gebhart/patrepeval huggingface dataset:
The BRCA1 and BRCA2 breast cancer genes (1997)

Between 5% and 10% of breast cancer cases result from an inherited predisposition. The majority of hereditary forms of breast and ovarian cancer can be accounted for by mutations in two recently identified genes, BRCA1 and BRCA2. Inactivating mutations have been found throughout both genes, and the majority are predicted to result in truncated proteins. Surprisingly, whereas germline mutations have been identified in a growing number of breast or breast and ovarian cancer families, few mutations have been reported in sporadic forms of breast or ovarian cancer. Alternative mechanisms of inactivation have been proposed, but there is currently no strong evidence that these genes are involved in sporadic forms of cancer. Recent studies suggest a role for BRCA1 in transcriptional regulation, as it possesses a conserved amino terminal RING finger domain and an acidic carboxyl domain. Although this role would be consistent with the reported localization of the BRCA1 protein to the nucleus, a cytoplasmic localization and a secretory role for BRCA1 has also been proposed. Current findings suggest that BRCA1 may play an as yet undefined protective role in cells, as it is strongly expressed in epithelial cells undergoing high levels of proliferation in association with differentiation.
Social Textiles (2015)

Wearable commodities are able to extend beyond the temporal span of a particular community event, offering omnipresent vehicles for producing icebreaking interaction opportunities. We introduce a novel platform, which generates social affordances to facilitate community organizers in aggregating social interaction among unacquainted, collocated members beyond initial hosted gatherings. To support these efforts, we present functional work-in-progress prototypes for Social Textiles, wearable computing textiles which enable social messaging and peripheral social awareness on non-emissive digitally linked shirts. The shirts serve as catalysts for different social depths as they reveal common interests (mediated by community organizers), based on the physical proximity of users. We provide 3 key scenarios, which demonstrate the user experience envisioned with our system. We present a conceptual framework, which shows how different community organizers across domains such as universities, brand communities and digital self-organized communities can benefit from our technology.
From stem cell to red cell: regulation of erythropoiesis at multiple levels by multiple proteins, RNAs, and chromatin modifications (2011)

This article reviews the regulation of production of RBCs at several levels. We focus on the regulated expansion of burst-forming unit-erythroid erythroid progenitors by glucocorticoids and other factors that occur during chronic anemia, inflammation, and other conditions of stress. We also highlight the rapid production of RBCs by the coordinated regulation of terminal proliferation and differentiation of committed erythroid colony-forming unit-erythroid progenitors by external signals, such as erythropoietin and adhesion to a fibronectin matrix. We discuss the complex intracellular networks of coordinated gene regulation by transcription factors, chromatin modifiers, and miRNAs that regulate the different stages of erythropoiesis.
Hepatitis B surface antigen (HBsAg) expression in plant cell culture: Kinetics of antigen accumulation in batch culture and its intracellular form (2002)

The production of edible vaccines in transgenic plants and plant cell culture may be improved through a better understanding of antigen processing and assembly. The hepatitis B surface antigen (HBsAg) was chosen for study because it undergoes substantial and complex post-translational modifications, which are necessary for its immunogenicity. This antigen was expressed in soybean (Glycine max L. Merr. cv Williams 82) and tobacco NT1 (Nicotiana tabacum L.) cell suspension cultures, and HBsAg production in batch culture was characterized. The plant-derived antigen consisted predominantly of disulfide cross-linked HBsAg protein (p24(s)) dimers, which were all membrane associated. Similar to yeast, the plant-expressed HBsAg was retained intracellularly. The maximal HBsAg titers were obtained with soybean suspension cultures (20-22 mg/L) with titers in tobacco cultures being approximately 10-fold lower. For soybean cells, electron microscopy and immunolocalization demonstrated that all the HBsAg was localized to the endoplasmic reticulum (ER) and provoked dilation and proliferation of the ER network. Sucrose gradient analysis of crude extracts showed that HBsAg had a complex size distribution uncharacteristic of the antigen's normal structure of uniform 22-nm virus-like particles. The extent of authentic epitope formation was assessed by comparing total p24(s) synthesized to that reactive by polyclonal and monoclonal immunoassays. Depending on culture age, between 40% and 100% of total p24(s) was polyclonal antibody reactive whereas between 6% and 37% was recognized by a commercial monoclonal antibody assay. Possible strategies to increase HBsAg production and improve post-translational processing are discussed.
Spontaneous Oxygen Radical Production at Sites of Antigen Challenge in Allergic Subjects (1995)

