gebhart/patrepeval huggingface dataset:
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake (2010)

The intestinal microbiota consists of over 1000 species, which play key roles in gut physiology and homeostasis. Imbalances in the composition of this bacterial community can lead to transient intestinal dysfunctions and chronic disease states. Understanding how to manipulate this ecosystem is thus essential for treating many disorders. In this study, we took advantage of recently developed tools for deep sequencing and phylogenetic clustering to examine the long-term effects of exogenous microbiota transplantation combined with and without an antibiotic pretreatment. In our rat model, deep sequencing revealed an intestinal bacterial diversity exceeding that of the human gut by a factor of two to three. The transplantation produced a marked increase in the microbial diversity of the recipients, which stemmed from both capture of new phylotypes and increase in abundance of others. However, when transplantation was performed after antibiotic intake, the resulting state simply combined the reshaping effects of the individual treatments (including the reduced diversity from antibiotic treatment alone). Therefore, lowering the recipient bacterial load by antibiotic intake prior to transplantation did not increase establishment of the donor phylotypes, although some dominant lineages still transferred successfully. Remarkably, all of these effects were observed after 1 mo of treatment and persisted after 3 mo. Overall, our results indicate that the indigenous gut microbial composition is more plastic that previously anticipated. However, since antibiotic pretreatment counterintuitively interferes with the establishment of an exogenous community, such plasticity is likely conditioned more by the altered microbiome gut homeostasis caused by antibiotics than by the primary bacterial loss.
Wear debris. An environmental issue in total joint replacement. (1994)

There is a growing concern that osteolytic lesions, often adjacent to otherwise stable implants, are a recent phenomenon caused by some recent change in polyethylene, metal, or other aspect of the total hip construction. This study investigates the possibility that bearings and modular connections used in modern hip replacements are an unappreciated source of particulate debris. Measurements taken from contemporary femoral bearings show a significant mismatch in both surface finish and sphericity of mating metal and polyethylene components, with sphericity of inserts being much worse then sphericity of femoral heads. The tolerances for sphericity of polyethylene inserts were further changed by the placement of an insert into its metal shell. Hip simulator tests of assembled inserts and shells showed greater polyethylene weight loss for metal-backed shells than for inserts alone. Bending and torsional tests of metal/metal modular connections showed that dynamic loads can release large numbers of debris particles from taper junctions. Because osteolytic lesions clearly are associated with overload of tissue by debris particles, the design, manufacture, and tolerances of modular connections in total hip replacement all seem to require reevaluation.
Detecting disease-predisposing variants: the haplotype method. (1997)

For many HLA-associated diseases, multiple alleles-- and, in some cases, multiple loci--have been suggested as the causative agents. The haplotype method for identifying disease-predisposing amino acids in a genetic region is a stratification analysis. We show that, for each haplotype combination containing all the amino acid sites involved in the disease process, the relative frequencies of amino acid variants at sites not involved in disease but in linkage disequilibrium with the disease-predisposing sites are expected to be the same in patients and controls. The haplotype method is robust to mode of inheritance and penetrance of the disease and can be used to determine unequivocally whether all amino acid sites involved in the disease have not been identified. Using a resampling technique, we developed a statistical test that takes account of the nonindependence of the sites sampled. Further, when multiple sites in the genetic region are involved in disease, the test statistic gives a closer fit to the null expectation when some--compared with none--of the true predisposing factors are included in the haplotype analysis. Although the haplotype method cannot distinguish between very highly correlated sites in one population, ethnic comparisons may help identify the true predisposing factors. The haplotype method was applied to insulin-dependent diabetes mellitus (IDDM) HLA class II DQA1-DQB1 data from Caucasian, African, and Japanese populations. Our results indicate that the combination DQA1#52 (Arg predisposing) DQB1#57 (Asp protective), which has been proposed as an important IDDM agent, does not include all the predisposing elements. With rheumatoid arthritis HLA class II DRB1 data, the results were consistent with the shared-epitope hypothesis.
Neuropsychopharmacology : The Fifth Generation of Progress (2002)

