gebhart/patrepeval huggingface dataset:
Developmental Regulation of Wnt/β-Catenin Signals Is Required for Growth Plate Assembly, Cartilage Integrity, and Endochondral Ossification (2005)

Studies have suggested that continuous Wnt/beta-catenin signaling in nascent cartilaginous skeletal elements blocks chondrocyte hypertrophy and endochondral ossification, whereas signaling starting at later stages stimulates hypertrophy and ossification, indicating that Wnt/beta-catenin roles are developmentally regulated. To test this conclusion further, we created transgenic mice expressing a fusion mutant protein of beta-catenin and LEF (CA-LEF) in nascent chondrocytes. Transgenic mice had severe skeletal defects, particularly in limbs. Growth plates were totally disorganized, lacked maturing chondrocytes expressing Indian hedgehog and collagen X, and failed to undergo endochondral ossification. Interestingly, the transgenic cartilaginous elements were ill defined, intermingled with surrounding connective and vascular tissues, and even displayed abnormal joints. However, when activated beta-catenin mutant (delta-beta-catenin) was expressed in chondrocytes already engaged in maturation such as those present in chick limbs, chondrocyte maturation and bone formation were greatly enhanced. Differential responses to Wnt/beta-catenin signaling were confirmed in cultured chondrocytes. Activation in immature cells blocked maturation and actually de-stabilized their phenotype, as revealed by reduced expression of chondrocyte markers, abnormal cytoarchitecture, and loss of proteoglycan matrix. Activation in mature cells instead stimulated hypertrophy, matrix mineralization, and expression of terminal markers such as metalloprotease (MMP)-13 and vascular endothelial growth factor. Because proteoglycans are crucial for cartilage function, we tested possible mechanisms for matrix loss. Delta-beta-catenin expression markedly increased expression of MMP-2, MMP-3, MMP-7, MMP-9, MT3-MMP, and ADAMTS5. In conclusion, Wnt/beta-catenin signaling regulates chondrocyte phenotype, maturation, and function in a developmentally regulated manner, and regulated action by this pathway is critical for growth plate organization, cartilage boundary definition, and endochondral ossification.
Synthetic peptide analogs differentially alter the binding affinities of cyclic nucleotide-dependent protein kinases for nucleotide substrates (1988)

Analogues of a synthetic heptapeptide substrate corresponding to the sequence around a phosphorylation site in histone H2B [Glass, D. B. & Krebs, E. G. (1982) J. Biol. Chem. 257, 1196-1200] were used to assess interactions between the peptide substrate and the ATP binding sites of cGMP-dependent protein kinase and the catalytic subunit of cAMP-dependent protein kinase. The affinity of each protein kinase for lin-benzo-ADP was determined in the absence and presence of substrate peptide by fluorescence anisotropy titrations [Bhatnagar, D., Roskoski, R., Jr., Rosendahl, M. S., & Leonard, N. J. (1983) Biochemistry 22, 6310-6317]. The Kd values of cGMP-dependent protein kinase for lin-benzo-ADP in the absence and presence of cGMP were 7.6 and 9.7 microM, respectively. Histone H2B(29-35) (Arg-Lys-Arg-Ser-Arg-Lys-Glu) had no effect on nucleotide affinity in either the absence or presence of cGMP. However, when lysine-34 located two residues after the phosphorylatable serine is replaced with an alanyl residue, the resulting [Ala34]histone H2B(29-35) and its analogue peptides interact with cGMP-dependent protein kinase and/or the nucleotide in a fashion that decreases nucleotide binding affinity approximately 3-fold. This amino acid replacement had previously been shown to cause an increase in Vmax and a decrease in the pH optimum for the phosphotransferase reaction. Replacement of positively charged residues at positions 30 and 31 of the peptide also decreased nucleotide affinity. Other analogues of histone H2B(29-35) failed to affect binding of lin-benzo-ADP to the active site of the cGMP-dependent enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)
Disorders of Gastrointestinal Motility Associated with Diabetes Mellitus (1983)