Allergic reactions in the lung are characterized by the production of mediators, an influx of inflammatory cells, increased vascular permeability, and changes in airway mechanics. The mechanisms responsible for these airway changes have not been fully defined but may involve the production of reactive oxygen species (ROS) produced by the inflammatory cells. To examine whether ROS are produced by inflammatory cells at sites of antigen exposure, bronchoalveolar lavage (BAL) was performed in airway segments 19 h after challenge with saline or antigen in 14 allergic subjects. Antigen challenge increased cell recovery, predominantly as a result of an influx of eosinophils. Using electron paramagnetic resonance (EPR) spectroscopy with the spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), BAL cells from saline-challenged sites produced minimal ROS. Cells from antigen-challenged sites spontaneously produced a prominent DMPO-OH signal that was inhibited by superoxide dismutase (SOD), indicating the production of superoxide anions (O2-.). Reduction of ferricytochrome c and production of luminol-dependent chemiluminescence via SOD-inhibitable reactions confirmed the spontaneous production of O2-. Following density gradient separation of the antigen-challenged BAL cells, the granulocytic cells, which were predominantly eosinophils, not the mononuclear cells, were the major source of the ROS. At the sites of antigen challenge, the degree of airway permeability as assessed by albumin concentration in BAL fluid was correlated with O2- production by BAL cells measured by EPR spectroscopy. These results demonstrate that cells at sites of antigen challenge generate ROS that may contribute to the airway injury associated with allergic inflammation.
Prolonged retention of estradiol by human breast cancer cells in tissue culture. (1979)

Conditions are described under which prolonged estradiol retention and estrogenic activity are observed in human breast cancer cells in tissue culture. The cells were incubated for three hr with a physiological concentration of [3H]estradiol (3 to 5 nM) and then were washed with 3 successive exchanges of medium 3, 17, and 24 or 48 hr following incubation with [3H]estradiol. The total wash period was 78 hr. The following parameters were monitored to assess the duration of estrogen action in MCF-7 human breast cancer cells in tissue culture; (a) the concentration of [3H]estradiol and [3H]estradiol metabolites in the media washes; (b) the intracellular concentration of [3H]estradiol and [3H]estradiol metabolites; and (c) the time course of estradiol-enhanced rates of radiolabeled thymidine incorporation. The [3H]estradiol concentration in the final medium wash was approximately 0.05 nM. The total intracellular concentration of tritium was about 50 nM prior to wash and 9 nM following 78 hr of wash. The intracellular concentration of specifically bound [3H]estradiol was initially 18 nM, and after 78 hr of wash, it was 2.8 nM. After 48 hr of wash, nearly all specifically bound [3H]estradiol was present in the nucleus. Following incubation of the cells with 5 nM estradiol and an identical wash procedure, estrogenic activity as measured by a stimulation of thymidine incorporation was observed throughout the 78 hr monitored. When 10(-6) M tamoxifen or 10(-7) M unlabeled estradiol was included in the medium washes, the washout of nonspecific binding was unaffected; however, specifically bound [3H]estradiol was essentially eliminated within 24 hr. When bovine serum albumin was included in the medium washes, total, nonspecific, and specific [3H]estradiol binding was reduced in a parallel and dose-dependent fashion. After 48 hr, cells washed with medium containing 3.5 or 7% bovine serum albumin contained one-tenth of the [3H]estradiol present in cells washed with medium alone. We conclude that medium exchanges alone do not effectively remove estradiol from MCF-7 cells, and suggest that estrogen retention by estrogen-responsive cells may mask in vitro assessments of such responsiveness in this and other systems. Inclusion of bovine serum albumin in the washes may alleviate this problem.
Inactivation of viruses in serum with binary ethyleneimine (1976)

The inactivation os six strains from three different groups of viruses with 0.001 M binary ethyleneimine at 37 C proceeded at the same rate in either bovine serum or cell culture medium. The inactivant did not impair the growth-promoting capacity of bovine serum used in cell culture, nor did it affect the antibody activity of guinea pig hyperimmune serum.
Polymer modification of fiber optic chemical sensors as a method of enhancing fluorescence signal for pH measurement (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer modification of fiber optic chemical sensors as a method of enhancing fluorescence signal for pH measurementChristiane Munkholm, David R. Walt, Fred P. Milanovich, and Stanley M. KlainerCite this: Anal. Chem. 1986, 58, 7, 1427–1430Publication Date (Print):June 1, 1986Publication History Published online22 September 2008Published inissue 1 June 1986https://doi.org/10.1021/ac00298a034RIGHTS & PERMISSIONSArticle Views566Altmetric-Citations167LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (485 KB) Get e-Alerts Get e-Alerts
Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum ‘Verrucomicrobia’, isolated from a sponge (Porifera) (2006)