Section 1. Neurotransmitter and Signal Transduction / Eric Nestler, Ronald Duman Section 2. Emerging Methods in Molecular Biology and Genetics / Samuel H. Barondes Section 3. Emerging Imaging Technologies and Their Application to Psychiatric Research Section 4. Drug Discovery and Evaluation / Herbert Meltzer Section 5. Disorders of Development / Joseph Coyle Section 6. Schizophrenia and Related Disorders / Daniel Weinberger Section 7. Anxiety and Stress Disorders / Dennis Charney Section 8. Affective Disorders / Charles Nemeroff Section 9. Alzheimers and Other Dementias / Kenneth L. Davis Section 10. Substance Use Disorders / Charles O'Brien, Marian Fischman Section 11. Impulsive and Compulsive Disorders / Eric Hollander Section 12. Movement Disorders and Paroxysmal Disorders / Carol Tamminga INDEX
RNA secondary structure prediction (2005)

Abstract The field of RNA secondary structure prediction matured in the last 10 years with the development of many readily available software packages. The thermodynamic parameters for predicting the free energy of an RNA secondary structure are continuing to be revised on the basis of new experiments. This article reviews the available secondary structure prediction algorithms for both a single sequence and multiple sequences.
Blood-Based Analyses of Cancer: Circulating Tumor Cells and Circulating Tumor DNA (2014)

Recent advances in technologies to analyze circulating tumor cells and circulating tumor DNA are setting the stage for real-time, noninvasive monitoring of cancer and providing novel insights into cancer evolution, invasion, and metastasis.
Report of the European Myeloma Network on multiparametric flow cytometry in multiple myeloma and related disorders (2008)

The European Myeloma Network (EMN) organized two flow cytometry workshops. The first aimed to identify specific indications for flow cytometry in patients with monoclonal gammopathies, and consensus technical approaches through a questionnaire-based review of current practice in participating laboratories. The second aimed to resolve outstanding technical issues and develop a consensus approach to analysis of plasma cells. The primary clinical applications identified were: differential diagnosis of neoplastic plasma cell disorders from reactive plasmacytosis; identifying risk of progression in patients with MGUS and detecting minimal residual disease. A range of technical recommendations were identified, including: 1) CD38, CD138 and CD45 should all be included in at least one tube for plasma cell identification and enumeration. The primary gate should be based on CD38 vs. CD138 expression; 2) after treatment, clonality assessment is only likely to be informative when combined with immunophenotype to detect abnormal cells. Flow cytometry is suitable for demonstrating a stringent complete remission; 3) for detection of abnormal plasma cells, a minimal panel should include CD19 and CD56. A preferred panel would also include CD20, CD117, CD28 and CD27; 4) discrepancies between the percentage of plasma cells detected by flow cytometry and morphology are primarily related to sample quality and it is, therefore, important to determine that marrow elements are present in follow-up samples, particularly normal plasma cells in MRD negative cases.
The omniguide antenna; An omnidirectional waveguide array for UHF-TV broadcasting (2005)

The Omniguide antenna is a new type of high-gain antenna developed for UHF-TV broadcasting. Waveguide components are employed in the design instead of coaxial line elements to increase the power-handling capacity, Separate picture and sound inputs are provided which are decoupled independent of frequency, thus eliminating the need for a frequency-selective combining Filter. A reflection-absorbing circuit increases the picture input bandwidth.
Theory of morphology-dependent resonances: shape resonances and width formulas (1993)

The theory of morphology-dependent resonances of a spherical particle is developed in analogy with the theory of quantum-mechanical shape resonances. Exact analytic formulas for predicting the widths of the resonances for both real and complex indices of refraction are developed.
Human Retinal Pigment Epithelium Cell Changes and Expression of αB-Crystallin (2007)

The detection of alphaB-crystallin in the RPE of patients with early and advanced AMD implicates this as an AMD biomarker. Sporadic expression of alphaB-crystallin by RPE cells localized adjacent to drusen in early AMD indicates that changes in the gene expression of RPE cells accompany early stages of the disease and introduces novel potential targets for AMD therapy.
Utilization of monoclonal‐antibody‐based assay (hemocardtm) in screening for and differentiating between genotypes of sickle cell disease and other hemoglobinopathies (1995)