Gastrointestinal symptoms such as vomiting, constipation, diarrhea, and fecal incontinence occur frequently in patients with diabetes mellitus. In a survey of 136 diabetic outpatients, 76% had one or more gastrointestinal symptoms, the commonest symptom being constipation (found in 60%). In many cases these symptoms are thought to be due to abnormal gastrointestinal motility that, in turn, may be a manifestation of diabetic autonomic neuropathy involving the gastrointestinal tract. The pathophysiology of these gastrointestinal symptoms, clarified in recent studies, and the clinical features and treatment of these problems in diabetic patients are reviewed.
Growth Inhibition Effects of Cancer Cell Lines by Gloiopeltis furcata Fractions in Vitro (2005)

본 실험은 홍조해조류의 하나인 불등가사리를 추출 후 각 용매별로 분획하여 암세포 성장억제 효과와 QR 유도활성 효과 등 생리활성을 연구하였다. 불등가사리를 이용하여 4종의 인체 암세포주 HepG2, HeLa, MCF-7 및 HT-29와 정상 간세포에 대한 암세포 증식억제 실험을 한 결과 사용한 4종의 암세포주에서 모두 시료첨가 농도에 의존적으로 증식 저지 효과가 나타났고, 특히 불등가사리의 methanol 분획층인 GFMM에서는 매우 낮은 농도의 시료첨가에도 불구하고 괄목할 만한 높은 암세포 성장 억제효과를 나타내었으며, 정상 간세포에서는 모든 분획층에서 약한 세포증식 억제율을 나타내어 정상 세포에 미치는 독성이 낮음을 확인하였다. 특히 본 시료는 여성암의 대표적인 유방암과 자궁경부암의 암세포 성장저지효과가 탁월하였다. 한편, 사용한 4가지 암세포주 중 유일하게 QR을 가지고 있는 HepG2를 이용한 암예방지표인 QR 효소 유도 활성 여부를 측정한 결과 분획물 첨가농도를 10, 20, 30 및 40 ㎍/mL로 첨가하였을 때 GFMM의 첨가농도 20 ㎍/mL에서 대조군에 비해 약 2배 이상의 높은 QR 유도효과를 나타내어 최종농도 40 ㎍/mL에서는 2.6의 암예방 QR 유도효과를 나타내었다.
A two‐component signal‐transducing system is involved in competence and penicillin susceptibility in laboratory mutants of Streptococcus pneumoniae (1994)

Penicillin resistance in Streptococcus pneumoniae has been attributed so far to the production of penicillin-binding protein (PBP) variants with decreased affinities for beta-lactam antibiotics. Cefotaxime-resistant laboratory mutants, selected after several steps on increasing concentrations of this beta-lactam, become deficient in transformation as well. A DNA fragment conferring both cefotaxime resistance and transformation deficiency was isolated and cloned from the mutant C306. The cefotaxime resistance associated with this resistance determinant was not accompanied with apparent changes in PBP properties, and it mapped on the chromosome distinct from the known resistance determinants, genes encoding PBP2x, PBP1a or PBP2b. Determination of a 2265 bp DNA sequence of the resistance determinant revealed two open reading frames, ciaR and ciaH, whose deduced amino acid sequence identified the corresponding proteins as the response regulator and histidine kinase receptor, respectively (members of the two families of bacterial signal-transducing proteins). Two hydrophobic peptide regions divided the histidine kinase CiaH into two putative domains: an N-terminal extracellular sensor part, and an intracellular C-terminal domain with the conserved His-226 residue, the presumed phosphorylation site. The single point mutations responsible for cefotaxime-resistance and transformation deficiency of C306 and of another two independently isolated cefotaxime-resistant mutants were each located in the C-terminal half of CiaH. A small extracellular protein, the competence factor, is required for induction of competence. Neither C306 nor the transformants obtained with the mutated ciaH gene produced competence factor, and exogenous competence factor could not complement the transformation deficiency, indicating that the signal-transducing system cia is involved in early steps of competence regulation.
Binding of Hepatitis C Virus Envelope Protein E2 to CD81 Up-regulates Matrix Metalloproteinase-2 in Human Hepatic Stellate Cells (2004)