A marine bacterium, strain Pol012(T), was isolated from the Mediterranean sponge Axinella polypoides and subsequently characterized as belonging to subphylum 1 of the phylum 'Verrucomicrobia'. Strain Pol012(T) was non-motile, Gram-negative, coccoid or rod-shaped and red in colour. The menaquinones MK-8 and MK-9 were detected. The G+C content of the genomic DNA was 50.9 mol%. Growth was possible at temperatures between 8 and 30 degrees C and at pH values between 6.8 and 8.2. The closest cultured relative of strain Pol012(T) was Akkermansia muciniphila (83 % sequence similarity), while the closest environmental 16S rRNA gene sequence was the marine clone Arctic96BD-2 (95 % sequence similarity). Strain Pol012(T) is the first marine pure-culture representative of 'Verrucomicrobia' subphylum 1 and represents a novel genus and species, for which the name Rubritalea marina gen. nov., sp. nov. is proposed. The type strain is Pol012(T) (=DSM 177716(T)=CIP 108984(T)).
Mesenchymal Stem Cell-Mediated Immature Dendritic Cells Induce Regulatory T Cell-Based Immunosuppressive Effect (2011)

Immature dendritic cells (imDCs) are increasingly viewed as mediators of T-cell tolerance. We investigated factors enabling induction of regulatory T (Treg) cells through syngeneic imDC/mesenchymal stem cell (MSC) co-cultures in vitro and immunosuppressive effects of MSC-mediated imDCs (MSCs were excluded after 72 h co-culture) in vivo. In these experiments, we found that Foxp3(+) Treg cell population remarkably increased after the T cell priming phase when splenocytes were co-cultured with both imDCs and MSCs, presumably inducing naïve T cells into Treg cells by MSCs and imDCs. In parallel, TGF-β secretion was markedly induced from the imDC+MSC+splenocyte culture supernatant to a significant level at 72-h co-culture, compared to the MSC or imDC+splenocyte co-culture. Based on these results, using a murine melanoma tumor model, we confirmed that the subcutaneous injection of B16 cells induced a perfect tumor incidence in allogeneic recipients when MSC-mediated DCs were coinjected. Consequently, these results suggested that immune tolerance with MSC-mediated DCs leads to immunosuppression induced by at least Foxp3-specific Treg cells. This tool may be useful in clinical trials due to the yet unknown side effects of stem cell therapy.
A comparison of the bovine uterine and plasma proteome using iTRAQ proteomics (2012)

Early embryo loss is a key factor affecting fertility in dairy and beef herds. Prior to implantation, the bovine embryo spends around 16 days free-floating in the uterine environment and is dependent on the composition of uterine fluid for normal growth and development. However, there is a lack of information regarding the protein composition of the bovine uterus and how it relates to plasma. In this study, uterine flushings (UF) (n = 6) and blood plasma (n = 4) were collected from beef heifers on day 7 of the oestrous cycle, albumin depleted and compared using iTRAQ proteomics. A total of 35 proteins were higher and 18 were lower in UF including metabolic enzymes, proteins with anti-oxidant activity and those involved in modulation of the immune response. This study confirms the dynamic nature of the bovine uterine proteome and that it differs from plasma. Factors affecting the uterine proteome and how it impacts on embryo survival warrant further study.
AN ANTIMALARIAL ALKALOID FROM HYDRANGEA. XIV. SYNTHESIS OF 5-, 6-, 7-, AND 8-MONOSUBSTITUTED DERIVATIVES (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAN ANTIMALARIAL ALKALOID FROM HYDRANGEA. XIV. SYNTHESIS OF 5-, 6-, 7-, AND 8-MONOSUBSTITUTED DERIVATIVESB. R. BAKER, ROBERT E. SCHAUB, JOSEPH P. JOSEPH, FRANCIS J. McEVOY, and JAMES H. WILLIAMSCite this: J. Org. Chem. 1952, 17, 1, 141–148Publication Date (Print):January 1, 1952Publication History Published online1 May 2002Published inissue 1 January 1952https://pubs.acs.org/doi/10.1021/jo01135a014https://doi.org/10.1021/jo01135a014research-articleACS PublicationsRequest reuse permissionsArticle Views520Altmetric-Citations43LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Three Camelid VHH Domains in Complex with Porcine Pancreatic α-Amylase (2002)

Camelids produce functional antibodies devoid of light chains and CH1 domains. The antigen-binding fragment of such heavy chain antibodies is therefore comprised in one single domain, the camelid heavy chain antibody VH (VHH). Here we report on the structures of three dromedary VHH domains in complex with porcine pancreatic alpha-amylase. Two VHHs bound outside the catalytic site and did not inhibit or inhibited only partially the amylase activity. The third one, AMD9, interacted with the active site crevice and was a strong amylase inhibitor (K(i) = 10 nm). In contrast with complexes of other proteinaceous amylase inhibitors, amylase kept its native structure. The water-accessible surface areas of VHHs covered by amylase ranged between 850 and 1150 A(2), values similar to or even larger than those observed in the complexes between proteins and classical antibodies. These values could certainly be reached because a surprisingly high extent of framework residues are involved in the interactions of VHHs with amylase. The framework residues that participate in the antigen recognition represented 25-40% of the buried surface. The inhibitory interaction of AMD9 involved mainly its complementarity-determining region (CDR) 2 loop, whereas the CDR3 loop was small and certainly did not protrude as it does in cAb-Lys3, a VHH-inhibiting lysozyme. AMD9 inhibited amylase, although it was outside the direct reach of the catalytic residues; therefore it is to be expected that inhibiting VHHs might also be elicited against proteases. These results illustrate the versatility and efficiency of VHH domains as protein binders and enzyme inhibitors and are arguments in favor of their use as drugs against diabetes.
Antibacterial Activity of Lidocaine in Combination with a Bicarbonate Buffer (1993)