Sickle cell disease covers a group of conditions in which pathology may be attributed to the presence of sickle hemoglobin (HbS). The identification of HbS and other variants including those in combination with HbS is commonly achieved by cellulose acetate electrophoresis at alkaline pH. Because many hemoglobin variants with similar charges have similar electrophoretic migration patterns, they are difficult to differentiate by electrophoresis. The HemoCard assays address this concern through the use of monoclonal antibodies capable of specifically recognizing the unique amino acid substitution in the variant hemoglobin. The panel of HemoCard monoclonal antibodies confirms the absence and presence of HbA, HbC, HbE, HbS, and other sickling hemoglobin variants. The combination of alkaline cellulose acetate electrophoresis and HemoCard assays allows the technologist to reach a final conformation of both common and much less common sickle cell disease genotypes, combinations of HbS with other hemoglobins that ordinarily do not produce sickle cell disease, and other clinically important hemoglobinopathies including HbE/beta-thalassemia and hemoglobin C disease.
Effect of the administration schedule on the therapeutic efficacy of oral pancreatic enzyme supplements in patients with exocrine pancreatic insufficiency: a randomized, three‐way crossover study (2005)

The efficacy of pancreatic enzyme supplements for the treatment of exocrine pancreatic insufficiency may be optimized by administration during or after meals.
NetScape Communicator 4 for Windows (Visual QuickStart Guide) (1997)

From the Publisher:
Takes an easy, visual approach to teaching Netscape Communicator, where pictures guide you through the software and show you what to do. 
Works like a reference book - you look up what you need and then get straight to work. 
No long-winded passages - concise, straight-forward commentary explains what you need to know. 
Affordably priced, because buying a computer book shouldn't be an investment in itself.
The abnormal occurrence and the differentiation-dependent distribution of N-acetyl and N-glycolyl species of the ganglioside GM2 in human germ cell tumors a study with specific monoclonal antibodies (1990)

Human primary germ cell tumors were analyzed for the presence of the ganglioside GM2 using three specific monoclonal antibodies which can distinguish the molecular species of the sialic acid moiety: the antibody MK1-16 is specific for N-acetyl GM2, MK2-34 is specific for N-glycolyl GM2, and MK1-17 detects both N-acetyl and N-glycolyl GM2. When the occurrence of the GM2 antigen was tested in 107 cases of human germ cell tumors by the immunohistochemical technique using these antibodies, seminoma was characterized as having the highest frequency of N-acetyl GM2 (89.4%, 42 of 47 cases) among germ cell tumors, followed by embryonal carcinoma (40.0%), and teratocarcinoma (26.6%). Compared with this, yolk sac tumors and choriocarcinoma had a much lower positive incidence of the N-acetyl GM2 antigen. On the other hand, the N-glycolyl GM2 antigen was not found at all in 47 cases of seminoma (0%), and the positive incidence was very low in embryonal carcinoma (6.6%), although considerably higher incidences were obtained with choriocarcinoma (25.0%), yolk sac tumor (22.2%), and teratocarcinoma (13.3%). The presence and molecular species of the GM2 antigens in these human germ cell tumors were also ascertained chemically by the thin-layer chromatography (TLC) immunostaining of the ganglioside fractions prepared from primary germ cell tumors. These results indicate that seminoma specifically contains N-acetyl GM2 and no N-glycolyl GM2, suggesting that N-acetyl GM2 could be a good marker for seminoma. On the other hand, non-seminomatous germ cell tumors were characterized by the presence of N-glycolyl GM2, one of the Hanganutziu-Deicher antigens (H-D antigens). Moreover, the positive occurrence of N-glycolyl GM2 correlated very well with the degree of differentiation of non-seminomatous germ cell tumors, i.e., the differentiated tumors such as yolk sac tumors, choriocarcinoma, and teratocarcinoma had a higher positive incidence of N-glycolyl GM2 type H-D antigen but a lower positive incidence of N-acetyl GM2 when compared with embryonal carcinoma, the most undifferentiated tumors among non-seminomatous germ cell tumors.
Methylation mediated silencing of TMS1/ASC gene in prostate cancer (2006)

Our study demonstrates that methylation-mediated silencing of TMS1/ASC is a frequent event in prostate cancer, thus identifying a new potential diagnostic and prognostic marker for the treatment of the disease. Racial differences in TMS1/ASC methylation patterns implicate the probable role of molecular markers in determining in susceptibility to prostate cancer in different ethnic groups.
Innate signals overcome acquired TCR signaling pathway regulation and govern the fate of human CD161hi CD8α+ semi-invariant T cells (2011)