The hepatitis C virus (HCV) envelope E2 glycoprotein is a key molecule regulating the interaction of HCV with cell surface proteins. E2 binds the major extracellular loop of human CD81, a tetraspanin expressed on various cell types including hepatocytes and B lymphocytes. Regardless, information on the biological functions originating from this interaction are largely unknown. Since human hepatic stellate cells (HSC) express high levels of CD81 at the cell surface, we investigated the E2/CD81 interaction in human HSC and the possible effects arising from this interaction. Matrix metalloproteinase-2 (MMP-2; gelatinase A), a major enzyme involved in the degradation of normal hepatic extracellular matrix, was up-regulated following the interaction between E2 and CD81. In particular, by employing zymography and Western blot, we observed that E2 binding to CD81 induces a time-dependent increase in the synthesis and activity of MMP-2. This effect was abolished by preincubating HSC with an anti-CD81 neutralizing antibody. Similar effects were detected in NIH3T3 mouse fibroblasts transfected with human CD81 with identical time course features. In addition, E2/CD81 interaction in human HSC induced the up-regulation of MMP-2 by increasing activator protein-2/DNA binding activity via ERK/MAPK phosphorylation. Finally, suppression of CD81 by RNA interference in human HSC abolished the described effects of E2 on these cells, indicating that CD81 is essential for the activation of the signaling pathway leading to the up-regulation of MMP-2. These results suggest that HSC may represent a potential target for HCV. The interaction of HCV envelope with CD81 on the surface of human HSC induces an increased expression of MMP-2. Increased degradation of the normal hepatic extracellular matrix in areas where HCV is concentrated may favor inflammatory infiltration and further parenchymal damage.
Prodiginine (prodigiosin-like) pigments from Streptomyces and other aerobic Actinomycetes (1976)

About 95 microorganisms, mainly streptomycetes, were examined for prodiginine pigments. The test methods, including some media for stimulating pigment production, are given. All nine strains which produced prodiginine pigments were characterized and the pigments identified. The results were used to propose structures for five prodigiosin-like pigments from actinomycetes reported in the literature between 1947 and 1964. Streptoverticillium sp. 26-1 furnished good yields of butylcycloheptylprodiginine (I), whose antimicrobial activity is given.
Treatment of patients with arthrosis of hip or knee with an aqueous extract of Devil's Claw (Harpagophytum procumbens DC.) (2003)

Preparations made from the secondary tubers of Devil's claw (Harpagophytum procumbens) are successfully used in patients with rheumatic diseases (arthrosis and low back pain). In order to add data on the efficacy and long-term safety of an aqueous extract (Doloteffin; 2400 mg extract daily, corresponding to 50 mg harpagoside), which has been tested successfully in patients with low back pain, an uncontrolled multicentre drug surveillance study for about 12 weeks was conducted in 75 patients with arthrosis of the hip or knee. To standardize the assessment of treatment effects, the Western Ontario and McMaster Universities (WOMAC) osteoarthritis index (10 point scale) as well as the 10 cm VAS pain scale were used. The results of the study revealed a strong reduction of pain and the symptoms of osteoarthritis. There was a relevant improvement of each WOMAC subscale as well as of the total WOMAC index: 23.8% for the pain subscale, 22.2% for the stiffness subscale and 23.1% for the physical function subscale. The WOMAC total score was reduced by 22.9%. VAS pain scores were decreased by 25.8% for actual pain, 25.2% for average pain, 22.6% for worst pain and 24.5% for the total pain score. The physicians reported a continuous improvement in typical clinical findings such as 45.5% for pain on palpation, 35% for limitation of mobility and 25.4% for joint crepitus. Only two cases of possible adverse drug reactions were reported (dyspeptic complaints and a sensation of fullness). Although this was an open clinical study, the results suggest that this Devil's claw extract has a clinically beneficial effect in the treatment of arthrosis of the hip or knee.
Activation of phenotypic expression of human globin genes from nonerythroid cells by chromosome-dependent transfer to tetraploid mouse erythroleukemia cells (1979)