The results of this study indicate that NaHCO3 enhances the killing effect that has been described for lidocaine alone. The inability to recover common pathogenic bacteria from biopsy specimens could be the result of exposure to local anesthetic agents such as lidocaine that are buffered with NaHCO3.
Differential absorption of amoxicillin from the human small and large intestine (1994)

Differences in extent of amoxicillin absorption from various regions of the gastrointestinal tract were determined and compared with the same dose administered orally. Nine healthy men were intubated at a proximal (duodenum or jejunum) or distal (ileum or colon) site with use of a 15-foot double lumen nasointestinal tube. Amoxicillin solutions (375 mg in 120 ml water) were delivered on 2 successive days as a bolus or a 4-hour infusion. Subjects were reintubated at another site and amoxicillin administration was repeated. Subjects with colonic intubation received only infusions. Finally, all subjects received an oral dose of amoxicillin solution. Plasma samples were obtained at 16 time points over a 10-hour period and assayed for amoxicillin by use of an HPLC method. Area under the concentration-time curve and the maximum plasma concentration were computed to evaluate amoxicillin absorption. Amoxicillin absorption was rate and site dependent in the gastrointestinal tract. The drug was well absorbed in the duodenum and jejunum, with no significant differences in absorption when administered as a bolus or 4-hour infusion, but absorption was decreased and rate dependent in the ileum, where more drug was absorbed as an infusion compared with a bolus. Amoxicillin was unabsorbed when infused in all colonic regions.
Elevated Expression of Tyrosine Kinase DDR2 in Primary Biliary Cirrhosis (2002)

DDR2, a TK that is stimulated by fibrillar collagens that accumulate in cirrhotic livers, is present at elevated levels in the small bile ducts of PBC patients. DDR2 is part of a positive feedback loop in which its enhanced expression leads to enhanced deposition of fibrillar collagens (types I andIII). These fibrillar collagens can also provide binding sites for immune mediators, such as cytokines and chemokines. Therefore, unusually high DDR2 expression in the bile ducts of PBC patients could contribute to duct injury by altering local cytokine levels and thereby increasing immune-mediated damage.
Experimental evaluation of smart antenna system performance for wireless communications (1998)

In wireless communications, smart antenna systems (or antenna arrays) can be used to suppress multipath fading with antenna diversity and to increase the system capacity by supporting multiple co-channel users in reception and transmission. This paper presents experimental results of diversity gain, interference cancellation, and mitigation of multipath fading obtained by using a smart antenna system in typical wireless scenarios. Also given are experimental results for the signal-to-interference ratio (SIR) of two moving users, comparing different beamforming algorithms in typical wireless scenarios. All of the experiments were performed using the 900-MHz smart antenna testbed at The University of Texas at Austin.
A Simplified Technique of Distal Femoral Screw Insertion for the Grosse-Kempf Interlocking Nail (1988)

Failure accurately to determine distal femoral screw hole position can sometimes prolong operating time for placing an interlocking Grosse-Kempf rod. The described technique allows the distal femoral screw holes to be localized accurately with minimal radiation exposure. This technique utilizes readily available instruments and is not technically demanding.
Fine Mapping of a Mouse Metallothionein Gene Metal Response Element (1989)

Metal-regulated transcription of metallothionein (MT) genes in higher eucaryotes involves multiple copies of a highly conserved 17-base-pair metal-regulatory element (MRE). We have assayed by transient transfection the ability of mouse MT-I element d (MREd) to confer metal responsivity to constructs containing the mouse MT-I TATA box and the bacterial chloramphenicol acetyltransferase indicator gene. A single copy of MREd works bidirectionally to afford a three- to fourfold induction, and dual copies act cooperatively to yield a 10- to 20-fold response. Element d responds to the same spectrum of heavy metals as doses the complete MT gene promoter. The sequences involved in induction by metals were delineated by analyzing point mutations in MREd. While nucleotides of the highly conserved core sequence TGCPuCXC are critical, substitutions in the less conserved regions affect the induction response only marginally. These sequences include residues of a potential Sp1-binding site, suggesting that if Sp1 binds to MREd, it has little if any role in induction by metals.