Type 17 programmed CD161(hi)CD8α(+) T cells contribute to mucosal immunity to bacteria and yeast. In early life, microbial colonization induces proliferation of CD161(hi) cells that is dependent on their expression of a semi-invariant Vα7.2(+) TCR. Although prevalent in adults, CD161(hi)CD8α(+) cells exhibit weak proliferative and cytokine responses to TCR ligation. The mechanisms responsible for the dichotomous response of neonatal and adult CD161(hi) cells, and the signals that enable their effector function, have not been established. We describe acquired regulation of TCR signaling in adult memory CD161(hi)CD8α(+) T cells that is absent in cord CD161(hi) cells and adult CD161(lo) cells. Regulated TCR signaling in CD161(hi) cells was due to profound alterations in TCR signaling pathway gene expression and could be overcome by costimulation through CD28 or innate cytokine receptors, which dictated the fate of their progeny. Costimulation with IL-1β during TCR ligation markedly increased proinflammatory IL-17 production, while IL-12-induced Tc1-like function and restored the response to TCR ligation without costimulation. CD161(hi) cells from umbilical cord blood and granulocyte colony stimulating factor-mobilized leukaphereses differed in frequency and function, suggesting future evaluation of the contribution of CD161(hi) cells in hematopoietic stem cell grafts to transplant outcomes is warranted.
Comparison of smoking-induced gene expression on Affymetrix Exon and 3'-based expression arrays. (2007)

Cigarette smoke is the major cause of lung cancer and chronic obstructive pulmonary disease in the United States. We have previously defined the impact of tobacco smoke on intrathoracic airway gene expression among healthy nonsmokers and smokers using standard 3'-based expression U133A arrays [12]. In this report, we compared the performance of the Affymetrix GeneChip Human Exon 1.0 ST array with the HG-U133A array for detecting smoking-related gene expression changes in large airway epithelium obtained at bronchoscopy. RNA obtained from the same bronchial airway epithelial cell samples of four current smokers and three never smokers was hybridized to both arrays. Out of 22,215 probe sets on HG-U133A, 14,741 RefSeq transcripts were mapped to 17,800 core transcripts on the Exon array and the 2 platforms were compared for this overlapping transcript set. While the reproducibility of both platforms was high, the Exon array had a slightly stronger correlation for technical replicates. A majority of the genes with the largest smoking-related fold changes were tightly correlated between platforms, but there were a number of smoking-related changes in gene expression that were detected only on the Exon arrays. Furthermore, while the HG-U133A study did not have enough power to detect any differentially expressed genes between the 4 current vs. 3 never smokers at a False Discovery Rate (FDR) < 0.05, seventy differential expressed genes were detected at FDR < 0.05 in the same set of samples using the Exon platform. These findings suggest that the all-Exon array is a more robust platform for measuring airway epithelial gene expression and can serve as an effective tool for exploring host response to and damage from cigarette smoke.
Experimental study of a novel photosensitizer for sensitive and multidrug-resistant gastric cancer treatment (2017)

Objective
To study the photodynamic therapeutical efficacy of a novel photosensitizer DTP on sensitive gastric cancer cells (SGC7901) and vincristine-resistant gastric cancer cells (SGC7901/VCR).


Methods
The P-gp expression on the SGC7901 and SGC7901/VCR cell membrane was indirectly confirmed by fluorescence microscopy. The survival rates of SGC7901 and SGC7901/VCR cells were evaluated by cell counting kit (CCK-8) after photodynamic therapy with DTP. The intracellular DTP uptake levels of two types of cell were determined using a fluorescence spectrophotometer, and the intracellular DTP distributions were observed by laser scanning confocal microscopy.


Results
The novel photosensitizer DTP has considerable photodynamic cytotoxic effect on SGC7901 and SGC7901/VCR cells. However, this effect on the SGC7901/VCR cells was relatively weak (P 0.05). The DTP uptake level in SGC7901 cells was higher than that in SGC7901/VCR cells (P 0.05). It was found that DTP distributed in the lysosomes of SGC7901 cells and in the lysosomes and mitochondria of SGC7901/VCR cells.