Chromosome-dependent gene transfer mediated by cell fusion was used to show that it is possible to activate phenotypic expression of human alpha globin genes derived from nonerythroid cells. Hybrid cells containing the human alpha globin structural genes were derived by fusion of populations of adult human peripheral blood mononuclear cells (devoid of identifiable erythroid cells) with adenine phosphoribosyl-transferase-deficient mouse erythroleukemia cells that contained close to a tetraploid complement of mouse chromosomes. The hybrid cells retained a near tetraploid complement of mouse chromosomes but had lost 80% of the chromosomes of the human parent cell. All of these hybrid cells and their subclones, which contained human chromosome 16, exhibited synthesis of human alpha globin chains. Human alpha globin mRNA was also demonstrated to be present in one of these hybrid cells by RNA.cDNA molecular hybridization analysis. We conclude that the mechanism responsible for restricting expression of the human globin genes in nonerthroid cells is not irreversible, at least for those globin structural genes that are actively transcribed in erythroid cells during adult life. Moreover, some genetic factor or process in the tetraploid mouse erythroleukemia cell is, under the conditions of our experiments, capable of reactivating phenotypic expression (production of globin chains) of human globin genes derived from nonerythroid hematopoietic cells after chromosome-dependent gene transfer.
Computer Programs to Assist the Physician in the Analysis of Self-Monitored Blood Glucose Data (1988)

We have developed new computer programs and algorithms to assist the physician in the analysis of data from patients with diabetes mellitus using “home monitoring of blood glucose”. These programs accept data from files created using a glucose meter equipped with memory and clock calender. The programs include: 1. “SUGAR3”, which has achieved the desired level of performance in terms of ease of use, speed, clarity and quality of graphical displays. This program is primarily for use in “batch” mode. 2. “MARK1”, which incorporates new methods and techniques for interactive analysis of the dynamics of glucose values obtained over a period of time covering up to several months together with their temporal relationships to type and dose of insulin and special user defined events. 3. “INSULIN”, which permits one to visualize the approximate profile of insulin action, for a regimen involving multiple injections or types of insulin.
Transforming growth factor-1 promotes the transcriptional activation of plasminogen activator inhibitor type 1 in carcinoma-associated fibroblasts (2012)

Carcinoma-associated fibroblasts (CAFs) play a pivotal role in promoting the growth, invasion and metastasis of tumor cells. However, to date little is known about the oncogenic mechanisms of CAFs. This study aimed to identify the microenvironmental factors involved in tumor development and progression directed by CAFs in liver metastases. Tissue samples collected from 20 patients with colorectal liver metastases were used in this study. Histological and morphological characterization of the samples was performed using hybridization and immunohistological assays. The mRNA expression of α-smooth muscle actin (α-SMA) was measured by northern blotting. The expression of plasminogen activator inhibitor type 1 (PAI-1) was measured by enzyme-linked immunosorbent assay (ELISA). As a result, co-expression of Thy-1 (CD90) and α-SMA was identified in CAFs, while normal liver samples were negative for α-SMA and Thy-1. Compared with epidermal growth factor (EGF) and tumor necrosis factor (TNF) incubation, the expression of α-SMA increased significantly following transforming growth factor-1 (TGF-1) incubation (P<0.05), while platelet-derived growth factor (PDGF) caused a significant suppression of α-SMA expression (P<0.05). PAI-1 expression was significantly lower in unstimulated fibroblasts compared to TGF-1-treated fibroblasts (P<0.01). The levels of PAI-1 transcription were significantly higher in CAFs from the patient samples compared with the healthy controls. Taken together, our findings suggest that CAFs may be important in migration, matrix degradation, invasion and angiogenesis of tumors, and TGF-1 may promote the activation of PAI-1 transcription in CAFs.
Design by Directed Evolution (1998)

The stunning array of features and functions exhibited by proteins in nature should convince most scientists of the power of evolutionary design processes. Natural selection acting on populations over long periods of time has generated a vast number of proteins ideally suited to their biological functions. When we try to recruit these remarkable molecular machines for new tasksfrom serving as industrial catalysts to being used as additives for laundry detergentswe find that they are often not so well suited. (The chemist is not terribly impressed with a synthesis requiring a reactor the size of a football field simply because the enzyme functions in water and the substrate does not dissolve, nor is she pleased with a catalyst shut down by the products of its own reaction.) Evolution is usually the culprit: proteins are optimized, and often highly specialized, for specific biological tasks.&#13;\nMost protein reengineering efforts have been by so-called rational design. The filtering effect of scientific publication (successes get published, failures mostly do not) might lead one to believe that we can, with reasonable probability of success, identify and modify the amino acids responsible for key properties such as an enzyme's substrate preference, stability, or activity in a nonnatural environment. In reality, we are far from being able to do this reliably. This is true even for the relatively small number of enzymes for which considerable structural and mechanistic data are available. Admitting ineptitude in rational design, however, frees us to consider other approaches which are hardly irrational. An alternative and highly effective design strategy can be found by looking to the processes by which all these proteins came about in the first place.&#13;\nMy research has been devoted to recreating in the laboratory the key processes of evolution and doing it in such a way that we can design scientifically interesting and technologically useful molecules. The challenge is to collapse the time scale for evolution from millions of years to months or even weeks.
Advanced chemical vapor deposition silicon carbide barrier technology for ultralow permeability applications (2006)

