed 97% conjugation. The activated disulfide polymer was also patterned on gold via microcontact printing. The pyridyl disulfide allowed for ready immobilization of the glycopolymer into 200 microm sized features on the surface.