Conclusions
The novel photosensitizer DTP is not the substrate of multidrug transporter P-gp, and its weaker photodynamic cytotoxic effect on SGC7901/VCR cells is independent of the P-gp overexpression on its cell membrane, which may be related to the distribution of intracellular DTP in the two types of cell.


Key words: 
Photodynamic therapy; Novel photosensitizer; Multidrug resistance; Photosensitizer uptake; Intracellular localization
Noninvasive Prenatal Methylomic Analysis by Genomewide Bisulfite Sequencing of Maternal Plasma DNA (2013)

We successfully analyzed fetal and placental methylomes on a genomewide scale, noninvasively and serially. This development offers a powerful method for research, biomarker discovery, and clinical testing for pregnancy-related disorders.
Repression of rat kidney L-arginine:glycine amidinotransferase synthesis by creatine at a pretranslational level. (1984)

The first committed reaction in the biosynthesis of creatine is catalyzed by the enzyme L-arginine:glycine amidinotransferase, commonly called transamidinase. Creatine, the end product of the biosynthetic pathway, is known to alter the levels of kidney transamidinase activity. Rats fed a diet containing 0.3% creatine had 26% of the kidney transamidinase activity of the rats fed a creatine-free diet. This reduction in transamidinase activity was correlated with a decrease in transamidinase protein in the creatine-fed rats. The relative synthetic rates and mRNA functional activities of transmidinase were measured in control and creatine-fed rats. The relative synthetic rate of transamidinase in creatine-fed rats was 21% of that found in the control animals. The functional transamidinase mRNA in creatine-fed rats was correspondingly reduced to 37% of the amount in the control animals. Thus, creatine affects transamidinase activity by altering its rate of synthesis at a pretranslational step and represents an example of end-product repression in a higher eukaryote.
Pharmacodynamic and kinetic basis for the selection of pneumococcal resistance in the upper respiratory tract (2002)

The oropharynx is both the reservoir where antibiotic-resistant Streptococcus pneumoniae strains are selected and the focus for further spread of these organisms. In order to select antibiotic-resistant organisms, the antibiotic must be able to eradicate the susceptible population. How an antibiotic acts on oropharyngeal flora is not fully understood, although data on salivary antibiotic concentrations could be useful for establishing some correlation. Many beta-lactam antibiotics are very active against S. pneumoniae, and although their saliva concentrations are very low, there may be enough to eradicate the majority of beta-lactam-sensitive strains. Other antibiotics achieve salivary concentrations in the range 10-30% of serum concentrations (erythromycin, clindamycin, doxycycline and rifampicin), and are also able to eradicate the antibiotic-susceptible population. Antibiotics achieving higher salivary concentrations (>/=40% of the serum levels) are not very active against S. pneumoniae (ciprofloxacin) or are able to eradicate antibiotic-sensitive and -intermediate strains (clarithromycin, azithromycin and telithromycin). Only antibiotics for which there are no highly resistant pneumococcal strains, for instance some beta-lactams administered at very high dose and for a short course, are associated with a lower risk of antibiotic resistance selection. To diminish the risk, the antibiotics should be dosed in order to obtain inhibitory quotients (maximal serum concentration/MIC ratios) >/= 4, which depends not only on the antibiotic concentration achieved but also on the lack of highly resistant organisms.
PD-1 and PD-L1 expression in molecularly selected non-small-cell lung cancer patients (2014)

PD-1 and PD-L1 are differentially expressed in oncogene-addicted NSCLC supporting further investigation of specific checkpoint inhibitors in combination with targeted therapies.
Inflammation in Atherosclerosis (2012)

Experimental work has elucidated molecular and cellular pathways of inflammation that promote atherosclerosis. Unraveling the roles of cytokines as inflammatory messengers provided a mechanism whereby risk factors for atherosclerosis can alter arterial biology, and produce a systemic milieu that favors atherothrombotic events. The discovery of the immune basis of allograft arteriosclerosis demonstrated that inflammation per se can drive arterial hyperplasia, even in the absence of traditional risk factors. Inflammation regulates aspects of plaque biology that trigger the thrombotic complications of atherosclerosis. Translation of these discoveries to humans has enabled both novel mechanistic insights and practical clinical advances.