Plasma-enhanced chemical vapor deposition (PECVD) processes have been developed to produce prototype barrier coatings for protection from detrimental gases. The strategy used is based on a combination of molecular precursor design and advanced plasma processing and represents a route to an effective, barrier solution. Silicon carbide room temperature deposition processes have been established on several reactor systems. The impact of process-operating factors on the structure and barrier performance has been analyzed and a wide range of tunability has been found. A metrology has been developed to estimate the optical, mechanical, and application-relevant barrier properties. In addition, coatings have been analyzed for subnanometer structural defects by positronium annihilation lifetime spectroscopy (PALS). None of the barriers present evidence of any mesopores or open porosity. Furthermore, the amount of nanostructural defects in layers has been found to depend on both plasma chemistry and power. Based on the PALS results, structural models of different types of barrier layers are proposed. Significant progress in barrier performance has been demonstrated in terms of water vapor transmission rate down in the range of 10−4g∕m2d.
现代振动光谱学和微光谱学 理论、仪器和生物医药应用 (2016)

作者在1993年曾撰写了《IntroductionofVibrationalSpectroscopy》（振动光谱学入门）一书，该书论述了振动光谱的基本原理和理论。在此书出版后的20多年间，出现了快速数据采集系统，皮秒和飞秒激光器的广泛应用，计算能力的快速提高使得振动光谱成像技术成为可能。计算机的飞速发展使数据处理能力和统计分析能力大幅提高。
OnabotulinumtoxinA injections in chronic migraine, targeted to sites of pericranial myofascial pain: an observational, open label, real-life cohort study (2017)

OnabotulinumtoxinA has proven its efficacy in reducing the number of headache days in chronic migraine (CM) patients. The usual paradigm includes 31 pericranial injection sites with low dose (5 U) per site. The aim of this study is to present the results obtained using a simpler injection protocol of onabotulinumtoxinA, with injection sites targeted to pericranial myofascial sites of pain. Observational, open label, real-life, cohort study. We enrolled 63 consecutive patients fulfilling the diagnostic criteria of CM, and refractory to conventional treatments. The patients were injected using a “follow-the-pain” pattern into the corrugator and/or temporalis and/or trapezius muscles. The doses per muscle were fixed. According to the number of muscles injected, the total dose could vary from 70 to 150 U per session. Patients were considered responders if they had a ≥ 50% decrease in number of headache days in at least two consecutive injection cycles. Forty one patients (65.1% in intention to treat analysis) responded to treatment. In 70.7% of responders, the effect size was even higher, with a reduction ≥70% in the number of headache days. The associated cervical pain and muscle tenderness, present in 33 patients, was reduced by ≥50% in 31 patients (94%). Triptan consumption dramatically decreased (81%) in responders. The trapezius was the most frequently injected muscle. We observed no serious adverse event. The mean patient satisfaction rate was 8.5/10. This study provides additional robust evidence supporting the efficacy of onabotulinumtoxinA injections in CM. Furthermore, the paradigm we used, with reduced number of injection sites targeted to pericranial myofascial sites of pain, may provide evidence in favor of the implication of myofascial trigger points in migraine chronicization. ClinicalTrials.gov Protocol Record I17022 ClinicalTrials.gov Identifier: NCT03175263 . Date of registration: June 7, 2017. Retrospectively registered.
The Correlation of Skeletal and Cardiac Muscle Dysfunction in Duchenne Muscular Dystrophy (2016)

Our findings allow us to conclude that in this population, there exists a significant relationship between skeletal muscle and cardiac function in non-ambulatory DMD patients. While this does not imply a causal relationship, a possible association between skeletal and cardiac muscle function suggests that researchers should carefully monitor cardiac function, even when the primary outcome measures are not cardiac in nature.